Thermodynamics of G⋅A mispairs in DNA: Continuum electrostatic model

Abstract

An analysis of the stability of a duplex containing G•A mispairs or G•A/A•G tandem during DNA melting has revealed that duplex stability depends on both DNA sequences and on the conformations of the G•A mispairs. The thermodynamics of single pair opening for G(anti)•A(syn) and G(anti)•A(anti) conformations adopted by G•A mispairs is found to strongly correlate with that of the canonical base pairs, while for sheared conformation a significant difference is observed.

Anharmonic vibrations of nucleobases: Structural basis of one- and two-dimensional infrared spectra for canonical and mismatched base pairs

“…For the A-T and G-C pairs, the H-bond lengths listed here are in good agreement with a previous report [67]. However, it is well known that the HF method tends to overestimate the H-bond length by a few percent in comparison with DFT results using B3LYP functionals, for example, with a similar basis set [59]. The computed H-bond lengths, even though these are obtained as gas phase structures, are still comparable with experimentally determined ones.…”

“…No basis set superposition error was considered either since our focus is mainly on evaluating the vibrational parameters. The interaction energy corresponds to the in-vacuum standard free energy for pair formation [59] at a given temperature (here it is 298.15 K). All calculations were performed using Gaussian 03 [60].…”

Quantum transport anomalies in DNA containing mispairs

“…A recent study indicates a negative correlation between the cancer risk and sensitivity of charge transport property of the gene to a mutation. [6] Understanding how mispairs modify the electric properties of DNA then becomes very important [7][8][9] and, together with the usage of other properties, [10,11] may improve mutation detecting techniques. [12][13][14][15] In addition, thanks to its perfect self-assembling and self-recognition properties found in nature, DNA is also expected to be a potentially functional material for molecular devices.…”

“…This result has also been simulated by simple tight-binding models. [25][26][27] It is known that G.A mispair in various conformations [11] is the most stable mispair and often present in the DNA. [5] The magnetic properties of DNA was studied earlier and found to be significantly influenced by the presence of the G.A mispair.…”

The Peculiarities of Polaron Motion in the Molecular Polynucleotide Chains of Finite Length In The Presence Of Localized Excitations in the Chain

“…Основным носителем тока в однородных синтетических полинуклеотидных последовательностях считается полярон [13,14,15,16]. Поляронный перенос заряда исследовался при воздействии температурных флуктуаций [17,18], в постоянном и переменном электрических полях [19]- [23], при импульсном силовом воздействии [24,25]. В ряде работ рассматривался перенос заряда как в однородных, так и в регулярных цепочках ДНК [26,27].…”