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Mesoscopic model confirms strong base pair metal mediated bonding for T-Hg 2 + -T and weaker for C-Ag + -C
Abstract
Metal mediated DNA are mismatches where a metal ion bridges the base pairs and are of interest for biosensors. Here, we study T-Hg2+-T, which is known to be stabilized by base pair metal mediated bonds, and C-Ag+-C whose stabilization mechanism is less well understood. We use a mesoscopic model and published melting temperatures of sequences containing CC or TT mismatches in the presence of the metal ions. For T-Hg2+-T we obtain a strong base pair bond potential and moderate one for C-Ag+-C, only one stacking potential for each configuration is stronger than usual.
... They found that helix stability is additive for high ion concentrations and long helices and non-additive for low ion concentrations and short helices [72]. Recently, Silva and Weber [73] used a mesoscopic model and published melting temperatures of sequences containing CC or TT mismatches in the presence of metal ions. These metal-mediated base pairs are becoming increasingly popular in sensing applications and DNA nanotechnology. ...
Deoxyribonucleic acid (DNA) is a fundamental biomolecule for correct cellular functioning and regulation of biological processes. DNA’s structure is dynamic and has the ability to adopt a variety of structural conformations in addition to its most widely known double-stranded DNA (dsDNA) helix structure. Stability and structural dynamics of dsDNA play an important role in molecular biology. In vivo, DNA molecules are folded in a tightly confined space, such as a cell chamber or a channel, and are highly dense in solution; their conformational properties are restricted, which affects their thermodynamics and mechanical properties. There are also many technical medical purposes for which DNA is placed in a confined space, such as gene therapy, DNA encapsulation, DNA mapping, etc. Physiological conditions and the nature of confined spaces have a significant influence on the opening or denaturation of DNA base pairs. In this review, we summarize the progress of research on the stability and dynamics of dsDNA in cell-like environments and discuss current challenges and future directions. We include studies on various thermal and mechanical properties of dsDNA in ionic solutions, molecular crowded environments, and confined spaces. By providing a better understanding of melting and unzipping of dsDNA in different environments, this review provides valuable guidelines for predicting DNA thermodynamic quantities and for designing DNA/RNA nanostructures.
The redox properties of metallo-base pairs remain to be elucidated. Herein, we report the detailed 1H/13C/109Ag NMR spectroscopic and cyclic voltammetric characterisation of the [Ag(cytidine)2]+ complex as isolated cytosine-Ag+-cytosine (C-Ag+-C) base pairs. We also performed comparative studies between cytidine/Ag+ and other nucleoside/Ag+ systems by using cyclic voltammetry measurements. In addition, to evaluate the effect of [Ag(cytidine)2]+ formation on the chemical reduction of Ag+ to Ag, we utilised the redox reaction between Ag+ and tetrathiafulvalene (TTF). We found that Ag+-mediated base pairing lowers the redox potential of the Ag+/Ag couple. In addition, C-Ag+-C base pairing makes it more difficult to reduce captured Ag+ ions than in other nucleoside/Ag+ systems. Remarkably, the cytidine/Ag+ system can be utilised to control the redox potential of the Ag+/Ag couple in DMSO. This feature of the cytidine/Ag+ system may be exploited for Ag nanoparticle synthesis by using the redox reaction between Ag+ and TTF.
Unlike the canonical base pairs AT and GC, the molecular properties of mismatches such as hydrogen bondings and stacking interactions are strongly dependent on the identity of the neighbouring base pairs. As a result, due to the sheer number of possible combinations of mismatches and flanking base pairs, only a fraction of these have been studied in varying experiments or theoretical models. Here, we report on the melting temperature measurement and mesoscopic analysis of contiguous DNA mismatches in nearest-neighbours and next-nearest neighbour contexts. A total of 4032 different mismatch combinations, including single, double and triple mismatches were covered. These were compared with 64 sequences containing all combination of canonical base pairs in the same location under the same conditions. For a substantial number of single mismatch configurations, 15%, the measured melting temperatures were higher than the least stable AT base pair. The mesoscopic calculation, using the Peyrard-Bishop model, was performed on the set of 4096 sequences, and resulted in estimates of on- site and nearest-neighbour interactions that can be correlated to hydrogen bonding and base stacking. Our results confirm many of the known properties of mismatches, including the peculiar sheared stacking of tandem GA mismatches. More intriguingly, it also reveals that a number of mismatches present strong hydrogen bonding when flanked on both sites by other mismatches. To highlight the applicability of our results, we discuss a number of practical situations such as enzyme binding affinities, thymine DNA glycosylase repair activity, and trinucleotide repeat expansions.
We report a biased QM/MM molecular dynamics study of the dissociation process of cytosine-cytosine complexes mediated by Ag⁺ or H⁺ ions in monomeric and dimeric forms. We performed calculations under explicit solvent conditions and obtained the free energy profiles by thermodynamic integration technique to give deep insights on the dissociation process. For all geometries corresponding to key points on energy profiles the noncovalent interaction descriptors were calculated and the details of dissociation mechanism were revealed. Our findings by means of dissociation energy barrier analysis for Ag⁺-mediated cytosines suggested more favorable cis-configuration of C(Ag⁺)C with the energy of 17.8 kcal/mol over trans-configuration with the energy of 12.2 kcal/mol in monomeric form, in contrast to H⁺ mediated cytosines. Also, it is shown that the QM/MM-MD global minimum of dissociation free energy profiles for both monomer isomers (cis- and trans-) doesn't correspond to the geometries found in crystal data and previous theoretical studies of equilibrium geometries. But the addition of an adjacent silver mediated cytosine pair, in which additional stabilizing factors arise such as interplane H-bonding, π-π stacking or argentophilic interaction, leads to a change in the dissociation profiles and improving the agreement with experiment. The trans-configuration of (C(Ag⁺)C)2 with the energy barrier of 16.6 kcal/mol is more favorable in the dissociation process then cis-configuration with the energy of 15.6 kcal/mol.
Metal-mediated base pairs expand the repertoire of nucleic acid structures and dynamics. Here we report solution structures and dynamics of duplex DNA containing two all-natural C-Hg II-T metallo base pairs separated by six canonical base pairs. NMR experiments reveal a 3:1 ratio of well-resolved structures in dynamic equilibrium. The major species contains two (N3)T-Hg II-(N3)C base pairs in a predominantly B-form helix. The minor species contains (N3)T-Hg II-(N4)C base pairs and greater A-form characteristics. Tenfold different 1 J coupling constants (15 N, 199 Hg) are observed for (N3)C-Hg II (114 Hz) versus (N4)C-Hg II (1052 Hz) connectivities, reflecting differences in cytosine ionization and metal-bonding strengths. Dynamic interconversion between the two types of C-Hg II-T base pairs are coupled to a global conformational exchange between the helices. These observations inspired the design of a repetitive DNA sequence capable of undergoing a global B-to-A-form helical transition upon adding Hg II , demonstrating that C-Hg II-T has unique switching potential in DNA-based materials and devices.
Spectroscopic characterization of AgI‐ion‐mediated C‐AgI‐A and C‐AgI‐T base pairs found in primer extension reactions catalyzed by DNA polymerases was conducted. UV melting experiments revealed that C‐A and C‐T mismatched base pairs in oligodeoxynucleotide duplexes are specifically stabilized by AgI ions in 1:1 stoichiometry in the same manner as a C‐C mismatched base pair. Although the stability of the mismatched base pairs in the absence of AgI ions is in the order C‐A≈C‐T>C‐C, the stabilizing effect of AgI ions follows the order C‐C>C‐A≈C‐T. However, the comparative susceptibility of dNTPs to AgI‐mediated enzymatic incorporation into the site opposite templating C is dATP>dTTP≫dCTP, as reported. The net charge, as well as the size and/or shape complementarity of the metal‐mediated base pairs, or the stabilities of mismatched base pairs in the absence of metal ions, would be more important than the stability of the metallo‐base pairs in the replicating reaction catalyzed by DNA polymerases.
DNA is an attractive candidate for integration into nanoelectronics as a biological nanowire due to its linear geometry, definable base sequence, easy, inexpensive and non-toxic replication and self-assembling properties. Recently we discovered that by intercalating Ag+ in polycytosine-mismatch oligonucleotides, the resulting C-Ag+-C duplexes are able to conduct charge efficiently. To map the functionality and biostability of this system, we built and characterized internally-functionalized DNA nanowires through non-canonical, Ag+-mediated base pairing in duplexes containing cytosine-cytosine mismatches. We assessed the thermal and chemical stability of ion-coordinated duplexes in aqueous solutions and conclude that the C-Ag+-C bond forms DNA duplexes with replicable geometry, predictable thermodynamics, and tunable length. We demonstrated continuous ion chain formation in oligonucleotides of 11–50 nucleotides (nt), and enzyme ligation of mixed strands up to six times that length. This construction is feasible without detectable silver nanocluster contaminants. Functional gene parts for the synthesis of DNA- and RNA-based, C-Ag+-C duplexes in a cell-free system have been constructed in an Escherichia coli expression plasmid and added to the open-source BioBrick Registry, paving the way to realizing the promise of inexpensive industrial production. With appropriate design constraints, this conductive variant of DNA demonstrates promise for use in synthetic biological constructs as a dynamic nucleic acid component and contributes molecular electronic functionality to DNA that is not already found in nature. We propose a viable route to fabricating stable DNA nanowires in cell-free and synthetic biological systems for the production of self-assembling nanoelectronic architectures.
Metal‐mediated base pairs (MMBPs) formed by natural or artificial nucleobases have recently been developed. The metal ions can be aligned linearly in a duplex by MMBP formation. The development of a three‐ or more‐metal‐coordinated MMBPs has the potential to improve the conductivity and enable the design of metal ion architectures in a duplex. This study aimed to develop artificial self‐bases coordinated by three linearly aligned AgI ions within an MMBP. Thus, artificial nucleic acids with a 1,3,9‐triaza‐2‐oxophenoxazine (9‐TAP) nucleobase were designed and synthesized. In a DNA/DNA duplex, self‐base pairs of 9‐TAP could form highly stable MMBPs with three AgI ions. Nine equivalents of AgI led to the formation of three consecutive 9‐TAP self‐base pairs with extremely high stability. The complex structures of 9‐TAP MMBPs were determined by using electrospray ionization mass spectrometry and UV titration experiments. Highly stable self‐9‐TAP MMBPs with three AgI ions are expected to be applicable to new DNA nanotechnologies.
Binding reactions of HgII and AgI to pyrimidine-pyrimidine mismatches in duplex DNA were characterized using fluorescent nucleobase analogs, thermal denaturation and 1H NMR. Unlike AgI, HgII exhibited stoichiometric, site-specific binding of C-T mismatches. The on- and off-rates of HgII binding were approximately 10-fold faster to C-T mismatches (kon ≈ 105 M-1 s-1, koff ≈ 10-3 s-1) as compared to T-T mismatches (kon ≈ 104 M-1 s-1, koff ≈ 10-4 s-1), resulting in very similar equilibrium binding affinities for both types of 'all natural' metallo base pairs (Kd ≈ 10-150 nM). These results are in contrast to thermal denaturation analyses, where duplexes containing T-T mismatches exhibited much larger increases in thermal stability upon addition of HgII (ΔTm = 6-19°C), as compared to those containing C-T mismatches (ΔTm = 1-4°C). In addition to revealing the high thermodynamic and kinetic stabilities of C-HgII-T base pairs, our results demonstrate that fluorescent nucleobase analogs enable highly sensitive detection and characterization of metal-mediated base pairs - even in situations where metal binding has little or no impact on the thermal stability of the duplex.
Owing to their great potentials in genetic code extension and the development of nucleic acid-based functional nanodevices, DNA duplexes containing Hg(II)-mediated base pairs have been extensively studied during the past 60 years. However, structural basis underlying these base pairs remains poorly understood. Herein, we present five high-resolution crystal structures including one first-time reported C-Hg(II)-T containing duplex, three T-Hg(II)-T containing duplexes and one native duplex containing T-T pair without Hg(II) Our structures suggest that both C-T and T-T pairs are flexible in interacting with the Hg(II) ion with various binding modes including N3-Hg(II)-N3, N4-Hg(II)-N3, O2-Hg(II)-N3 and N3-Hg(II)-O4. Our studies also reveal that the overall conformations of the C-Hg(II)-T and T-Hg(II)-T pairs are affected by their neighboring residues via the interactions with the solvent molecules or other metal ions, such as Sr(II) These results provide detailed insights into the interactions between Hg(II) and nucleobases and the structural basis for the rational design of C-Hg(II)-T or T-Hg(II)-T containing DNA nanodevices in the future.
DMA
T is a new fluorescent thymidine mimic composed of 2′-deoxyuridine fused to dimethylaniline. DMAT exhibits the same pKa and base pairing characteristics as native thymidine residues, and its fluorescence properties are highly sensitive to nucleobase ionization, base pairing and metal binding.
Recently, metal-mediated base-pairs (metallo-base-pairs) have been studied extensively with the aim of exploring novel base-pairs; their structures, physicochemical properties, and applications have been studied. This trend has become more evident after the discovery of Hg(II)-mediated thymine-thymine (T-Hg(II)-T) and Ag(I)-mediated cytosine-cytosine (C-Ag(I)-C) base-pairs. In this article, we focus on the basic science and applications of these metallo-base-pairs, which are composed of natural bases.
DNA oligomers can form silver-mediated duplexes, stable in gas phase and solution, with potential for novel biomedical and technological applications. The nucleobase-metal bond primarily drives duplex formation, but hydrogen (H−) bonds may also be important for structure selection and stability. To elucidate the role of H-bonding, we conducted theoretical and experimental studies of a duplex formed by silver-mediated cytosine homopobase DNA strands, two bases long. This silver-mediated cytosine tetramer is small enough to permit accurate, realistic modeling by DFT-based quantum mechanics/molecular mechanics methods. In gas phase, our calculations found two energetically favorable configurations distinguished by H-bonding, one with a novel interplane H-bond, and the other with planar H-bonding of silver-bridged bases. Adding solvent favored silver-mediated tetramers with interplane H-bonding. Overall agreement of electronic circular dichroism spectra for the final calculated structure and experiment validates these findings. Our results can guide use of these stabilization mechanisms for devising novel metal-mediated DNA structures.
We have determined the three-dimensional (3D) structure of DNA duplex that includes tandem Hg(II)-mediated T-T base pairs (thymine-Hg(II)-thymine, T-Hg(II)-T) with NMR spectroscopy in solution. This is the first 3D structure of metallo-DNA (covalently metallated DNA) composed exclusively of 'NATURAL' bases. The T-Hg(II)-T base pairs whose chemical structure was determined with the (15)N NMR spectroscopy were well accommodated in a B-form double helix, mimicking normal Watson-Crick base pairs. The Hg atoms aligned along DNA helical axis were shielded from the bulk water. The complete dehydration of Hg atoms inside DNA explained the positive reaction entropy (ΔS) for the T-Hg(II)-T base pair formation. The positive ΔS value arises owing to the Hg(II) dehydration, which was approved with the 3D structure. The 3D structure explained extraordinary affinity of thymine towards Hg(II) and revealed arrangement of T-Hg(II)-T base pairs in metallo-DNA.
The mesoscopic statistical physics models, known generically as Peyrard-Bishop (PB) models, have found many applications for the study of oligonucleotide properties. Unfortunately, PB models have not reached a wider non-specialized audience for the lack of freely available software implementations. Here we present an extensible C++ implementation of four variants of the PB model, which allows the user to calculate melting temperatures from tested model parameters. Even for a non-specialist, it should be straightforward to change these parameters to reflect different experimental environments or different types of oligonucleotides. For users with some proficiency in C++ programming, it should be feasible to extend the code to other PB models owing to the generic programming implementation adopted for TfReg. Pre-calculated parameters are included that allow the immediate calculation of melting temperatures and thermal equivalence indexes for DNA and RNA.
Availability:
C++ source code and compiled binaries for several Linux distributions are available from https://sites.google.com/site/geraldweberufmg/tfreg and from OpenSuse build service at http://build.opensuse.org.
Contact:
gweberbh@gmail.com
Supplementary information:
Supplementary data are available at Bioinformatics online.
Pyrimidine
base pairs in DNA duplexes selectively capture metal ions to form metal ion-mediated base pairs, which can be evaluated by thermal denaturation, isothermal titration calorimetry, and nuclear magnetic resonance spectroscopy. In this critical review, we discuss the metal ion binding of pyrimidine bases (thymine, cytosine, 4-thiothymine, 2-thiothymine, 5-fluorouracil) in DNA duplexes. Thymine–thymine (T–T) and cytosine–cytosine (C–C) base pairs selectively capture Hg(II) and Ag(I) ions, respectively, and the metallo-base pairs, T-Hg(II)-T and C-Ag(I)-C, are formed in DNA duplexes. The metal ion binding properties of the pyrimidine–pyrimidine pairs can be changed by small chemical modifications. The binding selectivity of a metal ion to a 5-fluorouracil–5-fluorouracil pair in a DNA duplex can be switched by changing the pH of the solution. Two silver ions bind to each thiopyrimidine–thiopyrimidine pair in the duplexes, and the duplexes are largely stabilized. Oligonucleotides containing these bases are commercially available and can readily be applied in many scientific fields (86 references).
The microscopic flexibility of DNA is a key ingredient for understanding its interaction with proteins and drugs but is still poorly understood and technically challenging to measure. Several experimental methods probe very long DNA samples, but these miss local flexibility details. Others mechanically disturb or modify short molecules and therefore do not obtain flexibility properties of unperturbed and pristine DNA. Here, we show that it is possible to extract very detailed flexibility information about unmodified DNA from melting temperatures with statistical physics models. We were able to retrieve, from published melting temperatures, several established flexibility properties such as the presence of highly flexible TATA regions of genomic DNA and support recent findings that DNA is very flexible at short length scales. New information about the nanoscale Na+ concentration dependence of DNA flexibility was determined and we show the key role of ApT and TpA steps when it comes to ion-dependent flexibility and melting temperatures.
Very specific binding of the Ag(i) ion unexpectedly stabilized DNA duplexes containing the naturally occurring cytosine-cytosine (C-C) mismatch-base pair; because the C-C pair selectively binds to the Ag(i) ion, we developed a DNA-based Ag(i) sensor that employed an oligodeoxyribonucleotide containing C-C pairs used for Ag(i) binding sites.
From the perspective of the preparation of a DNA-based nanowire containing an array of metal ions, DNA-polymerase-catalyzed primer extension reactions were investigated and the formation of up to ten consecutive T-HgII-T base pairs was achieved by the HgII-mediated primer extension reaction in the presence of MnII ions. This enzymatic approach may be one of the promising techniques for preparing a DNA-based metal array.
The applicability of the caged nucleoside CNPP (2’-deoxycytidine bearing an ortho-nitrophenylpropyl group at the exocyclic N4 position) in the light-triggered formation of three silver(I)-mediated base pairs was probed, namely C–Ag(I)–C, Im–Ag(I)–C and P–Ag(I)–C (Im = imidazole 2’-deoxyribonucleoside; P = nucleoside analogue with a 1H-imidazo[4,5-f][1], [10]phenanthroline nucleobase surrogate). Generally, an increase in the duplex melting temperature was observed upon photo-deprotection in the presence of Ag(I), indicating the formation of the respective silver(I)-mediated base pair. Nevertheless, a complete photo-deprotection could not be achieved even under optimized conditions. A comparison of the results obtained for the three base pairs allows to derive some general conclusions regarding the optimal design of a metal-mediated base pair whose formation can be triggered by light.
TNA/DNA hybrids share several similarities to RNA/DNA, such as the tendency to form A-type helices and a strong dependency of their thermodynamic properties on purine/pyrimidine ratio. However, unlike RNA/DNA, not much is known about the base-pair properties of TNA. Here, we use a mesoscopic analysis of measured melting temperatures to obtain an estimate of hydrogen bonds and stacking interactions. Our results reveal that the AT base pairs in TNA/DNA have nearly identical hydrogen bond strengths than their counterparts in RNA/DNA, but surprisingly CG turned out to be much weaker despite similar stability.
The effects of metal ions on the stabilities of duplexes containing a D-homochiral and heterochiral mismatched base pairs were studied. In some duplexes containing an internal mismatched base pair, significant stabilization by HgII and AgI ions was observed. While, in duplexes containing a terminal mismatched base pair, only the duplexes containing T-T and LT-T mispairs were significantly stabilized by HgII ions, and the stabilities of the duplexes containing T-T and LT-T mispairs exceeded those of the corresponding homochiral matched duplex. The results suggest that the formation of homo- and heterochiral T-HgII-T base pairs at duplex termini would be useful for the thermal and enzymatic stabilization of DNA-based nanodevice.
A highly selective and sensitive sensor for mercury was designed based on a new fluorescent nucleobase, dioxT. Its metal-sensing ability was investigated using mismatched dioxT-T and dioxT-C base pairing. The...
1,3-Diaza-2-oxophenoxazine (X) has been introduced as a ligand in silver(I)-mediated base pairing in a parallel DNA duplex. This fluorescent cytosine analog is capable of forming stabilizing X–Ag(I)–X and X–Ag(I)–C base pairs in DNA duplexes, as confirmed by temperature-dependent UV spectroscopy and luminescence spectroscopy. DFT calculations of the silver(I)-mediated base pairs suggest the presence of a synergistic hydrogen bond. Molecular dynamics (MD) simulations of entire DNA duplexes nicely underline the geometrical flexibility of these base pairs, with the synergistic hydrogen bond facing either the major or the minor groove. Upon silver(I) binding to the X:X or X:C base pairs, the luminescence emission maximum experiences a red shift from 448 to 460 nm upon excitation at 370 nm. Importantly, the luminescence of the 1,3-diaza-2-oxophenoxazine ligand is not quenched significantly upon binding a silver(I) ion. In fact, the luminescence intensity even increases upon formation of a X–Ag(I)–C base pair, which is expected to be beneficial for the development of biosensors. As a consequence, the silver(I)-mediated phenoxazinone base pairs represent the first strongly fluorescent metal-mediated base pairs.
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Metal-mediated base pairs represent a topical area of research at the border of bioinorganic chemistry, supramolecular coordination chemistry and DNA nanotechnology. In a metal-mediated base pair, the hydrogen bonds of a canonical base pair are formally replaced by coordinate bonds to one or more metal ions located in the interior of the duplex. These base pairs can be created by using natural pyrimidine or purine nucleosides but may also involve artificial nucleosides. The review gives a survey of experimental nucleic acid structures containing one or more metal-mediated base pairs, including X-ray crystal structures as well as NMR solution structures. Starting with a selection of small-molecule structures involving model nucleobases, the overview is extended to nucleic acids structures with T–Hg(II)–T and C–Ag(I)–C base pairs formed from canonical pyrimidine bases, other metal-mediated base pairs involving natural nucleobases, and fully artificial metal-mediated base pairs. A comparison of the structures obtained under different experimental conditions allows to draw significant conclusions with respect to the conformational flexibility of metal-modified nucleic acids.
Despite the importance of DNA/RNA hybrids, a mesoscopic approach is still missing. We developed a mesoscopic model for DNA/RNA hybrids and obtained the complete parametrization from published melting temperatures. The new parameters show very clearly the reduced strength of the hydrogen bond of dArU base pairs, resulting in a weakened stabilization of the double helix and a strong stability dependence on deoxypyrimidine content. The stacking parameters show no correlation to B-DNA, however we obtain a moderate correlation to A-RNA. We discuss some example sequences with variable deoxypyrimidine contents and for polipurine tracts (PPT).
Various human activities lead to the pollution of ground, drinking, and wastewater with toxic metals. It is well known that metal ions preferentially bind to DNA phosphate backbones or DNA nucleobases, or both. Foreman et al. (Environ Toxicol Chem 30(8):1810–1818, 2011) reported the use of a DNA-dye based assay suitable for use as a toxicity test for potable environmental water. They compared the results of this test with the responses of live-organism bioassays. The DNA-based demonstrated that the loss of SYBR Green I fluorescence dye bound to calf thymus DNA was proportional to the toxicity of the water sample. However, this report raised questions about the mechanism that formed the basis of this quasi-quantitatively test. In this review, we identify the unique and preferred DNA-binding sites of individual metals. We show how highly sensitive and selective DNA-based sensors can be designed that contain multiple binding sites for 21 heavy metal cations that bind to DNA and change its structure, consistent with the release of the DNA-bound dye.
The 2′‐O,4′‐C‐methylene‐bridged nucleic acid (2′,4′‐BNA/LNA), having an N‐type sugar conformation, effectively improves duplex‐forming ability. 2′,4′‐BNA/LNA is widely used to improve gene knockdown in nucleic acid‐based therapies and is used in gene diagnosis. Metal‐mediated base pairs (MMBPs) such as thymine(T)‐HgII‐T and cytosine(C)‐AgI‐C have been developed and used as attractive tools in DNA nanotechnology studies. This study aimed to investigate the application of 2′,4′‐BNA/LNA in the field of MMBP. 2′,4′‐BNA/LNA with 5‐methylcytosine stabilized MMBP of C with AgI ion. Moreover, the 2′,4′‐BNA/LNA sugar significantly improved the duplex‐forming ability of the DNA/DNA complex compared to that by the unmodified sugar. These results suggest that the sugar conformation is important for improving the stability of duplex‐containing MMBPs. Our results indicate that 2′,4′‐BNA/LNA can be applied not only to nucleic acid‐based therapies but also to MMBP technologies.
The double-helix structure of DNA, in which complementary strands reversibly hybridize to each other, not only explains how genetic information is stored and replicated, but also has proved very attractive for the development of nanomaterials. The discovery of metal-mediated base pairs has prompted the generation of short metal–DNA hybrid duplexes by a bottom-up approach. Here we describe a metallo-DNA nanowire—whose structure was solved by high-resolution X-ray crystallography—that consists of dodecamer duplexes held together by four different metal-mediated base pairs (the previously observed C–Ag–C, as well as G–Ag–G, G–Ag–C and T–Ag–T) and linked to each other through G overhangs involved in interduplex G–Ag–G. The resulting hybrid nanowires are 2 nm wide with a length of the order of micrometres to millimetres, and hold the silver ions in uninterrupted one-dimensional arrays along the DNA helical axis. The hybrid nanowires are further assembled into three-dimensional lattices by interactions between adenine residues, fully bulged out of the double helix.
Metal ions are essential to many chemical, biological, and environmental processes. In the past two decades, many DNA-based metal sensors have emerged. While the main biological role of DNA is to store genetic information, its chemical structure is ideal for metal binding via both the phosphate backbone and nucleobases. DNA is highly stable, cost-effective, easy to modify, and amenable to combinatorial selection. Two main classes of functional DNA were developed for metal sensing: aptamers and DNAzymes. While a few metal binding aptamers are known, it is generally quite difficult to isolate such aptamers. On the other hand, DNAzymes are powerful tools for metal sensing since they are selected based on catalytic activity, thus bypassing the need for metal immobilization. In the last five years, a new surge of development has been made on isolating new metal-sensing DNA sequences. To date, many important metals can be selectively detected by DNA often down to the low parts-per-billion level. Herein, each metal ion and the known DNA sequences for its sensing are reviewed. We focus on the fundamental aspect of metal binding, emphasizing the distinct chemical property of each metal. Instead of reviewing each published sensor, a high-level summary of signaling methods is made as a separate section. In principle, each signaling strategy can be applied to many DNA sequences for designing sensors. Finally, a few specific applications are highlighted, and future research opportunities are discussed.
The synthesis of a metalled double-helix containing exclusively silver-mediated C*-C* base pairs is reported herein (C* = N1hexylcytosine). Remarkably, it is the first crystal structure containing infinite and consecutive C*-AgI-C* base pairs that form a double helix. The AgI ion occupies the center between two C* residues with N(3)-Ag bond distances of 2.1 Å and short AgI-AgI distances (3.1 Å) suggesting an interesting argentophilic attraction as a stabilization source of the helical disposition. The solid state structure is further stabilized by metal-mediated base-pairs, hydrogen bonding and π-stacking interactions. Moreover, the angle N(3)-Ag-N(3) is almost linear in the [Ag(N1hexylcytosine)2]+ motif and the bases are not coplanar thus generating a double strand helical aggregate in the solid state. The noncovalent and argentophilic interactions have been rationalized by means of DFT calculations.
The structure of an AgI-mediated cytosine–cytosine base pair, C–AgI–C, was determined with NMR spectroscopy in solution. The observation of 1-bond 15N-109Ag J-coupling (1J(15N,109Ag): 83 and 84 Hz) recorded within the C–AgI–C base pair evidenced the N3–AgI–N3 linkage in C–AgI–C. The triplet resonances of the N4 atoms in C–AgI–C demonstrated that each exocyclic N4 atom exists as an amino group (−NH2), and any isomerization and/or N4–AgI bonding can be excluded. The 3D structure of AgI–DNA complex determined with NOEs was classified as a B-form conformation with a notable propeller twist of C–AgI–C (−18.3±3.0°). The 109Ag NMR chemical shift of C-AgI-C was recorded for cytidine/AgI complex (δ(109Ag): 442 ppm) to completed full NMR characterization of the metal linkage. The structural interpretation of NMR data with quantum mechanical calculations corroborated the structure of the C–AgI–C base pair.
Silver(I) ions can stabilize cytosine–cytosine, cytosine (C)–methylcytosine (5mC) and cytosine–hydroxymethylcytosine (5hmC) mismatched-base pairs. While cytosine modifications regulate DNA stability to regulate cellular functions, silver ions can modulate the stability of C–C, C–5mC and C–5hmC containing DNA duplexes in a salt concentration dependent manner.
The metallo DNA duplex containing mercury-mediated T-T base pairs is an attractive biomacromolecular nanomaterial which can be applied to nanodevices such as ion sensors. Reported herein is the first crystal structure of a B-form DNA duplex containing two consecutive T-Hg(II) -T base pairs. The Hg(II) ion occupies the center between two T residues. The N3-Hg(II) bond distance is 2.0 Å. The relatively short Hg(II) -Hg(II) distance (3.3 Å) observed in consecutive T-Hg(II) -T base pairs suggests that the metallophilic attraction could exist between them and may stabilize the B-form double helix. To support this, the DNA duplex is largely distorted and adopts an unusual nonhelical conformation in the absence of Hg(II) . The structure of the metallo DNA duplex itself and the Hg(II) -induced structural switching from the nonhelical form to the B-form provide the basis for structure-based design of metal-conjugated nucleic acid nanomaterials.
We investigate, by first-principles density-functional calculations, fragments and periodic helices of CG- and AT-DNA, modified by incorporation of Zn2+ cations. We study the relative stability of different binding sites for the metal ions as well as different methods of charge neutralization. We find that binding the Zn cation to the N(7) atom of guanine or adenine leads always to lower energies than substitution of an imino proton between two H-bonded bases. Also, neutralizing with OH- groups bonded to Zn2+ is more stable than removing protons from the phosphate groups. Contrarily to common wisdom, we find that planarity of the base pairs is not an essential factor of stability, and that nonplanar base pairs can also be stacked effectively. Finally, we find that the most stable CG and AT helices, with Zn2+ bonded to N(7) atoms and neutralized by OH- ions, have wide band gaps of more than 2 eV, and we conclude that they are poor candidates for electronic conduction.
The complexing of DNA by mercury(II) is studied. In agreement with the prior investigations by Katz and Thomas, there is a decrease in the intrinsic viscosity and a spectral shift when Hg II adds to DNA. The reaction can be reversed by adding complexing agents for Hg II and the original native DNA recovered. The results indicate that Hg ++ rather than HgCl 2 is being bound and that it is adding to the base moieties, not to the phosphate groups. As Hg ++ is added, one type of complex with a characteristic spectrum forms up to a ratio of one Hg ++ to two bases for the several natural DNA's studied (calf thymus, E. coli and M. lysodeikticus), irrespective of the GC:AT ratio in the DNA. With excess Hg ++, a second higher complex forms. Protons are released when Hg ++ adds to DNA at pH 5.7. The initial values of ΔH +/ ΔHg ++ are in the range of 1.8-2.0. The strength of binding of Hg ++ as estimated by chloride titrations decreases in the order: AT polymer, heat-denatured calf thymus, native calf thymus, E. coli and M. lysodeikticus. Adding Hg ++ ion causes a rather small decrease in the denaturation temperature of calf-thymus DNA. The spectral and titration properties of AT polymer are quite different from those of the native DNA's. We are unable to propose a structure for the DNA-Hg II complex which explains all of the above-mentioned properties. It is probable, however, that a considerable degree of order in the base packing is retained in the complex.
The sodium salt of calf thymus nucleic acid is found to react with mercuric chloride to produce what is, essentially, an incomplete mercuric salt of nucleic acid. Two of the physical manifestations of the reaction are a decrease in viscosity and an increase in turbidity. These have been studied by appropriate methods. The reaction is accompanied by aggregation (but not precipitation) and can be completely reversed in solution as demonstrated for the first time by light scattering techniques. Data from binding experiments have been combined with those from light scattering measurements to give a consistent picture of the mechanisms involved.
Melting temperatures of oligonucleotides are useful for a number of molecular biology applications, such as the polymerase chain reaction (PCR). Although melting temperatures are often calculated with simplistic empirical equations, application of thermodynamics provides more accurate melting temperatures and an opportunity for students to apply rigorous thermodynamic analysis to an important biochemical problem. Because the stacking of base pairs on top of one another is a significant factor in the energetics of oligonucleotide melting, several investigators have applied van't Hoff analysis to melting temperature data using a nearest-neighbor model and have obtained entropies and enthalpies for the stacking of bases. The present article explains how the equilibrium constant for the dissociation of strands from double-stranded oligonucleotides can be expressed in terms of the total strand concentration and thus how the total strand concentration influences the melting temperature. It also presents a simplified analysis based on the entropies and enthalpies of stacking that is manually tractable so that students can work examples to help them understand the thermodynamics of oligonucleotide melting. Keywords (Audience): Upper-Division Undergraduate
A study of silver-ion binding by nucleic acids and synthetic ribo and deoxyribopolynucleotides, has been carried out by means of potentiometric titration, thermal transition, and difference spectra. It is clearly demonstrated that a strong complex between Ag+ and nitrogen atoms of bases is made reversibly. Binding constants and site numbers are determined for each type of polynucleotide. Base reactivity varies strongly with chain length, and a cooperative phenomenon is found in each case. Two successive complexes with DNA are seen in all the three techniques, and they have the same characteristics as complexes with respectively poly-dGC and poly dAT. In the first complex, Ag+ is linked to four bases, provided two of them are a G-C pair. Calculated and experimental values of site numbers agree very well for DNA of different G-C content. Thermal stabilization occurs simultaneously, and the increase of melting temperature corresponds to calculated changes of stacking energy between base pairs. In the second complex a new ordered structure insensitive to temperature is formed, with simultaneous release of protons. The stoichiometry can be related to base sequence. Complexing with silver increases the resistance of TMV RNA to both temperature and ribonuclease; a tentative explanation is given in the latter case.
The use of DNA as a molecular wire in nanoscale electronic architectures would greatly benefit from its capability of sequence-specific self-assembly. Although single electrons and positive charges have been shown to be transmitted by natural DNA over a distance of several base pairs, the high ohmic resistance of unmodified oligonucleotides imposes a serious obstacle. Exchanging some or all of the Watson–Crick base pairs in DNA by metal complexes may solve this problem and evolve DNA-like materials with superior conductivity for future nano-electronic applications. The so-called metal–base pairs are formed from suitable transition metal ions and ligand-like nucleosides which are introduced into both of the two pairing strands by automated DNA synthesis. This review illustrates the basic concepts of metal–base pairing and highlights recent developments in the field.
Metal-mediated base pairs formed by the interaction between metal ions and artificial bases in oligonucleotides have been developed for potential applications in nanotechnology. We recently found that a natural C:C mismatched base pair bound to an Ag(+) ion to generate a novel metal-mediated base pair in duplex DNA. Preparation of the novel C-Ag-C base pair involving natural bases is more convenient than that of metal-mediated base pairs involving artificial bases because time-consuming base synthesis is not required. Here, we examined the thermodynamic properties of the binding between the Ag(+) ion and each of single and double C:C mismatched base pair in duplex DNA by isothermal titration calorimetry. The Ag(+) ion specifically bound to the C:C mismatched base pair at a 1:1 molar ratio with 10(6) M(-1) binding constant, which was significantly larger than those for nonspecific metal ion-DNA interactions. The specific binding between the Ag(+) ion and the single C:C mismatched base pair was mainly driven by the positive dehydration entropy change and the negative binding enthalpy change. In the interaction between the Ag(+) ion and each of the consecutive and interrupted double C:C mismatched base pairs, stoichiometric binding at a 1:1 molar ratio was achieved in each step of the first and second Ag(+) binding. The binding affinity for the second Ag(+) binding was similar to that for the first Ag(+) binding. Stoichiometric binding without interference and negative cooperativity may be favorable for aligning multiple Ag(+) ions in duplex DNA for applications of the metal-mediated base pairs in nanotechnology.
In the presence of Ag(I) ions, the C-T and m(5)iC (5-methylisocytosine)-T base pairs showed comparable stability to the C-Ag(I)-C base pair, and the m(5)iC-C base pair was highly stabilized by the synergetic effect of Ag(I) coordination and possible hydrogen bonding.
Metal-mediated base pair formation, resulting from the interaction between metal ions and artificial bases in oligonucleotides, has been developed for its potential application in nanotechnology. We have recently found that the T:T mismatched base pair binds with Hg(II) ions to generate a novel metal-mediated base pair in duplex DNA. The thermal stability of the duplex with the T-Hg-T base pair was comparable to that of the corresponding T:A or A:T. The novel T-Hg-T base pair involving the natural base thymine is more convenient than the metal-mediated base pairs involving artificial bases due to the lack of time-consuming synthesis. Here, we examine the specificity and thermodynamic properties of the binding between Hg(II) ions and the T:T mismatched base pair. Only the melting temperature of the duplex with T:T and not of the perfectly matched or other mismatched base pairs was found to specifically increase in the presence of Hg(II) ions. Hg(II) specifically bound with the T:T mismatched base pair at a molar ratio of 1:1 with a binding constant of 10(6) M(-1), which is significantly higher than that for nonspecific metal ion-DNA interactions. Furthermore, the higher-order structure of the duplex was not significantly distorted by the Hg(II) ion binding. Our results support the idea that the T-Hg-T base pair could eventually lead to progress in potential applications of metal-mediated base pairs in nanotechnology.
We investigate the statistical mechanics of a simple lattice model for the denaturation of the DNA double helix. The model consists of two chains connected by Morse potentials representing the H bonds. We determine the temperature dependence of the interstrand separation and we show that a mechanism involving an energy localization analogous to self-focusing may initiate the denaturation.
We have generated a novel silver(I)-mediated unnatural DNA base pair consisting of two 2,6-bis(ethylthiomethyl)pyridine nucleobases SPy. This metallo-base pair has a remarkably high pairing stability and selectivity which rivals that of the natural base pairs dA:dT and dC:dG. UV-melting experiments revealed that the dSPy:dSPy self-pair can replace natural base pairs at multiple sites and still form stable DNA duplexes.
Very specific binding of of Hg(II) and Ag(I) cations unexpectedly and significantly stabilizes the naturally occurring miss-base pairs, thymine-thymine and cytosine-cytosine, in DNA duplexes.
Melting temperatures, T(m), were systematically studied for a set of 92 DNA duplex oligomers in a variety of sodium ion concentrations ranging from 69 mM to 1.02 M. The relationship between T(m) and ln [Na(+)] was nonlinear over this range of sodium ion concentrations, and the observed melting temperatures were poorly predicted by existing algorithms. A new empirical relationship was derived from UV melting data that employs a quadratic function, which better models the melting temperatures of DNA duplex oligomers as sodium ion concentration is varied. Statistical analysis shows that this improved salt correction is significantly more accurate than previously suggested algorithms and predicts salt-corrected melting temperatures with an average error of only 1.6 degrees C when tested against an independent validation set of T(m) measurements obtained from the literature. Differential scanning calorimetry studies demonstrate that this T(m) salt correction is insensitive to DNA concentration. The T(m) salt correction function was found to be sequence-dependent and varied with the fraction of G.C base pairs, in agreement with previous studies of genomic and polymeric DNAs. The salt correction function is independent of oligomer length, suggesting that end-fraying and other end effects have little influence on the amount of sodium counterions released during duplex melting. The results are discussed in the context of counterion condensation theory.
The very specific binding of the HgII ion unexpectedly and significantly stabilizes naturally occurring thymine-thymine base mispairing in DNA duplexes. Following this finding, we prepared DNA duplexes containing metal-mediated base pairs at the desired sites, as well as novel double helical architectures consisting only of thymine-HgII-thymine pairs.
N-N J-coupling across a metal center (2JNN) was clearly detected in a biological macromolecule (DNA duplex) for the first time. By using 2JNN, the base pairing mode of mercury-mediatedT-T pairs (T-HgII-T) was definitely determined. This pairing mode was found to be a novel metal ion-binding mode for DNA and RNA molecules, in which imino proton-metal exchange processes are included. Accordingly, 2JNN is highly important for the determination of the chemical structures of metal-mediated base pairs.
Highly selective oligonucleotide-based sensor for mercury (II) in aqueous solutions
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