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Mechanisms of HT and EET in DNA. (a) G-to-G consecutive hole hopping, (b) G–X–G (X = A, C, or T) hole tunnelling, (c) T-to-T consecutive excess electron hopping, and (d) T–Y–T excess electron tunnelling. Eox and Ered are oxidation and reduction potentials, respectively. Note: Eox(G) < Eox(X), while Ered(T) > Ered(Y)
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In the past few decades, charge transfer in DNA has attracted considerable attention from researchers in a wide variety of fields, including bioscience, physical chemistry, and nanotechnology. Charge transfer in DNA has been investigated using various techniques. Among them, time-resolved spectroscopic methods have yielded valuable information on c...
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Citations
... Marguet et al. state that the interpretation of Ref. [12] was oversimplified [13]. Moreover, the charge-transfer dynamics in DNA have also been studied by time-resolved spectroscopy [14]. More interestingly, the development of multipulse configuration has been extended to UV regions and its application in 2D ES was achieved by Prokhorenko and coworkers [15] in 2016. ...
Investigating exciton dynamics within DNA nucleobases is essential for comprehensively understanding how inherent photostability mechanisms function at the molecular level, particularly in the context of life’s resilience to solar radiation. In this paper, we introduce a mathematical model that effectively simulates the photoexcitation and deactivation dynamics of nucleobases within an ultrafast timeframe, particularly focusing on wave-packet dynamics under conditions of strong nonadiabatic coupling. Employing the hierarchy equation of motion, we simulate two-dimensional electronic spectra (2DES) and calibrate our model by comparing it with experimentally obtained spectra. This study also explores the effects of base stacking on the photo-deactivation dynamics in DNA. Our results demonstrate that, while strong excitonic interactions between nucleobases are present, they have a minimal impact on the deactivation dynamics of the wave packet in the electronic excited states. We further observe that the longevity of electronic excited states increases with additional base stacking and pairing, a phenomenon accurately depicted by our excitonic model. This model enables a detailed examination of the wave packet’s motion on electronic excited states and its rapid transition to the ground state. Additionally, using this model, we studied base stacks in DNA hairpins to effectively capture the primary exciton dynamics at a reasonable computational scale. Overall, this work provides a valuable framework for studying exciton dynamics from single nucleobases to complex structures such as DNA hairpins.
... Thymine-adenine-thymine (TAT) is a representative base triplet, which consists of one charge donor and two charge acceptors [11][12][13][14][15][16]. Adenine (A) is oxidized and can be used as a hole carrier, while thymine (T) is reduced and regarded as an electron carrier [17,18]. T and A form a dimer through the Watson-Crick structure, and the third base T is parallel to A and connected by hydrogen bonds to form a stable base triplet structure [19][20][21][22]. ...
The short-range charge transfer of DNA base triplets has wide application prospects in bioelectronic devices for identifying DNA bases and clinical diagnostics, and the key to its development is to understand the mechanisms of short-range electron dynamics. However, tracing how electrons are transferred during the short-range charge transfer of DNA base triplets remains a great challenge. Here, by means of ab initio molecular dynamics and Ehrenfest dynamics, the nuclear–electron interaction in the thymine-adenine-thymine (TAT) charge transfer process is successfully simulated. The results show that the electron transfer of TAT has an oscillating phenomenon with a period of 10 fs. The charge density difference proves that the charge transfer proportion is as high as 59.817% at 50 fs. The peak position of the hydrogen bond fluctuates regularly between −0.040 and −0.056. The time-dependent Marcus–Levich–Jortner theory proves that the vibrational coupling between nucleus and electron induces coherent electron transfer in TAT. This work provides a real-time demonstration of the short-range coherent electron transfer of DNA base triplets and establishes a theoretical basis for the design and development of novel biological probe molecules.
... This discovery, made in 1993, opened the field of charge transport through nucleic acids. Since then, the conductivity of DNA has been demonstrated in numerous experiments (Fujitsuka and Majima 2017;Genereux and Barton 2010;Wagenknecht 2006). Beyond the aim of understanding the biological relevance, the main focus has been on the distances that can be covered in the process and the different types and mechanisms of charge transport. ...
... Although so far the high complexity of the system has partially hindered a complete characterization of the charge transfer processes in DNA, recent technical advances in spectroscopic instrumentation contributed to enhance our understanding of the kinetics of such phenomena. That is, starting from the first direct measurement of the photoinduced hole transport in DNA by time-resolved spectroscopy [3], several experimental works have contributed to shed light on this subject [4][5][6][7][8][9][10][11]. In particular, DNA hole transfer kinetics through π-stack arrays have been proved to depend not only from the redox potential of the single nucleobases but also on the DNA specific sequence and conformation [12] as revealed by means of time-resolved spectroscopic data. ...
In this paper, we extend the previously described general model for charge transfer reactions, introducing specific changes to treat the hopping between energy minima of the electronic ground state (i.e., transitions between the corresponding vibrational ground states). We applied the theoretical–computational model to the charge transfer reactions in DNA molecules which still represent a challenge for a rational full understanding of their mechanism. Results show that the presented model can provide a valid, relatively simple, approach to quantitatively study such reactions shedding light on several important aspects of the reaction mechanism.
... Extensive investigation by researchers all over the world have discovered the amazing biochemical mechanisms, charge transfer, and semiconducting characteristics in DNA [5,6]. In the microscopic dimension compatible to a quantum well superlattice, the knowledge gained from semiconductor science can be applied and used to supplement to a better understanding of DNA [7][8][9] or vice versa. ...
This study presents a quantum well model using transfer matrix to analyse the charge transfer characteristic in DNA nanostructure sequences. The unconfined state or unbound state above the quantum well are used to investigate the carrier behaviours in nanostructure of semiconductor. Similar analysis and simulations can be applied to the understanding of charge transfer in DNA nanostructure with sequence of periodic and quasi-periodic sequences. The model was validated with experiments using photoreflectance spectroscopy on nanostructure in semiconductor superlattice. In addition, the results published by the study of Thermoelectric effect and its dependence on molecular length and sequence in single DNA molecules[1] were used to compare with the simulations by the quantum well model. The results show agreement and can provide new insight into charge transfer and transport in DNA nanostructure with different types of sequences.
... This figure is adapted from Ref. 34. transport over nanometer scales because the charge transfer dynamics is limited by hopping among specific DNA nucleobases or nucleobase "islands" (typically purines for hole transport). 30,31 Achieving ratcheted charge transport in nucleic acids or other macromolecules may create novel opportunities to realize moleculebased circuitry in self-assembling matter. 32,33 In contrast to prior studies, which focused mainly on solid-state electronics, the ratchets explored here are based on a bottom-up approach with selfassembling soft matter. ...
Ratcheted multi-step hopping electron transfer systems can plausibly produce directional charge transport over very large distances without requiring a source–drain voltage bias. We examine molecular strategies to realize ratcheted charge transport based on multi-step charge hopping, and we illustrate two ratcheting mechanisms with examples based on DNA structures. The charge transport times and currents that may be generated in these assemblies are also estimated using kinetic simulations. The first ratcheting mechanism described for nanoscale systems requires local electric fields on the 10⁹ V/m scale to realize nearly 100% population transport. The second ratcheting mechanism for even larger systems, based on electrochemical gating, is estimated to generate currents as large as 0.1 pA for DNA structures that are a few μm in length with a gate voltage of about 5 V, a magnitude comparable to currents measured in DNA wires at the nanoscale when a source–drain voltage bias of similar magnitude is applied, suggesting an approach to considerably extend the distance range over which DNA charge transport devices may operate.
... Indeed, this reactivity is by far the most involved in oxidative DNA damage, initiated by reactive oxygen species (ROS) generated by normal cellular metabolism, or by exogenous sources such as ionizing or ultraviolet irradiation [1][2][3]. In the thirty years since the discovery of long-range charge transport in DNA, as reviewed by Barton and coworkers [4][5][6], a large body of experimental data have accumulated showing that the one-electron oxidation of DNA produces a hole that can migrate through the double helix with the final destination at the G sites [4][5][6][7][8][9][10]. Among the four common DNA bases (A, G, T, and C), G is the most readily oxidized to the G radical cation (G •+ ), which is also the putative initial intermediate in the oxidative DNA damage. ...
... It is worth mentioning the redox reactions of guanine derivatives having methylation at the N1 position: the oxidation of 1-methyl guanosine (1-Me-Guo, 7) by Br2 •− and the reduction of 8-Br-1-Me-Guo (9) by eaq − showed identical absorption spectra having a band at 610-620 nm, which decays via second-order kinetics ( Figure 4). The transient is consistent with the 1-Me-G(N2-H) • radical (8) and the absence of tautomerization due to the N1-Me group [11,28]. The ESR and UV-visible spectra of 1-Me-G •+ 2 µs after the pulse (in red color); by monitoring the reaction at 620 nm (see red arrow), radical 3 is transformed to 2 with a first-order rate constant of 5 × 10 4 s −1 at room temperature with Arrhenius parameters reported in the insert (adapted from [11,28]). ...
... •− and the reduction of 8-Br-1-Me-Guo (9) by e aq − showed identical absorption spectra having a band at 610-620 nm, which decays via second-order kinetics ( Figure 4). The transient is consistent with the 1-Me-G(N2-H) • radical (8) and the absence of tautomerization due to the N1-Me group [11,28]. The ESR and UV-visible spectra of 1-Me-G •+ and its corresponding deprotonated 1-Me-G(N2-H) • are also recorded from the one-electronoxidized 1-Me-dGuo by Cl 2 ...
The guanyl radical or neutral guanine radical G(-H)• results from the loss of a hydrogen atom (H•) or an electron/proton (e–/H+) couple from the guanine structures (G). The guanyl radical exists in two tautomeric forms. As the modes of formation of the two tautomers, their relationship and reactivity at the nucleoside level are subjects of intense research and are discussed in a holistic manner, including time-resolved spectroscopies, product studies, and relevant theoretical calculations. Particular attention is given to the one-electron oxidation of the GC pair and the complex mechanism of the deprotonation vs. hydration step of GC•+ pair. The role of the two G(-H)• tautomers in single- and double-stranded oligonucleotides and the G-quadruplex, the supramolecular arrangement that attracts interest for its biological consequences, are considered. The importance of biomarkers of guanine DNA damage is also addressed.
... Sequences d-B n -a can be identified by different hopping rates between bases. Measured hopping rates for A-A or G-G present values to be 1.2 × 10 9 and 4.3 × 10 9 Hz, respectively (Fujitsuka and Majima, 2017). Long-range electron transfer is based on multistep hopping mechanisms and intra-and inter-strand hopping rates, as well as activation energy, between nucleotides depends on the bases involved. ...
... Long-range electron transfer is based on multistep hopping mechanisms and intra-and inter-strand hopping rates, as well as activation energy, between nucleotides depends on the bases involved. For example, GAC presents an intra-stand hole hopping rate ~10 6 Hz and an activation energy ~0.3eV, while GAAC ~10 4 Hz and ~0.53eV, respectively (Fujitsuka and Majima, 2017). Sequences as GAG and GAAG, again, present the more relevant changes due to insertion of an additional nucleotide A, going from ~5⋅10 7 (Hz) and ~0.2eV for GAG, to 10 5 (Hz) and ~0.45eV. ...
Protein-DNA interactions play a fundamental role in all life systems. A critical issue of such interactions is given by the strategy of protein search for specific targets on DNA. The mechanisms by which the protein are able to find relatively small cognate sequences, typically 15–20 base pairs (bps) for repressors, and 4–6 bps for re-striction enzymes among the millions of bp of non-specific chromosomal DNA have hardly engaged researchers for decades. Recent experimental studies have generated new insights on the basic processes of protein-DNA interactions evidencing the underlying complex dynamic phenomena involved, which combine three- dimensional and one-dimensional motion along the DNA chain. It has been demonstrated that protein mole-cules have an extraordinary ability to find the target very quickly on the DNA chain, in some cases, with two orders of magnitude faster than the diffusion limit. This unique property of protein-DNA search mechanism is known as facilitated diffusion. Several theoretical mechanisms have been suggested to describe the origin of facilitated diffusion. However, none of such models currently has the ability to fully describe the protein search strategy. In this paper, we suggest that the ability of proteins to identify consensus sequences on DNA is based on the entanglement of π-π electrons between DNA nucleotides and protein amino acids. The π-π entanglement is based on Quantum Walk (QW), through Coin-position entanglement (CPE). First, the protein identifies a dimer belonging to the consensus sequence, and localize a π on such dimer, hence, the other π electron scans the DNA chain until the sequence is identified. Focusing on the example of recognition of consensus sequences of EcoRV or EcoRI, we will describe the quantum features of QW on protein-DNA complexes during the search strategy, such as walker quadratic spreading on a coherent superposition of different vertices and environment-supported long- time survival probability of the walker. We will employ both discrete- or continuous-time versions of QW. Biased and unbiased classical Random Walk (CRW) have been used for a long time to describe the Protein-DNA search strategy. QW, the quantum version of CRW, has been widely studied for its applications in quantum information applications. In our biological application, the walker (the protein) resides at a vertex in a graph (the DNA structural topology). Differently to CRW, where the walker moves randomly, the quantum walker can hop along the edges in the graph to reach other vertices entering coherently a superposition across different vertices spreading quadratically faster than CRW analogous evidencing the typical speed up features of the QW. When applied to a protein-DNA target search problem, QW gives the possibility to achieve the experimental diffusional motion of proteins over diffusion classical limits experienced along DNA chains exploiting quantum features such as CPE and long-time survival probability supported by the environment. In turn, we come to the conclusion that, under quantum picture, the protein search strategy does not distinguish between one-dimensional (1D) and three-dimensional (3D) cases.
... Sequences d-B n -a can be identified by different hopping rates between bases. Measured hopping rates for A-A or G-G present values to be 1.210 9 and 4.310 9 Hz, respectively [69]. Long-range electron transfer is based on multistep hopping mechanisms and intra-and inter-strand hopping rates, as well as activation energy, between nucleotides depends by the bases involved. ...
... Long-range electron transfer is based on multistep hopping mechanisms and intra-and inter-strand hopping rates, as well as activation energy, between nucleotides depends by the bases involved. For example, GAC presents an intra-stand hole hopping rate ~10 6 Hz and an activation energy ~0.3eV, while GAAC ~10 4 Hz and ~0.53eV, respectively [69]. Sequences as GAG and GAAG, again, present the more relevant changes due to insertion of an additional nucleotide A, going from ~510 7 (Hz) and ~0.2eV for GAG, to 10 5 (Hz) and ~0.45eV. ...
Protein-DNA interactions play a fundamental role in all life systems. A critical issue of such interactions is given by the strategy of protein search for specific targets on DNA. The mechanisms by which the protein are able to find relatively small cognate sequences, typically 15-20 base pairs (bps) for repressors, and 4-6 bps for restriction enzymes among the millions of bp of non-specific chromosomal DNA have hardly engaged researcher for decades. Recent experimental studies have generated new insights on the basic processes of protein-DNA interactions evidencing the underlying complex dynamic phenomena involved, which combine three-dimensional and one-dimensional motion along the DNA chain. It has been demonstrated that protein molecules spend most of search time on the DNA chain with an extraordinary ability to find the target very quickly, in some cases, with two orders of magnitude faster than the diffusion limit. This unique property of protein-DNA search mechanism is known as facilitated diffusion . Several theoretical mechanisms have been suggested to describe the origin of facilitated diffusion. However, none of such models currently has the ability to fully describe the protein search strategy.
In this paper, we suggest that the ability of proteins to identify consensus sequence on DNA is based on the entanglement of π-π electrons between DNA nucleotides and protein amino acids. The π-π entanglement is based on Quantum Walk (QW), through Coin-position entanglement (CPE). First, the protein identifies a dimer belonging to the consensus sequence, and localize a π on such dimer, hence, the other π electron scans the DNA chain until the sequence is identified. By focusing on the example of recognition of consensus sequences by EcoRV or EcoRI, we will describe the quantum features of QW on protein-DNA complexes during search strategy, such as walker quadratic spreading on a coherent superposition of different vertices and environment-supported long-time survival probability of the walker. We will employ both discrete- or continuous-time versions of QW. Biased and unbiased classical Random Walk (CRW) has been used for a long time to describe Protein-DNA search strategy. QW, the quantum version of CRW, have been widely studied for its applications in quantum information applications. In our biological application, the walker (the protein) resides at a vertex in a graph (the DNA structural topology). Differently to CRW, where the walker moves randomly, the quantum walker can hop along the edges in the graph to reach other vertices entering coherently a superposition across different vertices spreading quadratically faster than CRW analogous evidencing the typical speed up features of the QW. When applied to protein-DNA target search problem, QW gives the possibility to achieve the experimental diffusional motion of proteins over diffusion classical limits experienced along DNA chains exploiting quantum features such as CPE and long-time survival probability supported by environment. In turn, we come to the conclusion that, under quantum picture, the protein search strategy does not distinguish between one-dimensional (1D) and three-dimensional (3D) case.
Significance
Most biological processes are associated to specific protein molecules binding to specific target sequences of DNA. Experiments have revealed a paradoxical phenomenon that can be synthesized as follows: proteins generally diffuse on DNA very slowly, but they can find targets very fast overwhelming two orders of magnitude faster than the diffusion limit. This paradox is known as facilitated diffusion . In this paper, we demonstrate that the paradox is solved by invoking the quantum walk picture for protein search strategy. This because the protein exploits quantum properties, such as long-time survival probability due to coherence shield induced by environment and coin-position entanglement to identify consensus sequence, in searching strategy. To our knowledge, this is the first application of quantum walk to the problem of protein-DNA target search strategy.
... In this work, the authors study terminated carbon chains of two to eight carbon atoms, and report that the increase of the wire length alters its function from an electron donor to an electron acceptor, but no transfer rate was reported. Experience from experiments of charge transfer along DNA shows that possibly a direct approach for this aim could be time-resolved spectroscopy [10][11][12][13][14][15][16]. ...
We investigate hole transfer in open carbynes, i.e., carbon atomic nanowires, using Real-Time Time-Dependent Density Functional Theory (RT-TDDFT). The nanowire is made of N carbon atoms. We use the functional B3LYP and the basis sets 3-21G, 6-31G*, cc-pVDZ, cc-pVTZ, cc-pVQZ. We also utilize a few Tight-Binding (TB) wire models, a very simple model with all sites equivalent and transfer integrals given by the Harrison ppπ expression (TBI) as well as a model with modified initial and final sites (TBImod) to take into account the presence of one or two or three hydrogen atoms at the edge sites. To achieve similar site occupations in cumulenes with those obtained by converged RT-TDDFT, TBImod is sufficient. However, to achieve similar frequency content of charge and dipole moment oscillations and similar coherent transfer rates, the TBImod transfer integrals have to be multiplied by a factor of four (TBImodt4times). An explanation for this is given. Full geometry optimization at the B3LYP/6-31G* level of theory shows that in cumulenes bond length alternation (BLA) is not strictly zero and is not constant, although it is symmetrical relative to the molecule center. BLA in cumulenic cases is much smaller than in polyynic cases, so, although not strictly, the separation to cumulenes and polyynes, approximately, holds. Vibrational analysis confirms that for N even all cumulenes with coplanar methylene end groups are stable, for N odd all cumulenes with perpendicular methylene end groups are stable, and the number of hydrogen atoms at the end groups is clearly seen in all cumulenic and polyynic cases. We calculate and discuss the Density Functional Theory (DFT) ground state energy of neutral molecules, the CDFT (Constrained DFT) "ground state energy" of molecules with a hole at one end group, energy spectra, density of states, energy gap, charge and dipole moment oscillations, mean over time probabilities to find the hole at each site, coherent transfer rates, and frequency content, in general. We also compare RT-TDDFT with TB results.
