Effect of the state ofh-b-1 hydrogen bond on the character of some atom vibrations in guanine-cytosine pair of the DNA molecule

Abstract

For the first hydrogen bond of the guanine-cytosine (G-C) pair, the potential function V(r, R ) is found for the nonequilibrium bond length R. A new form of the semiempirical potential function, Clementi's calculations for V ( r , R,) and some experimental data are used. New wave functions and energy levels as a function of the H-bond length for the ground and several excited states are obtained. This allows one to obtain frequencies and amplitudes of some vibrations of the G-C pair side groups involved in the formation of the hydrogen bond when the latter is not excited and when it is excited to the first energy level.

A Polymerase Tautomeric Model for Radiation Induced Bystander Effects: A Model for Untargeted Base Substitution Mutagenesis during Error Prone and SOS Replication of Double Stranded DNA Containing Thymine and Adenine in Rare Tautomeric Forms

“…Thus, the hydrogen atom will remain with their partner on hydrogen bond ( Figure 1e). The calculations [104][105][106][107][108]110,112,113] semi empirical potential function for protons of hydrogen bonds was used, it was developed by Tolpygo & Grebneva [109]. The proposed model is in a good agreement with the results obtained by other authors [114][115][116].…”

“…This results in a strong "local heating-up", followed by initiation of normal oscillations of the bases. After several oscillations, taking ~10 -14 -10 -12 sec [104][105][106][107][108], the vibratory system will reach equilibrium. The oscillations of atoms will cause changes in the distances between the paired bases, in other words, in the lengths of H-bonds.…”

“…The lifetime of the excited Н-bond is ~4 x 10 -9 sec [112,113]. In the same time the characteristic periods of atomic oscillations are 10 -14 -10 -12 sec [104][105][106][107][108]. Therefore, there will be not more than several 10s of oscillations up to 100 oscillations that influence the length of the H-bond.…”

“…When the hydrogen bond becomes weaker it becomes longer. In this case, there is a second minimum and the second minimum deepens [105,106,110]. Therefore, if under the thermal relaxation of the excitation energy the hydrogen atom will go to partner for the hydrogen bond, the new tautomeric state will be stable even with a small elongation of the hydrogen bond.…”

The nature and possible mechanisms of potential mutations formation due to the appearance of tymine dimers after irradiating two-stranded DNA by ultra-violet light

“…Это приводит к сильному «локальному разогреву» и как резуль тат -к возбуждению нормальных колебаний осно ваний. За время порядка нескольких периодов этих колебаний (их периоды ~10~1 4 -10" 12 с [106][107][108][109]) колебательная система перейдет в равновесие. Ко лебания атомов оснований вызовут изменения рас стояний между спаренными основаниями, другими словами, длин Н-связей.…”