The post-SCF quantum chemistry characteristics of the guanine–guanine stacking B-DNA

Abstract

The stacking interactions of two guanine molecules were analyzed detail at the DF-MP2/aug-cc-pVDZ level of theory for conformations appearing B-DNA. The dependence of intermolecular interaction energies on the pairs of step parameters (shift, slide, rise, tilt, roll and twist) was determined. The values of these parameters were chosen to cover the whole range of variability appearing crystallographic data. The scanning procedure was performed by subsequent changes of two variables with fixed values of the remaining base-pair and base-step BDNA parameters. Additionally, the hybrid variational-perturbational scheme was applied for the decomposition of the interaction energy into physically meaningful contributions at the MP2 level of theory. The significant impact of the mutual orientations of guanine bases was observed not only on the total intermolecular energy but also on its components. The second-order dispersion interaction is the most significant contribution to stabilization energy and is about eight times larger compared to the first-order electrostatic term with relaxation effects, which is also of stabilizing character. The dispersion interactions may vary up to 9.6 kcal mol(-1) between different guanine-guanine conformations. The parameters defining the mutual orientation of stacked guanine molecules have a different impact on the stabilization of the investigated complex. The following base-step parameters have only a minor impact on the stabilization energies: shift-slide, shift-roll, shift-twist, slide-twist and roll-twist. On the other hand, parameters such as rise and tilt significantly influence intermolecular interactions, i.e. strong attraction occurs only for a limited range of their values.

Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations?

“…[47][48][49] This is definitely a viable approach for the highest resolution and carefully refined structures (such as those of B-DNA decamers), provided the experimental nucleobase geometries are overlaid by QM-optimized monomers. 50,51 However, a small experimental error in interbase positions (mainly incorrect values of interbase angles) leading to close interatomic contacts may introduce large errors in energy calculations.…”

“…On the other hand, MP2/aug-cc-pVDZ calculations, which give more negative (i.e., more stable) stacking energies than the MP2/6-31G*(0.25) method, can be considered as a reasonable compromise between accuracy and computational demands. 25,47,48 Comment on Comparison with Experiments. The calculations provide intrinsic stacking energies that correspond to the gas phase environment.…”

Energy hyperspace for stacking interaction in AU/AU dinucleotide step: Dispersion‐corrected density functional theory study

“…following sequence-dependent interactions: (a) hydrogenbonding: this can be intra-or inter-base pair and can involve ribose interaction in case of RNA, (b) p-stacking interactions between the base aromatic rings and (c) external effects comprising of metal ion interaction, hydration, etc., which are mostly nonspecific. [15][16][17][18][19][20][21] Earlier, there were attempts to understand how base stacking energy obtained from van der Waals (vdW) and electrostatic interactions correlates with experimental data. Even recent quantum mechanical calculations of optimized structures of base pair steps have tried to focus on the equal contributions of both these interactions.…”

Theoretical insights into the nature of intermolecular interactions in cytosine dimer

“…It is well established that dispersion component is the main source of stabilization of stacked nucleic acid bases. The analysis of the nature of interactions in base pairs, however, has been settled on quantitative ground only quite recently [23][24][25][26][27][28][29][30][31]. Hill and collaborators analyzed the importance of electrostatics for stabilization of DNA bases [24].…”