Localization of a Hole on an Adenine−Thymine Radical Cation in B-Form DNA in Water

Kravec, Shane M.; Kinz-Thompson, Colin D.; Conwell, E. M.

doi:10.1021/jp110062y

Cited by 21 publications

(39 citation statements)

References 22 publications

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“…It was found that immediately upon introduction of the hole its wavefunction is spread over 5 adenines, the length of the QM region in this simulation [8,9]. Within 20 fs, however, the hole is localized on a single one of these adenines [8,10]. It was shown that the contraction of the hole, that we have called self-trapping, is due to the polarization set up by the hole in the surrounding water [10,11].…”

mentioning

confidence: 72%

“…Within 20 fs, however, the hole is localized on a single one of these adenines [8,10]. It was shown that the contraction of the hole, that we have called self-trapping, is due to the polarization set up by the hole in the surrounding water [10,11]. That this can happen on a fs time scale can be attributed to the librational motion of the water molecules [10].…”

mentioning

confidence: 97%

“…It was shown that the contraction of the hole, that we have called self-trapping, is due to the polarization set up by the hole in the surrounding water [10,11]. That this can happen on a fs time scale can be attributed to the librational motion of the water molecules [10]. The water molecule has two librational modes, L 1 and L 2 , with resonant frequencies of ~11.5 and 23 THZ [12].…”

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confidence: 99%

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The Role of Hole Traps in DNA

Conwell¹

2014

J Phys Chem Biophys

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confidence: 72%

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confidence: 97%

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confidence: 99%

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The Role of Hole Traps in DNA

Conwell¹

2014

J Phys Chem Biophys

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“…Geometric conformation, which is sensitive to various factors such as temperature, solvent, and counter ions, affects the electronic coupling that alters the CT rate. 56,57 They also reported that polar surroundings suppress charge delocalization in DNA and the charge in GC repeats localizes on individual G's. 35 Conwell et al suggested the formation of a large polaron that spreads in length over 56 base pairs in their earlier work, 40,56 although they recently reported the localization of the charge on a single A in an A/T consecutive sequence due to the polarization of the surrounding water by the charge.…”

Section: ¹1mentioning

confidence: 98%

“…35 Conwell et al suggested the formation of a large polaron that spreads in length over 56 base pairs in their earlier work, 40,56 although they recently reported the localization of the charge on a single A in an A/T consecutive sequence due to the polarization of the surrounding water by the charge. 57 They also proposed that interstranded CT would not occur in such GC repeats and the polaron wave function is predominantly for the CT in DNA. 40 On the other hand, Sugiyama and Saito demonstrated stabilization of the charge over a couple of G's based on theoretical calculations.…”

Section: ¹1mentioning

confidence: 99%

Kinetics of Charge Transfer through DNA across Guanine–Cytosine Repeats Intervened by Adenine–Thymine Base Pair(s)

Osakada

Kawai

Majima

2012

Bulletin of the Chemical Society of Japan

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Charge transfer (CT) in DNA has been studied extensively in the past decade. Several reasonable models, concerning delocalized charge over guanines (G's) as well as localized charge on individual G's, such as polaron and hopping mechanisms, are proposed based on theoretical and experimental research. It is likely that the dynamic nature of DNA such as electronic coupling and dynamic motion is important to promote this process. We previously reported the kinetic features of CT across the G and cytosine (C) repetitive sequence (GC repeats). Temperature-dependent experiments in GC repeats suggested the importance of the conformational flexibility and structure of DNA toward CT in DNA. In the present paper, we look further into the dynamic mechanisms of CT in DNA across GC repeats. Based on the nanosecond transient absorption measurement, we monitored the migration of a charge in DNA having GC repeats separated by A/T intervening base pair(s). Interestingly, the migration time of the charge varies depending on the position, where A/T base pair(s) are located among GC repeats. Thus, the data obtained here are not simply explained by G-hopping mechanisms, in which the charge localizes on individual G's. These results possibly indicate that CT in DNA across GC repeats proceeds via delocalization of the charge over G's to some extent, rather than localized G-hopping mechanisms.Charge transfer (CT) in DNA has been attracting considerable interest from both fundamental and practical points of view. 16 Understanding of the essential nature for CT in DNA is necessary to realize a novel class of DNA-based electrochemical sensing single-nucleotide polymorphisms as well as to figure out its significance toward biological systems such as repairing oxidative damage.712 CT in DNA has been characterized by the migration of a positive charge and excess electron, 1316 up to long distances through ³-stacking of DNA double helical structure. In particular, the long-range CT of positive charge, which we refer to as "CT in DNA" in the present paper, has been studied extensively over decades based on experimental and theoretical methodologies.In particular, tremendous progress in understanding the mechanistic underpinnings of CT in DNA has been accomplished by studies based on chemical analysis, such as guanine (G) oxidative products and the products of charge trapping molecules, 1721 although we would caution against the use of oxidative yield to discuss the kinetics based on these processes, as pointed out by Lewis et al. 22 and us, 23 since the kinetics of product formation is not fully understood. Long-range CT in DNA might occur via a hopping mechanism between G's, which have the lowest oxidation potential among nucleobases (E ox = 1.31 eV versus NHE). 17,2427 Alternative models also suggested that DNA dynamics, especially via delocalized charge such as polaron or domain, might play an important role in DNA-mediated CT.2830 Schuster et al. suggested the formulation of the phonon-assisted polaron hopping model for the charge migrati...

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Electron transfer in DNA

Siriwong

Voityuk

2012

WIREs Comput Mol Sci

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During the last two decades, electron transfer (ET) through DNA and its artificial analogues has been an area of extensive experimental and theoretical studies. This process plays an important role in biology (damage and repair of DNA in living cells) and is of potential interest in material sciences. Because structural dynamics of the π stack and its environment affect essentially the electron transport, some significant details of excess charge migration cannot be derived from experiments. Computer simulations of the ET process provide microscopic insights into mechanisms of this process. In the paper, we consider computational methods used to describe the propagation of excess charges through π stacks of DNA and related systems. © 2012 John Wiley & Sons, Ltd. This article is categorized under: Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods

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Localization of a Hole on an Adenine−Thymine Radical Cation in B-Form DNA in Water

Cited by 21 publications

References 22 publications

The Role of Hole Traps in DNA

The Role of Hole Traps in DNA

Kinetics of Charge Transfer through DNA across Guanine–Cytosine Repeats Intervened by Adenine–Thymine Base Pair(s)

Electron transfer in DNA

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