Charge transfer dynamics in DNA revealed by time-resolved spectroscopy

Fujitsuka, Mamoru; Majima, Tetsuro

doi:10.1039/c6sc03428d

Cited by 32 publications

(29 citation statements)

References 79 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Although works from the late 70′s to date have established that radiation-produced electrons in their various stages exhibit different reactivity towards DNA subunits-bases and the sugar-phosphate backbone—this field is hence under active debate [4,8,29,30,31,38,39,45,56,57,58,59,60,61,62,63,64,70,71,72,73,74,75,88,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113]. The consensus that emerged from extensive studies by various groups are the following:…”

Section: Ultrafast Hole and Electron Transfer Under Irradiationmentioning

confidence: 99%

“…A substantial volume of work has been focused on radiation-induced hole-mediated damage in DNA via the oxidation pathway, as this pathway may lead to cellular death [29,30,31,38,39,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68]. A fast base-to-base hole transfer process [29,30,31,38,39,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72] and backbone-to-base hole transfer process [30,31,38,39,43,…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Ultrafast Processes Occurring in Radiolysis of Highly Concentrated Solutions of Nucleosides/Tides

Denisov

Adhikary

et al. 2019

IJMS

View full text Add to dashboard Cite

Among the radicals (hydroxyl radical (•OH), hydrogen atom (H•), and solvated electron (esol−)) that are generated via water radiolysis, •OH has been shown to be the main transient species responsible for radiation damage to DNA via the indirect effect. Reactions of these radicals with DNA-model systems (bases, nucleosides, nucleotides, polynucleotides of defined sequences, single stranded (ss) and double stranded (ds) highly polymeric DNA, nucleohistones) were extensively investigated. The timescale of the reactions of these radicals with DNA-models range from nanoseconds (ns) to microseconds (µs) at ambient temperature and are controlled by diffusion or activation. However, those studies carried out in dilute solutions that model radiation damage to DNA via indirect action do not turn out to be valid in dense biological medium, where solute and water molecules are in close contact (e.g., in cellular environment). In that case, the initial species formed from water radiolysis are two radicals that are ultrashort-lived and charged: the water cation radical (H2O•+) and prethermalized electron. These species are captured by target biomolecules (e.g., DNA, proteins, etc.) in competition with their inherent pathways of proton transfer and relaxation occurring in less than 1 picosecond. In addition, the direct-type effects of radiation, i.e., ionization of macromolecule plus excitations proximate to ionizations, become important. The holes (i.e., unpaired spin or cation radical sites) created by ionization undergo fast spin transfer across DNA subunits. The exploration of the above-mentioned ultrafast processes is crucial to elucidate our understanding of the mechanisms that are involved in causing DNA damage via direct-type effects of radiation. Only recently, investigations of these ultrafast processes have been attempted by studying concentrated solutions of nucleosides/tides under ambient conditions. Recent advancements of laser-driven picosecond electron accelerators have provided an opportunity to address some long-term puzzling questions in the context of direct-type and indirect effects of DNA damage. In this review, we have presented key findings that are important to elucidate mechanisms of complex processes including excess electron-mediated bond breakage and hole transfer, occurring at the single nucleoside/tide level.

show abstract

Section: Ultrafast Hole and Electron Transfer Under Irradiationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Ultrafast Processes Occurring in Radiolysis of Highly Concentrated Solutions of Nucleosides/Tides

Denisov

Adhikary

et al. 2019

IJMS

View full text Add to dashboard Cite

show abstract

“…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 ~510 7 (Hz) and ~0.2eV for GAG, to 10 5 (Hz) and ~0.45eV.…”

Section: -D Searching Strategy and Coin-position Entanglement Ecorvmentioning

confidence: 98%

“…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 [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.…”

Section: -D Searching Strategy and Coin-position Entanglement Ecorvmentioning

confidence: 98%

Protein-DNA target search relies on Quantum Walk

D’Acunto¹

2020

Preprint

View full text Add to dashboard Cite

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.

show abstract

“…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 ].…”

Section: Introductionmentioning

confidence: 99%

Hole Transfer in Open Carbynes

2020

View full text Add to dashboard Cite

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.

show abstract

Charge transfer dynamics in DNA revealed by time-resolved spectroscopy

Abstract: Time-resolved study revealed kinetics of charge transfer in DNA.

Cited by 32 publications

References 79 publications

Ultrafast Processes Occurring in Radiolysis of Highly Concentrated Solutions of Nucleosides/Tides

Ultrafast Processes Occurring in Radiolysis of Highly Concentrated Solutions of Nucleosides/Tides

Protein-DNA target search relies on Quantum Walk

Hole Transfer in Open Carbynes

Contact Info

Product

Resources

About