Nucleic acid charge transfer: Black, white and gray

Venkatramani, Ravindra; Keinan, Shahar; Balaeff, Alexander; Beratan, David N.

doi:10.1016/j.ccr.2010.12.010

Cited by 117 publications

(143 citation statements)

References 120 publications

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“…[49][50][51] As an alternative to DNA, peptide nucleic acid (PNA) strands present certain advantages for long-range hole hopping. [58][59][60][61] The smaller helical twist of PNA, in comparison with DNA, improves the electronic coupling between neighboring bases. 58 Furthermore, PNA derivatives are not acids (despite the name) and they do not contain ionic charges along their backbones.…”

Section: Ct Molecular Electrets: Practical Ideas From Structural Biologymentioning

confidence: 99%

“…[58][59][60][61] The smaller helical twist of PNA, in comparison with DNA, improves the electronic coupling between neighboring bases. 58 Furthermore, PNA derivatives are not acids (despite the name) and they do not contain ionic charges along their backbones. Instead, PNA backbones comprise primary and secondary amides resulting in the intrinsic electric dipole reported for single-stranded structures.…”

Section: Ct Molecular Electrets: Practical Ideas From Structural Biologymentioning

confidence: 99%

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Bioinspired molecular electrets: bottom-up approach to energy materials and applications

2015

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Abstract. The diversity of life on Earth is made possible through an immense variety of proteins that stems from less than a couple of dozen native amino acids. Is it possible to achieve similar engineering freedom and precision to design electronic materials? What if a handful of nonnative residues with a wide range of characteristics could be rationally placed in sequences to form organic macromolecules with specifically targeted properties and functionalities? Referred to as molecular electrets, dipolar oligomers and polymers composed of non-native aromatic beta-amino acids, anthranilamides (Aa) provide venues for pursuing such possibilities. The electret molecular dipoles play a crucial role in rectifying charge transfer, e.g., enhancing charge separation and suppressing undesired charge recombination, which is essential for photovoltaics, photocatalysis, and other solar-energy applications. A set of a few Aa residues can serve as building blocks for molecular electrets with widely diverse electronic properties, presenting venues for bottom-up designs. We demonstrate how three substituents and structural permutations within an Aa residue widely alter its reduction potential. Paradigms of diversity in electronic properties, originating from a few changes within a basic molecular structure, illustrate the promising potentials of biological inspiration for energy science and engineering.

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Section: Ct Molecular Electrets: Practical Ideas From Structural Biologymentioning

confidence: 99%

Section: Ct Molecular Electrets: Practical Ideas From Structural Biologymentioning

confidence: 99%

Bioinspired molecular electrets: bottom-up approach to energy materials and applications

2015

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“…40 On the other hand, Sugiyama and Saito demonstrated stabilization of the charge over a couple of G's based on theoretical calculations. 58 Beratan et al also pointed out the delocalization of the charge to the neighboring base, and how flexibility produces a larger rate of CT. 39,42 Overall, theoretical research predominantly suggests the localization of the charge during transport.…”

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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“…The INDO/s method has been used in the past to calculate the electronic properties of DNA, as well as those of carbon nanotubes [50,[67][68][69][70][71][72], and showed accuracy comparable to that of higher-level quantum calculations [65,73,74]. The INDO/s electronic structure was calculated for each of the 6200 frames of the 3.1 ns molecular dynamics (MD) simulation [40] of two intertwined (GT) 30 DNA chains wrapped around a 70 Å-long fragment of (6,5) SWNT (see Fig.…”

Section: Theory and Simulationsmentioning

confidence: 99%

Two-color spectroscopy of UV excited ssDNA complex with a single-wall nanotube photoluminescence probe: Fast relaxation by nucleobase autoionization mechanism

et al. 2016

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SWNT ssDNADNA is capable to recover after absorbing ultraviolet (UV) radiation, for example, by autoionization (AI). Singlewall carbon nanotube (SWNT) two-color photoluminescence spectroscopy was combined with quantum mechanical calculations to explain the AI in self-assembled complexes of DNA wrapped around SWNT. DNA autoionization is a fundamental process wherein UV-photoexcited nucleobases dissipate energy by charge transfer to the environment without undergoing chemical damage. Here, single-wall carbon nanotubes (SWNT) are explored as a photoluminescent reporter for studying the mechanism and rates of DNA autoionization. Two-color photoluminescence spectroscopy allows separate photoexcitation of the DNA and the SWNTs in the UV and visible range, respectively. A strong SWNT photoluminescence quenching is observed when the UV pump is resonant with the DNA absorption, consistent with charge transfer from the excited states of the DNA to the SWNT. Semiempirical calculations of the DNA-SWNT electronic structure, combined with a Green's function theory for charge transfer, show a 20 fs autoionization rate, dominated by the hole transfer. Rate-equation analysis of the spectroscopy data confirms that the quenching rate is limited by the thermalization of the free charge carriers transferred to the nanotube reservoir. The developed approach has a great potential for monitoring DNA excitation, autoionization, and chemical damage both in vivo and in vitro arXiv:1512.00710v1 [cond-mat.mes-hall] 2 Dec 2015 2

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Nucleic acid charge transfer: Black, white and gray

Cited by 117 publications

References 120 publications

Bioinspired molecular electrets: bottom-up approach to energy materials and applications

Bioinspired molecular electrets: bottom-up approach to energy materials and applications

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

Two-color spectroscopy of UV excited ssDNA complex with a single-wall nanotube photoluminescence probe: Fast relaxation by nucleobase autoionization mechanism

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