Sequence dependent proton‐transfer reaction in stacked GC pair I: The possibility of proton‐transfer reactions

Abstract

ABSTRACT:We explored the possibilities of proton-transfer reactions between guanines (G) and cytosines (C) in stacking two GC pairs by means of density functional methods. There are two combinations of sequences, GC/GC (5Ј-dGpG-3Ј) and CG/GC (5Ј-dCpG-3Ј). We found that the simultaneous single proton transfer (SPT) in two base pairs, two independent double proton transfer (DPT), and continuous double SPT reactions strongly depend on the sequence of the DNA, because the SPT reaction occurs in specific sequences including CG/GC and the latter DPTs occur in those including GC/GC. The properties of the DPT products, such as effective charges, are almost the same as the original GC/GC, whereas the effective charges on G and C in the simultaneous SPT product become negative and positive in comparison with those in the original GC/GC. Coulomb attraction caused by the charge separation mainly contributes to the stability of the SPT product.

Theoretical Investigation of the Coupling between Hydrogen‐Atom Transfer and Stacking Interaction in Adenine–Thymine Dimers

“…Apart from the covalent bonds in the backbone, this structure is essentially held together by polar inter‐strand hydrogen bonds and apolar intra‐strand stacking π–π interactions. These two types of interactions have been widely considered in the literature, but only a few studies have been devoted to the coupling of the stacking and hydrogen‐bonding interactions in nucleic acid base pairs,1–6 and mainly the cytosine–guanine (C‐G) base pair.…”

Influence of Mg2+ on the Guanine–Cytosine Tautomeric Equilibrium: Simulations of the Induced Intermolecular Proton Transfer

“…Another major interaction is stacking, which deeply modifies the H-bond strengths [30] and also modulates the double proton transfer (DPT) energetic profile in metal-free DNA. [22,31,32] Recent efforts for assessing the relationship between PT reactions and spontaneous mutations have been performed using a central base pair under the influence of two neighboring base pairs, located below and above the investigated moiety, [21] and a similar model is used herein. As suggested by Chen and co-workers, [21] the PT in the GC radical anion is significantly influenced by stacking and hydration, as they increase the kinetic barrier and reaction energy by about 6 and 5 kcal mol À1 , respectively.…”

Metal-Assisted Proton Transfer in Guanine-Cytosine Pair: An Approach from Quantum Chemistry

“…However, these reactions hardly take place because of high energy barriers as seen in one GC pair [20]. For further research, it is natural to study what happens when two or more base pairs are stacked.…”