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Six-Helix and Eight-Helix DNA Nanotubes Assembled from Half-Tubes
Abstract
DNA nanotubes are cylinder-like structures formed from DNA double-helical molecules whose helix axes are fused at least twice by crossovers. It is potentially useful to use such tubes as sheaths around rodlike species that arise in biological systems and in nanotechnology. It seems easiest to obtain such sheathing by joining two or more components around an object rather than attempting to thread the object through a cavity in the tube. We report two examples of tubes containing a specific number of helices that are assembled from half-tube components. These tubes are a six-helix bundle and an eight-helix bundle, constructed respectively from two bent triple-crossover (BTX) molecules and from two four-helix arched motifs. Both species contain single strands in one molecule that are missing in its mate. The six-helix bundle is formed from two different BTX molecules, whereas the eight-helix species is a closed cyclic dimer of the same molecule. We demonstrate the formation of these species by gel electrophoresis, and we examine their arrangement into long one-dimensional arrays by means of atomic force microscopy.
... Several research groups, including ours, have used DNA nanotechnology to develop various DNA nanopores with different dimensions and sensing capabilities. Examples include DNA pores made up of a single 19 , four 20 , or six [21][22][23][24][25][26][27] DNA duplexes resulting in channel lumens of up to 2 nm in diameter. Larger structures with up to 9 nm channel diameters have also been created 21,[28][29][30][31] , along with a DNA cube that can function as a pore 32 . ...
... Following initial assembly and structural confirmation, some structures require purification (steps [9][10][11][12][13][14][15][16]. For directly visualizing DNA nanopores, transmission electron microscopy (TEM) (steps [17][18][19][20][21][22][23][24][25][26] and AFM (steps [27][28][29][30][31][32][33][34][35][36][37][38][39][40] can be used. The pores' membrane interaction and insertion can be probed with TEM and AFM, and a gel binding assay (steps [41][42][43][44][45][46][47][48][49][50][51]. ...
... PAUSE POINT Samples can now be stored for up to 2 years at RT, but they must be kept dry. [23][24][25][26]. Insert the stained TEM grids into a beamaligned TEM, wait for the indicators of the vacuum to turn green, rotate and load the sample inside. ...
DNA nanopores are bio-inspired nanostructures that control molecular transport across lipid bilayer membranes. Researchers can readily engineer the structure and function of DNA nanopores to synergistically combine the strengths of DNA nanotechnology and nanopores. The pores can be harnessed in a wide range of areas, including biosensing, single-molecule chemistry, and single-molecule biophysics, as well as in cell biology and synthetic biology. Here, we provide a protocol for the rational design of nanobarrel-like DNA pores and larger DNA origami nanopores for targeted applications. We discuss strategies for the pores’ chemical modification with lipid anchors to enable them to be inserted into membranes such as small unilamellar vesicles (SUVs) and planar lipid bilayers. The procedure covers the self-assembly of DNA nanopores via thermal annealing, their characterization using gel electrophoresis, purification, and direct visualization with transmission electron microscopy and atomic force microscopy. We also describe a gel assay to determine pore–membrane binding and discuss how to use single-channel current recordings and dye flux assays to confirm transport through the pores. We expect this protocol to take approximately 1 week to complete for DNA nanobarrel pores and 2–3 weeks for DNA origami pores.
... 59 Several groups have already synthesized DNTs with a defined structure and geometry. [60][61][62] Their structural, mechanical, and electrical properties are extensively studied both experimentally 60 and computationally. 49,[53][54][55][56]63 Though RNA is also one of the potential candidates to build nanopores, only a few studies have been reported on ring-based and origami RNA nanotubes. ...
... 59 Several groups have already synthesized DNTs with a defined structure and geometry. [60][61][62] Their structural, mechanical, and electrical properties are extensively studied both experimentally 60 and computationally. 49,[53][54][55][56]63 Though RNA is also one of the potential candidates to build nanopores, only a few studies have been reported on ring-based and origami RNA nanotubes. ...
... The Nucleic Acid Builder (NAB) 70 program has been used extensively to build all the structures. To start with, we have taken two different structures of RNTs and we refer to them as RNT1 60,61 and RNT2 65 in the rest of the article. RNT1 has identical crossover and nick design to the experimental design of the DNTs by Seeman et al.; 60,61 only the thymines are replaced by uracils. ...
We present a computational framework to model RNA based nanostructures and study their microscopic structures. We model hexagonal nanotubes made of 6 dsRNA (RNT) connected by double crossover (DX) at different positions. Using several hundred nano-seconds (ns) long all-atom molecular dynamics simulations, we study the atomic structure, conformational change and elastic properties of RNT in the presence of explicit water and ions. Based on several structural quantities such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), we find that the RNTs are almost as stable as DNA nanotubes (DNTs). Although the central portion of the RNTs maintain its cylindrical shape, both the terminal regions open up to give rise to a gating like behavior which can play a crucial role in drug delivery. From the bending angle distribution, we observe that the RNTs are more flexible than DNTs. The calculated persistence length of the RNTs is in the micron range which is order of magnitude higher than a single dsRNA. The stretch modulus of the RNTs from the contour length distribution is in the range of 4-7 nN depending on the sequence. The calculated persistence length and stretch modulus are in the same range of values as in the case of DNTs. To understand the structural properties of RNTs at the individual base-pair level we have also calculated all the helicoidal parameters and explain the relative flexibility and rigidity of RNTs having a different sequence. These findings emphasized the fascinating properties of RNTs which will expedite further theoretical and experimental studies in this field.
... In another approach namely 'DNA origami', recently established by P. Rothemund, a long DNA strand can be folded using small DNA staple strands and can be very efficient in designing complex DNA nanostructures [28]. DNA nanotube (DNT), a programable biomimicking ion-channel, is one of the recent additions of the expanding repository of DNA nanostructures [29][30][31][32][33]. Once properly derivatized, DNT can spontaneously insert into the lipid membrane and have appeared to function as an ion channel and can also transport drug molecules across the cell membranes [34][35][36][37][38][39][40][41][42]. ...
... Also, DNT can be operated as a robotic arm to carry and transport cargo across the cell and can also perform as a support system for other cell membrane channels [43]. Enhanced Rigidity of DNTs have widespread applications from nanoelectronics to nanomechanical devices [30,33,[44][45][46]. Thus, the mechanical strength of the DNTs is one of the most essential aspects and considerable effort has been put to measure and increase the mechanical strength of these nanotubes. ...
The flexibility and stiffness of small DNA molecules play a fundamental role ranging from several biophysical processes to nano-technological applications. Here, we estimate the mechanical properties of short double-stranded DNA (dsDNA) with lengths ranging from 12 base-pairs (bp) to 56 bp, paranemic crossover (PX) DNA and hexagonal DNA nanotubes (DNTs) using two widely used coarse-grained models - Martini and oxDNA. To calculate the persistence length (Lp) and the stretch modulus (γ) of the dsDNA, we incorporate the worm-like chain and elastic rod model, while for the DNTs, we implement our previously developed theoretical framework. We compare and contrast all of the results with previously reported all-atom molecular dynamics (MD) simulations and experimental results. The mechanical properties of dsDNA (Lp ∼ 50 nm, γ ∼ 800-1500 pN), PX DNA (γ ∼ 1600-2000 pN) and DNTs (Lp ∼ 1-10 μm, γ ∼ 6000-8000 pN) estimated using the Martini soft elastic network and oxDNA are in very good agreement with the all-atom MD and experimental values, while the stiff elastic network Martini reproduces values of Lp and γ which are an order of magnitude higher. The high flexibility of small dsDNA is also depicted in our calculations. However, Martini models proved inadequate to capture the salt concentration effects on the mechanical properties with increasing salt molarity. oxDNA captures the salt concentration effect on the small dsDNA mechanics. But it is found to be ineffective for reproducing the salt-dependent mechanical properties of DNTs. Also, unlike Martini, the time evolved PX DNA and DNT structures from the oxDNA models are comparable to the all-atom MD simulated structures. Our findings provide a route to study the mechanical properties of DNA and DNA based nanostructures with increased time and length scales and has a remarkable implication in the context of DNA nanotechnology.
... In another approach namely 'DNA origami', recently established by P. Rothemund, a long DNA strand can be folded using small DNA staple strands and can be very efficient in designing complex DNA nanostructures [23]. DNA nanotube (DNT), a programable biomimicking ion-channel, is one of the recent additions of the expanding repository of DNA nanostructures [24][25][26][27][28]. Once properly derivatized, DNT can spontaneously insert into the lipid membrane and have appeared to function as an ion channel and can also transport drug molecules across the cell membranes [29][30][31][32][33][34][35][36][37]. ...
... Also, DNT can be operated as a robotic arm to carry and transport cargo across the cell and can also perform as a support system for other cell membrane channels [38]. Enhanced Rigidity of DNTs have widespread applications from nanoelectronics to nanomechanical devices [25,28,[39][40][41]. Thus, the mechanical strength of the DNTs is one of the most essential aspects and considerable effort has been put to measure and increase the mechanical strength of these nanotubes. ...
The flexibility and stiffness of small DNA play a fundamental role ranging from several biophysical processes to nano-technological applications. Here, we estimate the mechanical properties of short double-stranded DNA (dsDNA) having length ranging from 12 base-pairs (bps) to 56 bps, paranemic crossover (PX) DNA, and hexagonal DNA nanotubes (DNTs) using two widely used coarse-grain models $-$ Martini and oxDNA. To calculate the persistence length ($L_p$) and the stretch modulus ($\gamma$) of the dsDNA, we incorporate the worm-like chain and elastic rod model, while for DNT, we implement our previously developed theoretical framework. We compare and contrast all the results with previously reported all-atom molecular dynamics (MD) simulation and experimental results. The mechanical properties of dsDNA ($L_p$ $\sim$ 50nm, $\gamma \sim$ 800-1500 pN), PX DNA ($\gamma \sim$ 1600-2000 pN) and DNTs ($L_p \sim 1-10\ \mu$m, $\gamma \sim$ 6000-8000 pN) estimated using Martini soft elastic network and oxDNA are in very good agreement with the all-atom MD and experimental values, while the stiff elastic network Martini reproduces order of magnitude higher values of $L_p$ and $\gamma$. The high flexibility of small dsDNA is also depicted in our calculations. However, Martini models proved inadequate to capture the salt concentration effects on the mechanical properties with increasing salt molarity. OxDNA captures the salt concentration effect on small dsDNA mechanics. But it is found to be ineffective to reproduce the salt-dependent mechanical properties of DNTs. Also, unlike Martini, the time evolved PX DNA and DNT structures from the oxDNA models are comparable to the all-atom MD simulated structures. Our findings provide a route to study the mechanical properties of DNA nanostructures with increased time and length scales and has a remarkable implication in the context of DNA nanotechnology.
... 最典型的核酸机器基于DNA链置换反应驱动, 由 于不同长度和序列DNA单链之间互补配对的结 合能力不同, 通过添加特定的DNA单链作为燃料 链, 驱动DNA分子机器构象变化 [51] . 由于一些特 定核酸序列对离子、小分子和蛋白质的特殊识别作 用, 还可以设计出具有底物识别作用的核酸机器 [52] , 图 1 典型框架核酸结构: DNA瓦块和DNA折纸结构 (a) DNA瓦块组装成的二维晶格 [28] ; (b) DNA四面体 [20] ; (c) 类富勒烯 结构 [21] ; (d) DNA折纸设计图及几种二维平面折纸结构 [22] ; (e) 球形 [40] 、花鸟图案 [42] 和兔子 [41] 线框DNA折纸结构; (f) DNA纳米 花瓶结构 [43] ; (g) 16个折纸模块组成的蒙娜丽莎图案 [50] Fig. 1. Typical FNAs: DNA tile and DNA origami: (a) DNA four-way junction [28] ; (b) DNA tetrahedron [20] ; (c) DNA buckyball selfassembled by three-point-star DNA tiles [21] ; (d) 2D DNA origami structures [22] ; (e) sphere [40] , flower-and-bird pattern [42] and bunnyshape [41] wireframe DNA origami structures; (f) nanoflask DNA origami structure with complex curvatures [43] ; (g) a Mona Lisa pattern self-assembled by 16 DNA origami tiles [50] . ...
... 由于一些特 定核酸序列对离子、小分子和蛋白质的特殊识别作 用, 还可以设计出具有底物识别作用的核酸机器 [52] , 图 1 典型框架核酸结构: DNA瓦块和DNA折纸结构 (a) DNA瓦块组装成的二维晶格 [28] ; (b) DNA四面体 [20] ; (c) 类富勒烯 结构 [21] ; (d) DNA折纸设计图及几种二维平面折纸结构 [22] ; (e) 球形 [40] 、花鸟图案 [42] 和兔子 [41] 线框DNA折纸结构; (f) DNA纳米 花瓶结构 [43] ; (g) 16个折纸模块组成的蒙娜丽莎图案 [50] Fig. 1. Typical FNAs: DNA tile and DNA origami: (a) DNA four-way junction [28] ; (b) DNA tetrahedron [20] ; (c) DNA buckyball selfassembled by three-point-star DNA tiles [21] ; (d) 2D DNA origami structures [22] ; (e) sphere [40] , flower-and-bird pattern [42] and bunnyshape [41] wireframe DNA origami structures; (f) nanoflask DNA origami structure with complex curvatures [43] ; (g) a Mona Lisa pattern self-assembled by 16 DNA origami tiles [50] . [60] ; (b) 三角形DNA纳米管封装的AuNP线 [62] ; (c) DNA折纸模块介导AuNPs形成平面阵列 [63] ; (d) DNA单链编码的AuNPs组装成分支状类分子结构 [65] Fig. 2. FNAs-directed nanoparticles assembly: (a) 2D AuNP arrays self-assembled by DNA tiles [60] ; (b) AuNP lines size-selective encapsulated within triangular DNA nanotubes [62] ; (c) 2D AuNP arrays directed by DNA origami tiles [63] ; (d) branched molecule-like structures self-assembled by single-stranded DNA encoded AuNPs [65] . ...
In recent years, the technology of traditional integrated circuit fabrication is facing a huge challenge. As the top-down lithography gradually approaches to its size limit, the development of atomic-scale precise fabrication for functional devices has already become a major scientific issue at present and might become a breakthrough in the development of information technology in the future. With the reference of the bottom-up self-assembly, which is the basic principle of constructing various advanced structures in living systems, the integrated assembly of atoms can be gradually constructed through a series of operations such as capturing, positioning, and moving atoms. The advent of framework nucleic acids (FNAs) happens to provide a new platform for manipulating single atom or integrating multiple atoms. As is well known, the nucleic acids are not only the carriers of genetic information, but also biological building blocks for constructing novel microscopic and macroscopic materials. The FNAs represent a new type of framework with special properties and features, constructed by nucleic acids’ bottom-up self-assembly. With the improvement of chemical synthesis and modification method of nucleic acids, various molecules and materials, such as fluorophores, nanoparticles, proteins, and lipids, can be spatially organized on FNAs with atomic precision, and these functionalized FNAs have been widely explored in the fields of biosensing, biocomputing, nano-imaging, information storage, nanodevices, etc. Based on the features of precise addressability, superior programmability and tailorable functionality, FNAs can be used for implementing the artificial self-assembly of objects with atomic precision to realize the precise arrangement in spatial and functional integration of basic assembly units, and even prompt the development of device fabrication from atomic scale to macroscopic scale. This review focuses on the intersection of FNAs and atomic fabrication, giving a systematically description of the feasibility and advantages of precisely atomic fabrication with FNAs from three aspects. First, the DNA/RNA nanoarchitectures from static state to dynamic state and general strategies for programmable functionalization of FNAs are briefly introduced. Then the applications of FNAs in device fabrication are highlighted, including single molecule reactors, single molecule sensors, nanodevices for cargo loading and transporting, nanophotonics, nanoelectronics and information processing devices. Finally, an outlook of the future development of atomic fabrication with FNAs is given as well.
... Approximately two decades earlier, Holliday had suggested that a branched DNA structure can naturally occur as a key intermediate of the chromosome synapses and recombination [2]. As opposed to the traditional linear conformation of DNA, Seeman realized an opportunity for using these branched DNA architectures, or 36 Page 2 of 34 Holliday junctions, as the basis for crystallizing proteins using the designed periodic DNA structures [1]. These structures are formed through the assembly of two-dimensional (2D) and three-dimensional (3D) networks of oligomeric nucleic acids. ...
... Two half-tube species were designed using two different bent TX (BTX) molecules and a single arched four-helix [4-helix bundle (4HB)] component to assemble a 6HB nanotube and an 8HB nanotube array, respectively. This work included an investigation of the influence of the external environment on the self-assembly of these objects into 1D arrays and reported the assemblies of DNA nanotubes with lengths of up to 500 nm [34]. ...
In bottom–up self-assembly, DNA nanotechnology plays a vital role in the development of novel materials and promises to revolutionize nanoscale manufacturing technologies. DNA shapes exhibit many versatile characteristics, such as their addressability and programmability, which can be used for determining the organization of nanoparticles. Furthermore, the precise design of DNA tiles and origami provides a promising technique to synthesize various complex desired architectures. These nanoparticle-based structures with targeted organizations open the possibility to specific applications in sensing, optics, catalysis, among others. Here we review progress in the development and design of DNA shapes for the self-assembly of nanoparticles and discuss the broad range of applications for these architectures.
... Hybridization of DNA tiles and wrapping by intrinsic or external factors Sticky ended 6HB (length 1-15 µm, inner diameter 2 nm) [19] DNA nanotubes (length 20 µm, width 25 nm) [53] DNA ribbons (length several microns, width 40-250 nm) [54] DNA nanotubes (persistence length 4 µm, diameter 7-20 nm) [55] DNA fibers (length over 20 µm, height 5.2-5.6 nm, width 55 nm) [56] 1D-3HB filaments (length hundreds nanometers to a few microns, outer diameter 2.0 ± 0.2 nm) [57] 6HB (length 4-4.5 µm, height 3.5 ± 0.4 nm), and 8HB (length 0.5 µm, height 4.5 ± 0.4 nm) [58] 4HB (length 1.5-2.0 µm, height 2.3 nm) [59] 6HB, 6HB+2, 6HB+3 (length 1-5 µm, inner diameter 2 nm) [60] DNA nanotubes (length over 10 µm) [61] DNA nanotubes (length 3-15 µm, outer diameter 10 nm) [62] 4-arm nanotubes (length 3 µm, height 7 nm) [63] 1×4 hexagon tiles (HT) (length 15.0 µm, width 0.26 ± 0.05 µm), 4×2 HT (length 5.5 µm, width 0.72 ± 0.09 µm for 2-bp connectors; length 10.1 µm, width 0.69 ± 0.05 µm for 1-bp connectors; length 6.8 µm, width 0.89 ± 0.07 µm for 1-bp-quasi-gap connectors), 2×4 HT (length 8.1 µm, width 0.95 ± 0.14 µm for 2-bp-quasi-gap connectors; length 6.5 µm, width 1.12 ± 0.04 µm for 1bp-gap connectors; length 13.6 µm, width 0.82 ± 0.13 µm for 1-bp-quasi-gap connectors) [64] Multi-rungs ...
... The stickyended structures could further assemble into nanotubes up to ~15 µm long. Later, to incorporate target species in the nanotubes, they designed 6HBs and eight-helix bundles (8HBs) assembled from two complementary half tubes [58] . The 6HBs were built from two different bent triple-crossover (BTX) molecules and joined face-to-face to produce integrated helixes. ...
Biomacromolecular nanotubes play important physiological roles in transmembrane ion/molecule channeling, intracellular transport, and inter‐cellular communications. While genetically encoded protein nanotubes are prevalent in vivo, the in vitro construction of biomimetic DNA nanotubes has attracted intense interest with the rise of structural DNA nanotechnology. The abiotic use of DNA assembly provides a powerful bottom‐up approach for the rational construction of complex materials with arbitrary size and shape at the nanoscale. More specifically, a typical DNA nanotube can be assembled either with parallel‐aligned DNA duplexes or by closing DNA tile lattices. These artificial DNA nanotubes can be tailored and site‐specifically modified to realize biomimetic functions including ionic or molecular channeling, bioreactors, drug delivery, and biomolecular sensing. In this Minireview, we aim to summarize recent advances in design strategies, including the characterization and applications of biomimetic DNA nanotubes.
... Sheets of helices can be generated by positioning crossovers a whole integer of half-helical turns apart (e.g. Figure 1B and C) (3,4). Such sheets can be stacked into hexagonal (5,6) or square lattices (7) by introducing multiple crossovers between many or all of the helices, whilst sheets or individual helices can be programmed to project at various angles by shifting the register of crossovers along adjacent inter-helical interfaces (e.g. Figure 1D and E) (8)(9)(10). Features may also be introduced by varying the length of adjacent domains and/or forcing deviations to the natural twist density (11,12). ...
... Features may also be introduced by varying the length of adjacent domains and/or forcing deviations to the natural twist density (11,12). Structures can be assembled through the hybridisation of a few short oligonucleotides (3,5,8,9) or by the folding of a long singlestranded scaffold (usually the 7249 nucleotide genome of the M13mp18 virus) by multiple short strands ('staples'), an approached termed DNA origami (4,6,7,(10)(11)(12). The size of these structures, often referred to as tiles, can be extended by over five orders of magnitude through the coaxial assembly of blunt (13) or sticky-ended segments (14)(15)(16) and the concomitant formation of duplexes containing discontinuities ('nicks') in their phosphodiester backbones (e.g. Figure 1B, D and E). ...
p>DNA self-assembly has proved to be a useful bottomup strategy for the construction of user-defined nanoscale objects, lattices and devices. The design of these structures has largely relied on exploiting simple base pairing rules and the formation of double-helical domains as secondary structural elements. However, other helical forms involving specific non-canonical base-base interactions have introduced a novel paradigm into the process of engineering with DNA. The most notable of these is a three-stranded complex generated by the binding of a third strand within the duplex major groove, generating a triple-helical ('triplex') structure. The sequence, structural and assembly requirements that differentiate triplexes from their duplex counterparts has allowed the design of nanostructures for both dynamic and/or structural purposes, as well as a means to target non-nucleic acid components to precise locations within a nanostructure scaffold. Here, we review the properties of triplexes that have proved useful in the engineering of DNA nanostructures, with an emphasis on applications that hitherto have not been possible by duplex formation alone.</p
... Sheets of helices can be generated by positioning crossovers a whole integer of half-helical turns apart (e.g. Figure 1B and C) (3,4). Such sheets can be stacked into hexagonal (5,6) or square lattices (7) by introducing multiple crossovers between many or all of the helices, whilst sheets or individual helices can be programmed to project at various angles by shifting the register of crossovers along adjacent inter-helical interfaces (e.g. Figure 1D and E) (8)(9)(10). Features may also be introduced by varying the length of adjacent domains and/or forcing deviations to the natural twist density (11,12). ...
... Features may also be introduced by varying the length of adjacent domains and/or forcing deviations to the natural twist density (11,12). Structures can be assembled through the hybridisation of a few short oligonucleotides (3,5,8,9) or by the folding of a long singlestranded scaffold (usually the 7249 nucleotide genome of the M13mp18 virus) by multiple short strands ('staples'), an approached termed DNA origami (4,6,7,(10)(11)(12). The size of these structures, often referred to as tiles, can be extended by over five orders of magnitude through the coaxial assembly of blunt (13) or sticky-ended segments (14)(15)(16) and the concomitant formation of duplexes containing discontinuities ('nicks') in their phosphodiester backbones (e.g. Figure 1B, D and E). ...
DNA self-assembly has proved to be a useful bottom-up strategy for the construction of user-defined nanoscale objects, lattices and devices. The design of these structures has largely relied on exploiting simple base pairing rules and the formation of double-helical domains as secondary structural elements. However, other helical forms involving specific non-canonical base-base interactions have introduced a novel paradigm into the process of engineering with DNA. The most notable of these is a three-stranded complex generated by the binding of a third strand within the duplex major groove, generating a triple-helical (‘triplex’) structure. The sequence, structural and assembly requirements that differentiate triplexes from their duplex counterparts has allowed the design of nanostructures for both dynamic and/or structural purposes, as well as a means to target non-nucleic acid components to precise locations within a nanostructure scaffold. Here, we review the properties of triplexes that have proved useful in the engineering of DNA nanostructures, with an emphasis on applications that hitherto have not been possible by duplex formation alone.
... [14][15][16][17] DNA tile-based nanotubes are typically formed by assembling short bundles of DNA helices for size-defined nanotubes or by wrapping twodimensional (2D) tile lattices with repeating DNA sequences for extended tubular structures. [18][19][20][21][22][23][24] Tiles comprised of a few DNA strands are frequently used as the modular building blocks for these extended structures, enabling dynamic control over the assembly and disassembly through strand displacement and enzymatic processes. [25][26][27][28][29][30][31][32] However, this method only offers rough control of the nanotube circumference and geometry by the inter-tile angles. ...
DNA nanotubes (NTs) have attracted extensive interest as artificial cytoskeletons for biomedical, synthetic biology, and materials applications. Here, we report the modular design and assembly of a minimalist yet robust DNA wireframe nanotube with tunable cross‐sectional geometry, cavity size, chirality, and length, while using only four DNA strands. We introduce an h‐motif structure incorporating double‐crossover (DX) tile‐like DNA edges to achieve structural rigidity and provide efficient self‐assembly of h‐motif‐based DNA nanotube (H‐NT) units, thus producing programmable, micrometer‐long nanotubes. We demonstrate control of the H‐NT nanotube length via short DNA modulators. Finally, we use an enzyme, RNase H, to take these structures out of equilibrium and trigger nanotube assembly at a physiologically relevant temperature, underlining future cellular applications. The minimalist H‐NTs can assemble at near‐physiological salt conditions and will serve as an easily synthesized, DNA‐economical modular template for biosensors, plasmonics, or other functional materials and as cost‐efficient drug‐delivery vehicles for biomedical applications.
... In our initial design, the DFSM is based on a previously reported six-helix DNA bundle structure with a length of ~22 nm and a diameter of ~7.5 nm (Fig. 1a) 36 . This structure comprises two three-helix half-tubular subunits that are fastened by four DNA locks (duplexes on the edges of the subunits, detailed in Supplementary Fig. 1, with sequences listed in Supplementary Table 1), allowing the formation of a complete six-helix bundle (defined as state S1) via DNA hybridization. ...
The environments in living cells are highly heterogeneous and compartmentalized, posing a grand challenge for the deployment of theranostic agents with spatiotemporal precision. Despite rapid advancements in creating nanodevices responsive to various cues in cellular environments, it remains difficult to control their operations based on the temporal sequence of these cues. Here, inspired by the temporally resolved process of viral invasion in nature, we design a DNA framework state machine (DFSM) that can target specific chromatin loci in living cells in a temporally controllable manner. The DFSM is composed of a six-helix DNA framework with multiple locks that can be opened via DNA strand displacement. The opening of locks at different locations results in distinct structural configurations of the DFSM. We show that the DFSM can switch among up to six structural states with reversibility, in response to the temporally ordered molecular inputs, including DNA keys, adenosine triphosphate or nucleolin. By implementing state switching of the DFSM in living cells, we demonstrate temporally controlled CRISPR–Cas9 targeting towards specific chromatin loci, which sheds light on biocomputing and smart theranostics in complex biological environments.
... [8][9][10] The external scaffold of DNA nanotubes possesses numerous ordered binding sites that can be used as templates to guide the precise assembly of other functional components along the tubes, including nanoparticles, [11][12] fluorescent dyes, 13 and proteins. 14 Prominent methods to synthesize DNA nanotubes, tile-based assembly and DNA origami, [15][16][17] have produced a range of cavity sizes and tube lengths but nevertheless have inherent limitations: nanotube length is uncontrolled when constructed with DNA tiles, which can furthermore propagate curvature and defects from the main tile building block; [18][19][20][21][22][23] the level of structural complexity achieved by DNA origami comes at the expense of using hundreds of unique staple strands and is limited by the size of the viral DNA scaffold; moreover, both structures require the use of magnesium concentrations that are significantly higher than in physiological conditions. [24][25][26][27] Alternatively, our group has reported a modular nanotube assembly method based on prefabricated DNA rungs and DNA linkers, showing their use as dynamic scaffolds for the organization of plasmonic nanoparticles and as vehicles for drug delivery. ...
Nanotubes built from DNA hold promise for several biological and materials applications, due to their high aspect ratio and encapsulation potential. A particularly appealing goal is to control the size, shape, and dynamic behaviour of DNA nanotubes with minimal design alteration, as nanostructures of varying morphologies and lengths have been shown to exhibit distinct cellular uptake, encapsulation behaviour, and in vivo biodistribution. Herein, we report a systematic investigation, combining experimental and computational design, to modulate the length, flexibility, and longitudinal patterns of wireframe DNA nanotubes. Subtle design changes govern the structure and properties of our nanotubes, which are built from a custom-made, long, and size-defined template strand to which DNA rungs and linkers are attached. Unlike DNA origami, these custom-made strands possess regions with repeating sequences at strategic locations, thereby reducing the number of strands necessary for assembly. Through strand displacement, the nanotubes can be reversibly altered between extended and collapsed morphologies. These design concepts enable fine-tuning of the nanotube stiffness and may pave the way for the development of designer nanotubes for a variety of applications, including the study of cellular internalization, biodistribution, and uptake mechanisms for structures of varied shapes and sizes.
... In 2005, Seeman et al. [19] introduced a bundle composed of six DNA double helices. In 2007, Kuzuya et al. [20] investigated the construction of six and eight-helix nanotubes each of which was created by two half-tubes composed of three and four DNA double helices, respectively. In 2008, Yin et al. [21] introduced the idea of making DNA tubes using DNA double helices. ...
Purpose
The purpose of this paper is to compare the stability of the three nanocarriers created by DNA origami method with different positions and numbers of crossovers
Design/methodology/approach
Nanocarriers are attractive components among a variety of nanostructures created by DNA origami and can have numerous applications in mechanical and medical engineering. For this reason, the current study compares three nanotubes with different positions and numbers of crossovers created by DNA origami method that can be utilized as nanocarriers. To investigate the structures, the DNA nanocarriers are studied at the human body temperature 310 K. Molecular dynamics simulations are used for this study. For a quantitative analysis of DNA nanocarriers, the areas of three hexagons at three different sites in each of the nanotubes are investigated. The results indicate that the number and position of crossovers are among the significant factors in the structure stability of nanocarriers. The analyses also revealed that although adding crossovers in locations with fewer crossovers increase structural stability, the position of crossovers can have different effects on the stability. DNA origami-based nanocarriers can be implemented in drug delivery, allow the nanocargoes to pass various surfaces and act as filters for passing cargoes of different dimensions and chemical structures.
Findings
The results indicate that the number and position of crossovers are among the significant factors in the structure stability of nanocarriers
Originality/value
In this paper, the stability of DNA origami nanocarriers with different positions and numbers of crossovers was investigated.
... Figure 9 shows the RNA nanotube structure solvated in aqueous solution. Importantly, in [146] two different structures of RNA nanotubes were used: (a) RNT1 that has identical crossover and nick design to the experimental design of the DNA nanotubes in [149,150] whereby the thymines are replaced by uracils, and (b) RNT2 that was taken from the experimental RNA origami tube design by [151] whereby owing to the computational difficulties in simulating the large origami nanotubes only a portion of the nanotube was used. A 56 bp long RNT2 was used to make it symmetric in both sides in comparison to 57 bp long RNT1. ...
Ribonucleic acid (RNA) is a fundamental molecule having several favourable structural properties that can be used for various potential applications in the field of nanotechnology including biomedicine and bioengineering. Here in this review, we describe the computational and mathematical modellings of the RNA nanoclusters, such as the molecular dynamics simulation, coarse-grained modelling and continuum modelling. The RNA nanocubes, nanotubes and nanorings are some of the typical nanosized structures derived from RNA strands, and the details about such nanostructures have also been presented in this review. The RNA nanoprisms made out of the RNA building blocks via self-assembly of the RNA nanotriangles and their potential applications have been described. Furthermore, special attention is given to the earlier developed RNA nanoscaffolds from the RNA building blocks. We also present some recent results to describe the physical behaviour of the RNA nanotubes in different kinds of physiological solutions using molecular dynamics simulations. Finally, the recent applications of these computational models in several areas of medical sciences such as radiotherapy and drug delivery for cancer treatment and construction of RNA nanodevices have been highlighted. Several potential applications of artificial intelligence in this fast-growing field of RNA engineering have also been presented.
... Recently, because of the biocompatibility and complex technologies of electrode surface modification (via those inorganic materials), DNA nanostructures 21,22 have been considered as a biocompatible alternative for miRNA detection processes. For example, Pei et al. demonstrated the use of a DNA tetrahedral probe, combined with varied amplification strategies (such as redox enzyme incorporation and hybridization chain reaction), to detect miRNAs with high sensitivity and specificity. ...
MicroRNAs (miRNAs) have emerged as the promising molecular biomarkers for early diagnosis and enhanced understanding of the molecular pathogenesis of cancers as well as certain diseases. Here, a facile, label-free, and amplification-free electrochemical biosensor was developed to detect miRNA by using DNA origami nanostructure-supported DNA probes, with methylene blue (MB) serving as the hybridization redox indicator, for the first time. Specifically, the use of cross-shaped DNA origami nanostructures containing multiple single-stranded DNA probes at preselected locations on each DNA nanostructure could increase the accessibility and the recognition efficiency of the probes (due to the rational controlled density of DNA probes). The successful immobilization of DNA origami probes and their hybridization with targeted miRNA-21 molecules was confirmed by electrochemical impedance spectroscopy and cyclic voltammetry methods. A differential pulse voltammetry technique was employed to record the oxidation peak current of MB before and after target hybridization. The linear detection range of this biosensor was from 0.1 pM to 10.0 nM, with a lower detection limit of 79.8 fM. The selectivity of the miRNA biosensor was also studied by observing the discrimination ability of single-base mismatched sequences. Because of the larger surface area and unprecedented customizability of DNA origami nanostructures, this strategy demonstrated great potential for sensitive, selective, and label-free determination of miRNA for translational biomedical research and clinical applications.
... Experimental techniques like cryoelectron microscopy, atomic force microscopy, and X-ray diffraction have been developed to study the complex atomic structures of the DNTs. 19,20,36,37 Also, several aspects of their structures at the nanoscale level have been investigated using computer simulations. 16,24,[29][30][31]36,38 It has been well-established that depending on the external environment, the DNT pores can have different topologies. ...
We report the enhancement of the structural stability of a DNA nanotube (DNT) by changing the salt concentrations for three different salt species, namely, NaCl, KCl, and MgCl2. Using fully atomistic molecular dynamics simulations, we find that, with the gradual increment in the NaCl salt concentration, the DNT becomes compact and rigid. The significant reduction in the average root-mean-square deviation, root-mean-square fluctuation, and effective radius of the DNT with an increase in the NaCl concentration quantifies our observation. We explain how the DNT–ion interactions play a vital role in the conformational fluctuation of the DNT. To understand the salt dependence of the mechanical properties of the DNTs, we have calculated the stretch modulus (γ) and persistence length (Lp) as a function of salt concentration. The calculated stretch moduli of the DNTs change from 8.3 to 13 nN, and the persistence length of the DNT varies from 6 to 10 μm when the NaCl salt concentration is varied from 0 to 1 M. Both the stretch modulus and the persistence length calculations reaffirm the structural stability of the DNT at higher salt concentrations. We find similar trends for another monovalent salt (KCl). However, for a divalent salt (MgCl2), we find minimal variation in the structural properties with an increase in the salt concentration.
... DNA nanostructures are usually stiff and cause more stability in the cellular environment. To date, DNA tiles were used for developing the several groups of fabricated periodicals one-dimensional tubes [194] and ribbons, two-dimensional arrays with strips, triangle [195], quadrilateral [196] and hexagon patterns [197] and three-dimensional crystal [198]. Keum et al., (2009) first time reported that the construction of DNA nanocages with dimensions with much less than 50 nm, the corresponding enzyme recognition process and started to follow the design of Turberfied and constructed DNA tetrahedral nanostructures with a theoretical diameter of about 7nm [199]. ...
Nucleic acid are the key unit and predominant genetic material for interpreting the fundamental basis of genetic information in an organism and now it's used for the evolution of a novel group of therapeutics. To identify the potential impact in the biological science, it receives high recognition in therapeutic applications.Due to their selective recognition of molecular targets and pathways, DNA significantly imparts tremendous specificity of action. With its high advantages in the assembly of device, interconnects and computational elements DNA has shown great potential fabrication and construction of nanostructures and devices. The interaction of low molecular weight small molecules with DNA is significant feature in pharmacology. Based on mode of binding mechanisms small molecules are categorized as intercalators and groove binders which has significant role in target-based drug development. The understanding mechanism of drug-DNA interaction plays a crucial part in the development of novel drug molecules with more effective and lesser side effects. This article is attempts to outline those interactions of drug-DNA with both experimental and computational advances, including ultraviolet (UV)-visible spectroscopy, fluorescent spectroscopy, circular dichroism, Nuclear magnetic resonance (NMR), molecular docking & dynamics and quantum mechanical applications.
... The self-assembly and molecular recognition abilities of DNA may solve the problems of wiring and positioning at the nanoscale [1][2][3][4][5][6]. DNA templates can be used for a large number of applications ranging from sensing technology to nanocomputers due to the ease in fabrication of nanostructures of any complexity and the possibility for the deposition and controlled alignment of the structures on a substrate by molecular self-assembly. ...
The use of self-assembly techniques may open new possibilities in scaling down electronic circuits to their ultimate limits. Deoxyribonucleic acid (DNA) nanotechnology has already demonstrated that it can provide valuable tools for the creation of nanostructures of arbitrary shape, thereforepresentinganidealplatformforthedevelopmentofnanoelectroniccircuits. Sofar,however, the electronic properties of DNA nanostructures are mostly insulating, thus limiting the use of the nanostructures in electronic circuits. Therefore, methods have been investigated that use the DNA nanostructures as templates for the deposition of electrically conducting materials along the DNA strands. The most simple such structure is given by metallic nanowires formed by deposition of metals along the DNA nanostructures. Here, we review the fabrication and the characterization of the electronic properties of nanowires, which were created using these methods.
... There are two widely known approaches to generate DNTs, namely tiles based self-assembly (32) and DNA origami techniques. It has been known that due to the simplicity of the construction methods, higher yields and lower molecular weight, DNTs assembled from crossover tiles are easy to customize further to assemble as membranes nanopore.(13) ...
Engineering the synthetic nanopores through lipid bilayer membrane to access the interior of a cell is a long persisting challenge in biotechnology. Here, we demonstrate the stability and dynamics of a tile-based 6-helix DNA nanotube (DNT) embedded in POPC lipid bilayer using the analysis of 0.2 microsecond long equilibrium MD simulation trajectories. We observe that the head groups of the lipid molecules close to the lumen cooperatively tilt towards the hydrophilic sugar-phosphate backbone of DNA and form a toroidal structure around the patch of DNT protruding in the membrane. Further, we explore the effect of ionic concentrations to the in-solution structure and stability of the lipid-DNT complex. Transmembrane ionic current measurements for the constant electric field MD simulation provide the I-V characteristics of the water filled DNT lumen in lipid membrane. With increasing salt concentrations, the measured values of transmembrane ionic conductance of the porous DNT lumen vary from 4.3 nS to 20.6 nS. Simulations of the DNTs with ssDNA and dsDNA overhangs at the mouth of the pore show gating effect with remarkable difference in the transmembrane ionic conductivities for open and close state nanopores.
... The results in this study further validate the long held belief in the field that LEGO approach with classic multi-stranded motifs are capable of self-assembly into complex 1D, 2D and 3D structures. The similar design principles from single-stranded tiles/bricks and multistranded motifs can be applied to the motifs in this study perfectly to form complex structures (22,25,(30)(31)(32)(33)(34). It is also worth noting that the yield of the 6H × 6H × 18T cuboid is higher than similar structures with DNA bricks (25). ...
Earlier studies in DNA self-assembly have foretold the feasibility of building addressable nanostructures with multi-stranded motifs, which is fully validated in this study. In realizing this feasibility in DNA nanotechnology, a diversified set of motifs of modified domain lengths is extended from a classic type. The length of sticky ends can be adjusted to form different dihedral angles between the matching motifs, which corresponds to different connecting patterns. Moreover, the length of rigidity core can also be tuned to result in different dihedral angles between the component helices of a certain motif therefore different numbers of component helices. The extended set of motifs is used for self-assembly of complex one dimensional, two dimensional and three dimensional structures.
... Tracing back to the earlier development in the DNA nanotechnology, there reveals that similar structural elements appeared in DNA origami and SST structures can also be found in those self-assembled from multi-stranded tiles, including junction tiles (16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31), planar tiles (31)(32)(33)(34)(35)(36)(37)(38)(39)(40)(41)(42) and other tiles (43)(44)(45)(46)(47)(48)(49)(50)(51)(52)(53)(54)(55)(56)(57)(58). Among a vast collection of tiles that have been developed, double crossover (DX) tile (32,33) was the first rigid tile introduced to the field. ...
DNA origami and single-stranded tile (SST) are two proven approaches to self-assemble finite-size complex DNA nanostructures. The construction elements appeared in structures from these two methods can also be found in multi-stranded DNA tiles such as double crossover tiles. Here we report the design and observation of four types of finite-size lattices with four different double crossover tiles, respectively, which, we believe, in terms of both complexity and robustness, will be rival to DNA origami and SST structures.
In structural DNA nanotechnology, E‐tiling DNA nanotubes are evidenced to be homogeneous in diameter and thus have great potential in biomedical applications such as cellular transport and communication, transmembrane ion/molecule channeling, and drug delivery. However, a precise structural description of chiral DNA nanotubes with chiral parameters was lacking, thus greatly hindering their application breadth and depth, until we recently raised and partly solved this problem. In this perspective, we summarize recent progress in defining the chiral indices and handedness of E‐tiling DNA nanotubes by microscopic imaging, especially atomic force microscopy (AFM) imaging. Such a detailed understanding of the chiral structures of E‐tiling DNA nanotubes will be very helpful in the future, on the one hand for engineering DNA nanostructures precisely, and, on the other, for realizing specific physicochemical properties and biological functions successfully.
DNA nanotubes (NTs) have attracted extensive interest as artificial cytoskeletons for biomedical, synthetic biology, and materials applications. Here, we report the modular design and assembly of a minimalist yet robust DNA wireframe nanotube with tunable cross‐sectional geometry, cavity size, chirality, and length, while using only four DNA strands. We introduce an h‐motif structure incorporating double‐crossover (DX) tile‐like DNA edges to achieve structural rigidity and provide efficient self‐assembly of H‐NT units, thus producing programmable, micrometer‐long nanotubes. We demonstrate control of the H‐NT nanotube length via short DNA modulators. Finally, we use an enzyme, RNase H, to take these structures out of equilibrium and trigger nanotube assembly at a physiologically relevant temperature, underlining future cellular applications. The minimalist H‐NTs can assemble at near‐physiological salt conditions and will serve as an easily synthesized, DNA‐economical modular template for biosensors, plasmonic or other functional materials and as cost‐efficient drug‐delivery vehicles for biomedical applications.
With the nanotechnology boom, artificially designed nucleic acid nanotubes have aroused interest due to their practical applications in nanorobotics, vaccine design, membrane channels, drug delivery, and force sensing. In this paper, computational study was performed to investigate the structural dynamics and mechanical properties of RNA nanotubes (RNTs), DNA nanotubes (DNTs), and RNA-DNA hybrid nanotubes (RDHNTs). So far, the structural and mechanical properties of RDHNTs have not been examined in experiments or theoretical calculations, and there is limited knowledge regarding these properties for RNTs. Here, the simulations were carried out using the equilibrium molecular dynamics (MD) and steered molecular dynamics (SMD) approaches. Using in-house scripting, we modeled hexagonal nanotubes composed of six double-stranded molecules connected by four-way Holliday junctions. Classical MD analyses were performed on the collected trajectory data to investigate structural properties. Analyses of the microscopic structural parameters of RDHNT indicated a structural transition from the A-form to a conformation between the A- and B-forms, which may be attributable to the increased rigidity of RNA scaffolds compared to DNA staples. Comprehensive research on the elastic mechanical properties was also conducted based on spontaneous thermal fluctuations of nanotubes and employing the equipartition theorem. The Young's modulus of RDHNT (E = 165 MPa) and RNT (E = 144 MPa) was found to be almost the same and nearly half of that found for DNT (E = 325 MPa). Furthermore, the results showed that RNT was more resistant to bending, torsional, and volumetric deformations than DNT and RDHNT. We also used non-equilibrium SMD simulations to acquire comprehensive knowledge of the mechanical response of nanotubes to tensile stress.
Understanding of DNA-mediated charge transport (CT) is significant for exploring circuits at the molecular scale. However, the fabrication of robust DNA wires remains challenging due to the persistence length and natural flexibility of DNA molecules. Moreover, CT regulation in DNA wires often relies on predesigned sequences, which limit their application and scalability. Here, we addressed these issues by preparing self-assembled DNA nanowires with lengths of 30-120 nm using structural DNA nanotechnology. We employed these nanowires to plug individual gold nanoparticles into a circuit and measured the transport current in nanowires with an optical imaging technique. Contrary to the reported cases with shallow or no length dependence, a fair current attenuation was observed with increasing nanowire length, which experimentally confirmed the prediction of the incoherent hopping model. We also reported a mechanism for the reversible CT regulation in DNA nanowires, which involves dynamic transitions in the steric conformation.
Structural diversity, emerged from its self-association property has made DNA a promising tool for its fabrication and construction into nanostructures and devices. With the advent of nanotechnology and biological molecules employed for drug delivery, DNA nanostructures as well as DNA origami structures emerged as potential candidate for suitable targeted nanovehicles in biological system. DNA can be manipulated in various nanosize scaffold/module to exploit it for drug delivery. Since decades, thorough research is going on worldwide to establish efficient drug delivery by employing nanostructures. DNA structures facilitate better solubility for drugs/small molecules, reduce side effects as well as improved therapeutic efficacy. In spite of its huge advantage in drug delivery, issues for major concerns are there which needs to be tackled/addressed. In order to viable in cell, DNA nanostructures has to cross biological barriers, immune system as well as nucleases, which can significantly reduce its stability and cause degradation. In this chapter our main focus is on detailed description of structural insight of DNA nanostructures/DNA origami structures, their pivotal role in drug delivery as well as the expectations and challenges associated with this extraordinary structural entity.
The transformation from disorder to order in self-assembly is an autonomous entropy-decreasing process. The spatial organization of nanoscale anisotropic building blocks involves the intrinsic heterogeneity in three dimensions and requires sufficiently precise control to coordinate intricate interactions. Only a few approaches have been shown to achieve the anisotropic extension from components to assemblies. Here, we demonstrate the ability to engineer three-dimensional low-entropy lattices at the nucleotide level from modular DNA origami frames. Through the programmable DNA bridging strategy, DNA domains of the same composition are periodically arranged in the crystal growth directions. We combine the site-specific positioning of guest nanoparticles to reflect the anisotropy control, which is validated by small-angle X-ray scattering and electron microscopy. We expect that our DNA origami-mediated crystallization method will facilitate both the exploration of refined self-assembly platforms and the creation of anisotropic metamaterials.
Over the past few decades, DNA nanotechnology engenders a vast variety of programmable nanostructures utilizing Watson–Crick base pairing. Due to their precise engineering, unprecedented programmability, and intrinsic biocompatibility, DNA nanostructures cannot only interact with small molecules, nucleic acids, proteins, viruses, and cancer cells, but also can serve as nanocarriers to deliver different therapeutic agents. Such addressability innate to DNA nanostructures enables their use in various fields of biomedical applications such as biosensors and cancer therapy. This review is begun with a brief introduction of the development of DNA nanotechnology, followed by a summary of recent applications of DNA nanostructures in biosensors and therapeutics. Finally, challenges and opportunities for practical applications of DNA nanotechnology are discussed.
DNA nanotechnology can be used to precisely construct nanostructures of different shapes, sizes and surface chemistry, which is appreciated in a variety of areas such as biomaterials, nanodevices, disease diagnosis, imaging, and drug delivery. Enzymatic degradation resistance and cell-targeting capability are indispensable for the applications of DNA nanostructures in biological and biomedical fields, and it remains challenging to rationally design the desirable nanoscale DNA materials suitable for the clinical translation by the existing assembly methodologies. Here, we present a simple and efficient method for the hierarchical assembly of three-level DNA ring-based nanostructure (DNA h-Nanoring) in a precise order, where the DNA compositions at the primary level, the second level and the third level are a single DNA ring, two-ring-hybridized duplex and uniform complex macro-cycle, respectively. Most as-assembled DNA h-Nanorings exhibit the regular two-dimensional cycle-shaped structure characterized by atomic force microscopy (AFM). The Nanoring exhibits a significantly enhanced resistance to enzymatic attack such that it can remain intact in 10% fetal bovine serum (FBS) for 24 h and even stably exist in the presence of nuclease at the high concentration. More importantly, it is very easy to modify the DNA h-Nanoring with the functional moieties (e.g., targeting ligand aptamer) because there are many single-stranded fragments available for further hybridization. By combining with receptor-targeted Sgc8, the nanoring can be used to accomplish the cell imaging and criminate target CEM cells from the control cells, demonstrating a potential platform for in vivo tumor imaging and targeted chemotherapeutics delivery.
Fluorescent copper nanoclusters (CuNCs) have been widely used in chemical sensors, biological imaging, and light‐emitting devices. However, individual fluorescent CuNCs have limitations in their capabilities arising from poor photostability and weak emission intensities. As one kind of aggregation‐induced emission luminogen (AIEgen), the formation of aggregates with high compactness and good order can efficiently improve the emission intensity, stability, and tunability of CuNCs. Here, DNA nanoribbons, containing multiple specific binding sites, serve as a template for in situ synthesis and assembly of ultrasmall CuNCs (0.6 nm). These CuNC self‐assemblies exhibit enhanced luminescence and excellent fluorescence stability because of tight and ordered arrangement through DNA nanoribbons templating. Furthermore, the stable and bright CuNC assemblies are demonstrated in the high‐sensitivity detection and intracellular fluorescence imaging of biothiols.
Ribbons and clusters: Individual copper nanoclusters (CuNCs) as building blocks are templated onto DNA nanoribbons to form compact and ordered CuNC self‐assemblies with strong and stable fluorescence. The assemblies have been used in the high‐sensitivity detection and intracellular fluorescence imaging of biothiols.
Abstract
Fluorescent copper nanoclusters (CuNCs) have been widely used in chemical sensors, biological imaging, and light‐emitting devices. However, individual fluorescent CuNCs have limitations in their capabilities arising from poor photostability and weak emission intensities. As one kind of aggregation‐induced emission luminogen (AIEgen), the formation of aggregates with high compactness and good order can efficiently improve the emission intensity, stability, and tunability of CuNCs. Here, DNA nanoribbons, containing multiple specific binding sites, serve as a template for in situ synthesis and assembly of ultrasmall CuNCs (0.6 nm). These CuNC self‐assemblies exhibit enhanced luminescence and excellent fluorescence stability because of tight and ordered arrangement through DNA nanoribbons templating. Furthermore, the stable and bright CuNC assemblies are demonstrated in the high‐sensitivity detection and intracellular fluorescence imaging of biothiols.
With silicon-based microelectronic technology pushed to its limit, scientists hunt to exploit biomolecules to power the bio-computer as substitutes. As a typical biomolecule, DNA now has been employed as a tool to create computing systems because of its superior parallel computing ability and outstanding data storage capability. However, the key challenges in this area lie in the human intervention during the computation process and the lack of platforms for central processor. DNA nanotechnology has created hundreds of complex and hierarchical DNA nanostructures with highly controllable motions by exploiting the unparalleled self-recognition properties of DNA molecule. These DNA nanostructures can provide platforms for central processor and reduce the human intervention during the computation process, which can offer unprecedented opportunities for biocomputing. In this review, recent advances in DNA nanotechnology are briefly summarized and the newly emerging concept of biocomputing with DNA nanostructures is introduced.
Nucleic acids hold great promise for bottom-up construction of nanostructures via programmable self-assembly. Especially, the emerging of advanced sequence design principles and the maturation of chemical synthesis of nucleic acids together have led to the rapid development of structural DNA/RNA nanotechnology. Diverse nucleic acids-based nano objects and patterns have been constructed with near-atomic resolutions and with controllable sizes and geometries. The monodispersed distribution of objects, the up-to-sub-millimeter scalability of patterns, and the excellent feasibility of carrying other materials with spatial and temporal resolutions have made DNA/RNA assemblies extremely unique in molecular engineering. In this review, we summarize recent advances in nucleic acids-based (mainly DNA-based) near-atomic fabrication by focusing on state-of-the-art design techniques, toolkits for DNA/RNA nano-engineering and related applications in a range of areas.
DNA tubes with prescribed circumferences are appealing to numerous multidisciplinary applications. DNA single-stranded tiles (SST) assembly method has demonstrated an unprecedented capability for programming the circumferences of DNA tubes in a modular fashion. Nevertheless, a distinct set of SSTs is typically required to assemble DNA tube of a specific circumference, with wider tubes requiring higher number of tiles of unique sequences, which not only increases the expense and design complexity, but also hampers the assembly yield. Herein, we introduce “offset-connection” to circumvent such challenges in conventional SST tube assembly. In this new connection scheme, the boundary SST tiles in an SST array are designed to connect in an offset manner. To compensate for the offset, the SST array has to grow wider until the array can close to form a wide tube with a tolerable degree of twist. Using this strategy, we have successfully assembled DNA tubes with prescribed circumferences consisting of 8-, 12-, 14-, 16-, 20-, 24-, 28-, 32-, 36-, 42-, 56-, 70-helices from two distinct sets of SSTs composed of 19×4 or 19×14 Tiles.
Biomacromolecular nanotubes play important physiological roles in transmembrane ion/molecule channeling, intracellular transport and inter‐cellular communications. While genetically encoded protein nanotubes are predominant in vivo, the in vitro construction of biomimetic DNA nanotubes has attracted intense interest with the rise of structural DNA nanotechnology. The abiotic use of DNA assembly provides a powerful bottom‐up approach for the rational construction of complex materials with arbitrary size and shape at the nanoscale. More specifically, a typical DNA nanotube can be assembled either with parallel‐aligned DNA duplexes or by closing DNA tile lattices. These artificial DNA nanotubes can be tailored and site‐specifically modified to realize biomimetic functions including ionic or molecular channeling, bioreactors, drug delivery and biomolecular sensing. In this Minireview, we aim to summarize recent advances in design strategies, including the characterization and applications of biomimetic DNA nanotubes.
DNA being a nanoscale molecule serving as a complete store-house of genetic information can be fabricated into geometrically fine nanostructures in one- (1D), two- (2D) and three- (3D) dimensions via bottom-up self-assembly of designed nucleotides with specified length. In 1982, Nadrian C. Seeman and his colleagues pioneered the field of DNA nanotechnology after taking the specific programmability of DNA under their consideration to construct a variety of nanostructures, nanofabrication and nanodevices. In fact, the construction of highly ordered and complex geometric structures and periodic arrays has been made possible merely due to distinct characteristics of DNA such as its nanoscale size, distinct base-pairing, excellent predictability and programmability. Also the advent of synthetic oligonucleotides has fast-tracked the self assembly of the complex nanoarchitecture. DNA nanotubes as an important component class in nanomachine can potentially template the growth of nanowires, act as drug delivery vehicles and molecular motors. In particular, drug delivery vehicles based on DNA are a promising class of biodegradable and biocompatible drug nanocarriers. Their size, shapes, and ligand-targeting are more precisely tunable than any of the currently available nanomaterials. The parallelogram framework yielding 2D arrays based on rigid DNA triangle tiles with Holliday junction at vertices are of promising importance on the ground of their usage, for example, for probing cooperative effects in ligand binding, for investigating proximity effect between proteins or other macromolecules and for the evaluation of their organizational power to position the target site. The parallelograms can further be implemented to construct sophisticated biomimetic nanostructures. The designed 2D DNA arrays can be used to manipulate signals for gene regulation as well as gene expression, as nano-medicine carrier and target specific drug release. DNA lattices could serve as a support for biological particles, for example protein complexes or viruses, for TEM imaging. In this dissertation, experiments rendered small circular DNA molecules as tiny building blocks to construct 1D and 2D nanostructures. This presents an endeavor to make the small circular oligonucleotides a new family member of DNA nanotechnology. The small circular DNA molecules (<100-nt) were assembled into 1D nanotubes and 2D crystalline arrays, described as follows. 1. The 5’-phosphorylated linear DNA strand was circularized with the help of a splint strand in the presence of T4 DNA Ligase. The small circular DNA strands with designed lengths of 48-, 50-, and 52-nt, are directed to self-assemble into four types of nanotubes after hybridization with complementary staple strands, following the folding strategy with each double crossover (DX) at 2.5 turns. Much smaller DNA circles such as the 32-nt ring were also tried to grow nanotubes. 2. We used small circularized DNA molecules of different lengths (≤84-nt) as core strands, and successfully synthesized two dimensional (2D) arrays consisting of lozenge framework based on Mao’s DNA tensegrity triangle tiles with four-arm junctions (Holliday junctions) at all vertices. Due to the intrinsic curvature of the triangle tile and the consecutive tile alignment, the 2D arrays are organized in the form of nanotubes. Two kinds of triangle tiles with equilateral side lengths of 1.5 and 2.5 full helical turns are connected by sticky ended cohesion of duplex with a length of 2.5 helical turns respectively. They were observed as parallel lozenge tiling lattices by high resolution AFM images, where the former has a unit cell of internal angles of 60o and side length of 13.6 nm, and the latter has the similar geometrical type of unit cells but with the side length of 17.0 nm. Modification of the triangle tile with infinitesimal side length disturbance and insertion of one T (thymine nucleotide) single stranded loop at every vertex of the triangle has also been tested.
In recent years, bio‐nanopore and solid‐state nanopore have been greatly improved for molecule bio‐sensing. Whereas, the development of this scientific field seems to have encountered a bottleneck due to their respective limitations. The small pore size of the former impedes the detection of large single molecule, and the latter is difficult to achieve similar accuracy and functional control. DNA origami plays a novel role to bring more opportunities for the development of nanopore technology since it is relatively easy to synthesize and modify. This review mainly focuses on introducing the DNA origami nanopore fabrication methods, characterization and application. Meanwhile, the challenges in the present DNA origami nanopore research are also discussed.
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Natural filaments, such as microtubules and actin filaments, are fundamental components of the cell. Despite their relatively simple linear structure, filaments play a number of crucial roles in living organisms, from scaffolding to cellular adhesion and motility. The mechanical properties of natural filaments mostly rely on the structural features of the component units and on the way they are connected together, thus providing an ideal molecular model for emulation purposes. In this review, we describe the progresses done in this field using DNA for the rational design of synthetic filamentous-like materials with tailored structural and physical characteristics. We firstly survey the strategies that have been adopted until now for the construction of individual DNA building components and their programmable selfassembly into linear oligomeric structures. We then describe the theoretical models of polymer elasticity applied to calculate the bending strength of DNA filaments, expressed in terms of persistence length. Finally, we report some of the most exciting examples of truly biomimetic DNA filaments, which are capable to mimic not only the sophisticated structural features of their natural counterparts but also their responsiveness to external stimuli, thus resulting in active motion and growing networks between distant loci.
Over the past decade, we have seen rapid advances in applying nanotechnology in biomedical areas including bioimaging, biodetection, and drug delivery. As an emerging field, DNA nanotechnology offers simple yet powerful design techniques for self-assembly of nanostructures with unique advantages and high potential in enhancing drug targeting and reducing drug toxicity. Various sequence programming and optimization approaches have been developed to design DNA nanostructures with precisely engineered, controllable size, shape, surface chemistry, and function. Potent anticancer drug molecules, including Doxorubicin and CpG oligonucleotides, have been successfully loaded on DNA nanostructures to increase their cell uptake efficiency. These advances have implicated the bright future of DNA nanotechnology-enabled nanomedicine. In this review, we begin with the origin of DNA nanotechnology, followed by summarizing state-of-the-art strategies for the construction of DNA nanostructures and drug payloads delivered by DNA nanovehicles. Further, we discuss the cellular fates of DNA nanostructures as well as challenges and opportunities for DNA nanostructure-based drug delivery.
In the beginning of the 21st century, therapeutic oligonucleotides have shown great potential for the treatment of many life-threatening diseases. However, effective delivery of therapeutic oligonucleotides to the targeted location in vivo remains a major issue. As an emerging field, DNA nanotechnology is applied in many aspects including bioimaging, biosensing, and drug delivery. With sequence programming and optimization, a series of DNA nanostructures can be precisely engineered with defined size, shape, surface chemistry, and function. Simply with hybridization, therapeutic oligonucleotides including unmethylated cytosine–phosphate–guanine dinucleotide oligos, small interfering RNA (siRNA) or antisense RNA, single guide RNA of the regularly interspaced short palindromic repeat–Cas9 system, and aptamers, are successfully loaded on DNA nanostructures for delivery. In this progress report, the development history of DNA nanotechnology is first introduced, and then the mechanisms and means for cellular uptake of DNA nanostructures are discussed. Next, current approaches to deliver therapeutic oligonucleotides with DNA nanovehicles are summarized. In the end, the challenges and opportunities for DNA nanostructure-based systems for the delivery of therapeutic oligonucleotides are discussed.
Plasmonic nanostructures with distinct spatial configuration and geometry are of considerable significance because of their desired optical response. These optical responses have close relationship with the inter-particle parameters in plasmonic nanostructures. However, the precise control of the consecutive variation of these parameters remains a formidable challenge. Here, we demonstrate a gold nanoparticle (AuNP) -based plasmonic nano-reporter, in which a AuNP performs as a walker to stepwise roll directionally and progressively on DNA origami. Using another AuNP as a stator, the rolling of the AuNP reporter could generate the inter-particle distance variation, which would be monitored by surface-enhanced Raman scattering (SERS). Our method opens up a door to develop an optical reporter that monitoring inter-particle variations in plasmonic nanostructures.
We discovered a promising metallo-β-lactamase inhibitor, DNA nanoribbon, by enzymatic kinetics and isothermal titration calorimetry evaluations. Atomic force microscopy, gel electrophoresis, competitive binding experiment, circular dichroic and thermal denaturation studies...
DNA origami has been established as addressable templates for site-specific anchoring of gold nanoparticles (AuNPs). Given that AuNPs are assembled by charged DNA oligonucleotides, it is important to reduce the charge repulsion between AuNPs-DNA and the template to realize high yields. Herein, we developed a cavity-type DNA origami as templates to organize 30-nm AuNPs, which formed dimer and tetramer plasmonic nanostructures. Transmission electron microscopy (TEM) images showed that high yields of dimer and tetramer plasmonic nanostructures were obtained by using the cavity-type DNA origami as the template. More importantly, we observed significant Raman signal enhancement from molecules covalently attached to the plasmonic nanostructures, which provides a new way to high-sensitivity Raman sensing.
The structures formed by mixtures of dissimilarly shaped nanoscale objects can significantly enhance our ability to produce nanoscale architectures. However, understanding their formation is a complex problem due to the interplay of geometric effects (entropy) and energetic interactions at the nanoscale. Spheres and rods are perhaps the most basic geometrical shapes and serve as convenient models of such dissimilar objects. The ordered phases formed by each of these individual shapes have already been explored, however, when mixed, spheres and rods have demonstrated only limited structural organization to date. Here, we show using experiments and theory that the introduction of directional attractions between rod ends and isotropically interacting spherical nanoparticles (NPs) through DNA base pairing leads to the formation of ordered three-dimensional lattices. The spheres and rods arrange themselves in a complex alternating manner, where the spheres can form either a face-centered cubic (FCC) or hexagonal close-packed (HCP) lattice, or a disordered phase, as observed by in situ X-ray scattering. Increasing NP diameter at fixed rod length yields an initial transition from a disordered phase to the HCP crystal, energetically stabilized by rod-rod attraction across alternating crystal layers, as revealed by theory. In the limit of large NPs, the FCC structure is instead stabilized over the HCP by rod entropy. We, therefore, propose that directionally specific attractions in mixtures of anisotropic and isotropic objects offer insight into unexplored self-assembly behavior of noncomplementary shaped particles.
Multihelical DNA bundles could enhance the functionality of nanomaterials and serve as model architectures to mimic protein filaments on the molecular and cellular level. We report the self-assembly of micrometer-sized helical DNA nanotubes with widely controllable helical diameters ranging from tens of nanometers to a few micrometers. Nanoscale helical shapes of DNA tile tubes (4, 6, 8, 10 and 12-helix tile tubes) are achieved by introducing discrete amounts of bending and twist through base pair insertions and/or deletions. Microscale helical diameters, which require smaller amounts of twist and bending, are achieved by controlling the intrinsic "supertwist" present in tile tubes with uneven number of helices (11, 13 and 15-helix tile tubes). Supertwist fine-tuning also allows us to produce helical nanotubes of defined chirality.
We proposed to address the scientific and engineering challenges associated with developing and demonstrating DNA-based wave-guiding devices that incorporate radiation-sensitive bio-molecules to define new architectures that can be used to control and manipulate information propagation at the nanoscale. Prof. N. Seeman, of New York University (NYU), has led the effort to define an advanced methodology for the precision-placement of self-assembled bio-systems and implement structures that incorporate frequency-selective, radiation-sensitive molecular elements. Prof. Seeman remains the world-leader in DNA-based nanofabrication and has pioneered methods (e.g., Seeman tiles) for the construction of periodic/aperiodic and symmetric/asymmetric bio-structures. Prof. H.-L. Cui, of Stevens Institute of Technology (SIT) has led the effort for defining the DNA-based photonic bandgap crystal devices and perform physics-based modeling of their wave-guiding properties. Prof. Cui is an expert in solid-state physics and electronics, and has extensive experience in developing physics-based software on high-performance computing (HPC) platforms for the study of nano/molecular electronics. We have produced a number of advances in the ability to build large DNA arrays, particularly in 3D. Key advances during the period include methods for self-assembling 3D crystals with multiple components and for making arrays of DNA origami crystals. Significant calculations were performed by the Cui group.
Sapropels-organic-matter rich layers-are common in Neogene sediments of the eastern Mediterranean Sea. The formation of these layers has been attributed to climate-related increases in organic-matter production and increased organic-matter preservation due to oxygen depletion in more stagnant bottom waters,. Here we report that eastern Mediterranean Pliocene sapropels contain molecular fossils of a compound (isorenieratene) known to be synthesized by photosynthetic green sulphur bacteria, suggesting that sulphidic (euxinic)-and therefore anoxic-conditions prevailed in the photic zone of the water column. These sapropels also have a high trace-metal content, which is probably due to the efficient scavenging of these metals by precipitating sulphides in a euxinic water column. The abundance and sulphur-isotope composition of pyrite are consistent with iron sulphide formation in the water column. We conclude that basin-wide water-column euxinia occurred over substantial periods during Pliocene sapropel formation in the eastern Mediterranean Sea, and that the ultimate degradation of the increased organic-matter production was strongly influential in generating and sustaining the euxinic conditions.
Algorithms and information, fundamental to technological and biological organization, are also an essential aspect of many elementary physical phenomena, such as molecular self-assembly. Here we report the molecular realization, using two-dimensional self-assembly of DNA tiles, of a cellular automaton whose update rule computes the binary function XOR and thus fabricates a fractal pattern--a Sierpinski triangle--as it grows. To achieve this, abstract tiles were translated into DNA tiles based on double-crossover motifs. Serving as input for the computation, long single-stranded DNA molecules were used to nucleate growth of tiles into algorithmic crystals. For both of two independent molecular realizations, atomic force microscopy revealed recognizable Sierpinski triangles containing 100-200 correct tiles. Error rates during assembly appear to range from 1% to 10%. Although imperfect, the growth of Sierpinski triangles demonstrates all the necessary mechanisms for the molecular implementation of arbitrary cellular automata. This shows that engineered DNA self-assembly can be treated as a Turing-universal biomolecular system, capable of implementing any desired algorithm for computation or construction tasks.
We developed a DNA nanomechanical device that enables the positional synthesis of products whose sequences are determined by the state of the device. This machine emulates the translational capabilities of the ribosome. The device has been prototyped to make specific DNA sequences. The state of the device is established by the addition of DNA set strands. There is no transcriptional relationship between the set strands and the product strands. The device has potential applications that include designer polymer synthesis, encryption of information, and use as a variable-input device for DNA-based computation.
We present a designed cyclic DNA motif that consists of six DNA double helices that are connected to each other at two crossover sites. DNA double helices with 10.5 nucleotide pairs per turn facilitate the programming of DNA double crossover molecules to form hexagonally symmetric arrangements when the crossover points are separated by seven or fourteen nucleotide pairs. We demonstrate by atomic force microscopy well-formed arrays of hexagonal six-helix bundle motifs both in 1D and in 2D.
Double cohesion has proved to be a useful tool to assemble robust 2D arrays of large tiles. Here we present a variety of examples showing the utility of this approach. We apply this principle to the 3 types of 2D lattice sections of arrays whose individual tiles are inherently 3 dimensional, because they contain three vectors that span 3-space. This application includes motifs which are based on the tensegrity triangle, the six-helix bundle motif and on three skewed triple crossover molecules. All of these designs have the potential to form 3 dimensional structures if all three directions of propagation are allowed. If one direction is blunted, 2D arrays form, and all 3 combinations are presented here. In addition, a large parallelogram array that was not attainable previously using single duplex cohesion was also constructed using double cohesion. For comparison, arrays which use another type of double cohesion, double paranemic (PX) cohesion are also presented. Double cohesion of sticky ends proved to be the more effective tool to assemble large motifs into arrays.
Relative mobility values for macromolecules in polyacrylamide gel electrophoresis at various gel concentrations are used to compute the retardation coefficient, KR, molecular radius, , free mobility, M0, and valence, V. Automated data processing and formal statistical analysis are applied. Results obtained with 29 proteins in 9 electrophoretic systems illustrate the utility of this approach, and also provide estimates of radius and total length of the acrylamide polymer.
This paper extends the study and prototyping of unusual DNA motifs, unknown in nature, but founded on principles derived from biological structures. Artificially designed DNA complexes show promise as building blocks for the construction of useful nanoscale structures, devices, and computers. The DNA triple crossover (TX) complex described here extends the set of experimentally characterized building blocks. It consists of four oligonucleotides hybridized to form three double-stranded DNA helices lying in a plane and linked by strand exchange at four immobile crossover points. The topology selected for this TX molecule allows for the presence of reporter strands along the molecular diagonal that can be used to relate the inputs and outputs of DNA-based computation. Nucleotide sequence design for the synthetic strands was assisted by the application of algorithms that minimize possible alternative base-pairing structures. Synthetic oligonucleotides were purified, stoichiometric mixtures were annealed by slow cooling, and the resulting DNA structures were analyzed by nondenaturing gel electrophoresis and heat-induced unfolding. Ferguson analysis and hydroxyl radical autofootprinting provide strong evidence for the assembly of the strands to the target TX structure. Ligation of reporter strands has been demonstrated with this motif, as well as the self-assembly of hydrogen-bonded two-dimensional crystals in two different arrangements. Future applications of TX units include the construction of larger structures from multiple TX units, and DNA-based computation. In addition to the presence of reporter strands, potential advantages of TX units over other DNA structures include space for gaps in molecular arrays, larger spatial displacements in nanodevices, and the incorporation of well-structured out-of-plane components in two-dimensional arrays.
DNA molecules containing two crossover sites between helical domains have been suggested as intermediates in recombination processes involving double-strand breaks. We have modeled these double-crossover structures in an oligonucleotide system. Whereas the relative orientations of the helical domains must be specified in designing these molecules, there are two broad classes of the molecules, the parallel, DP, and antiparallel, DA, molecules. The distance between crossover points must be specified as multiples of half-turns, in order to avoid torsional stress in this system; hence, there are two further subdivisions, those double-crossover molecules separated by odd, O, and even, E, numbers of half-turns. In addition, the parallel molecules with odd numbers of half-turns between crossovers must be divided into those with an excess major or wide-groove separation, W, or those with an excess minor- or narrow-groove separation, N. We have constructed models of all five of these classes, DAE, DAO, DPE, DPOW, and DPON. DPE molecules containing 1 and 2 helical turns between crossovers have been constructed; the DAE molecule contains 1 turn between crossovers, and the DAO, DPOW, and DPON molecules contain 1.5 helical turns between crossovers. None of the parallel molecules is well-behaved; the molecules either dissociate or form multimers when visualized on native polyacrylamide gels. In contrast, antiparallel molecules form single bands when assayed in this fashion. Hydroxyl radical autofootprinting analysis of these molecules reveals protection at expected sites of crossover and of occlusion, suggesting that all the complexes contain linear helix axes that are roughly coplanar between crossovers. However, the DPOW molecule and the DPE molecule with 2 turns between crossovers show decreased protection in the portion between crossovers, suggesting that their helices may bow in response to charge repulsion. We conclude that the helices between parallel double crossovers must be shielded from each other or distorted from linearity if they are to participate in recombination. We have analyzed the possibilities of branch migration and crossover isomerization in double-crossover molecules. Parallel molecules need no sequence symmetry beyond homology to branch migrate, but the sequence symmetry requirements for antiparallel molecules restrict migration to directly repetitive segments that iterate the sequence between crossovers. Crossover isomerization appears to be a very complex process in parallel double-crossover molecules, suggesting that it may be catalyzed by topoisomerases if it occurs within the cell.
Molecular self-assembly presents a `bottom-up' approach to the fabrication of objects specified with nanometre precision. DNA
molecular structures and intermolecular interactions are particularly
amenable to the design and synthesis of complex molecular objects. We
report the design and observation of two-dimensional crystalline forms
of DNA that self-assemble from synthetic DNA double-crossover
molecules. Intermolecular interactions between the structural units are
programmed by the design of `sticky ends' that associate according to
Watson-Crick complementarity, enabling us to create specific periodic
patterns on the nanometre scale. The patterned crystals have been
visualized by atomic force microscopy.
The assembly of synthetic, controllable molecular mechanical systems is one of the goals of nanotechnology. Protein-based molecular machines, often driven by an energy source such as ATP, are abundant in biology. It has been shown previously that branched motifs of DNA can provide components for the assembly of nanoscale objects, links and arrays. Here we show that such structures can also provide the basis for dynamic assemblies: switchable molecular machines. We have constructed a supramolecular device consisting of two rigid DNA 'double-crossover' (DX) molecules connected by 4.5 double-helical turns. One domain of each DX molecule is attached to the connecting helix. To effect switchable motion in this assembly, we use the transition between the B and Z forms of DNA. In conditions that favour B-DNA, the two unconnected domains of the DX molecules lie on the same side of the central helix. In Z-DNA-promoting conditions, however, these domains switch to opposite sides of the helix. This relative repositioning is detected by means of fluorescence resonance energy transfer spectroscopy, which measures the relative proximity of two dye molecules attached to the free ends of the DX molecules. The switching event induces atomic displacements of 20-60 A.
Double crossover molecules are DNA structures containing two Holliday junctions connected by two double helical arms. There are several types of double crossover molecules, differentiated by the relative orientations of their helix axes, parallel or antiparallel, and by the number of double helical half-turns (even or odd) between the two crossovers. They are found as intermediates in meiosis and they have been used extensively in structural DNA nanotechnology for the construction of one-dimensional and two-dimensional arrays and in a DNA nanomechanical device. Whereas the parallel double helical molecules are usually not well behaved, we have focused on the antiparallel molecules; antiparallel molecules with an even number of half-turns between crossovers (termed DAE molecules) produce a reporter strand when ligated, facilitating their characterization in a ligation cyclization assay. Hence, we have estimated the flexibility of antiparallel DNA double crossover molecules by means of ligation-closure experiments. We are able to show that these molecules are approximately twice as rigid as linear duplex DNA.
Terminal mono-oxo complexes of the late transition metal elements have long been considered too unstable to synthesize because
of repulsion between the oxygen electrons and the mostly filled metal d orbitals. A platinum(IV)-oxo compound flanked by two
polytungstate ligands, K7Na9[O=Pt(H2O)L2], L = [PW9O349–], has now been prepared and isolated at room temperature as air-stable brown crystals. X-ray and neutron diffraction at 30
kelvin revealed a very short [1.720(18) angstrom] Pt–O bond and no evidence of a hydrogen atom at the terminal oxygen, ruling
out a better precedented Pt–OH complex. Density functional theory and spectroscopic data account for the stability of the
Pt(IV)-oxo unit by electron withdrawal into delocalized orbitals of the polytungstates.
DNA self-assembly provides a programmable bottom-up approach for the synthesis of complex structures from nanoscale components. Although nanotubes are a fundamental form encountered in tile-based DNA self-assembly, the factors governing tube structure remain poorly understood. Here we report and characterize a new type of nanotube made from DNA double-crossover molecules (DAE-E tiles). Unmodified tubes range from 7 to 20 nm in diameter (4 to 10 tiles in circumference), grow as long as 50 microm with a persistence length of approximately 4 microm, and can be programmed to display a variety of patterns. A survey of modifications (1) confirms the importance of sticky-end stacking, (2) confirms the identity of the inside and outside faces of the tubes, and (3) identifies features of the tiles that profoundly affect the size and morphology of the tubes. Supported by these results, nanotube structure is explained by a simple model based on the geometry and energetics of B-form DNA.
A system of DNA "tiles" that is designed to assemble to form two-dimensional arrays is observed to form narrow ribbons several micrometers in length. The uniform width of the ribbons and lack of frayed edges lead us to propose that they are arrays that have curled and closed on themselves to form tubes. This proposal is confirmed by the observation of tubes with helical order.
A practical theoretical framework is presented for designing and classifying minimally strained nucleic acid nanotubes. The structures are based on the double crossover motif where each double-helical domain is connected to each of its neighbors via two or more Holliday-junction-like reciprocal exchanges, such that each domain is parallel to the main tube axis. Modeling is based on a five-parameter characterization of the segmented double-helical structure. Once the constraint equations have been derived, the primary design problem for a minimally strained N-domain structure is reduced to solving three simultaneous equations in 2N+2 variables. Symmetry analysis and tube merging then allow for the design of a wide variety of tubes, which can be tailored to satisfy requirements such as specific inner and outer radii, or multiple lobed structures. The general form of the equations allows similar techniques to be applied to various nucleic acid helices: B-DNA, A-DNA, RNA, DNA-PNA, or others. Possible applications for such tubes include nanoscale scaffolding as well as custom-shaped enclosures for other nano-objects.
DNAzymes are catalytically active DNA molecules, which have previously been described in solution. Here, we organize these molecules into a series of two-dimensional (2D) arrays using a periodic arrangement of DNA structures based on the DNA double crossover motif. We demonstrate by means of atomic force microscopy that the DNAzymes are organized according to the design and that they retain their activity when attached in linear strings within the context of the 2D array.
The bottom-up spatial organization of potential nanoelectronic components is a key intermediate step in the development of molecular electronics. We describe robust three-space-spanning DNA motifs that are used to organize nanoparticles in two dimensions. One strand of the motif ends in a gold nanoparticle; only one DNA strand is attached to the particle. By using two of the directions of the motif to produce a two-dimensional crystalline array, one direction is free to bind gold nanoparticles. Identical motifs, tailed in different sticky ends, enable the two-dimensional periodic ordering of 5 and 10 nm diameter gold nanoparticles.
The success of nanorobotics requires the precise placement and subsequent operation of specific nanomechanical devices at particular locations. The structural programmability of DNA makes it a particularly attractive system for nanorobotics. We have developed a cassette that enables the placement of a robust, sequence-dependent DNA robot arm within a two-dimensional (2D) crystalline DNA array. The cassette contains the device, an attachment site, and a reporter of state. We used atomic force microscopy to demonstrate that the rotary device is fully functional after insertion. Thus, a nanomechanical device can operate within a fixed frame of reference.
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