Advances in Quantum Systems in Chemistry, Physics, and Biology by Unknown

Author:Unknown
Language: eng
Format: epub
ISBN: 9783030349417
Publisher: Springer International Publishing

4 Regularities in the 3D Structures of BI and BII Conformational Families. Capabilities and Limitations of Computational Methods

Our previous theoretical study of elementary units of DNA revealed important regularities in 3D structure of BI and BII conformations of WCD [2, 3]. That work included DFT computations using PW91 functional and 6-31G(d) basis set applied to all 16 possible dDMPs. The geometry optimization started from the structure extracted from DNA fragments deposited in the NDB. Since we were unable to find BII conformations of dDMPs for some nucleosides sequences we constructed them by replacing the bases in other dDMPs. It appears that all these dDMPs with any nucleoside sequence retain the conformational characteristics of the family in the optimized local energy minima. This includes the regions of SPB torsion angles, deoxyribose puckering, and nearly parallel base arrangements [3]. These results reproduce the sequence dependence of base superposition patterns on nucleoside sequence observed for BI conformation duplex fragments in crystals, namely, the substantial base ring superposition for sequences with purine nucleosides in 5′-end of dDMP and the minor superposition for sequences with pyrimidine nucleosides in 5′-end. Confirmed based on additional computations using PW91 and PBE functionals, this regularity subsequently extends to AI and AII conformation families of dDMPs [4–6] as well as to cdDMPs with both chains belonging either to BI or AI conformation families [6, 7]. This leads to conclusion that many biologically important conformational characteristics of ‘canonical’ WCD preexist in the local energy minima of its elementary units, dDMPs and cdDMPs. These conformational regularities and their presence in DFT computations of the elemental units distinguish WCD from other polynucleotide duplexes having non-Watson-Crick geometry of nucleoside pairs [4–8] and, as we found recently, from other families of duplexes with Watson-Crick nucleoside pairs but with changed conformation of one or both SPB chains.

The regularities mentioned above have been additionally confirmed by ab initio computations of selected structures using MP2 level of theory and various basis sets up to 6-311++G** [6, 7]. Nevertheless, both QM approaches failed to reproduce the fine aspects of dDMP and cdDMP structures. DFT computations using PW91 and PBE functional systematically overestimate the distance between bases of dDMPs and between the stacked base pairs of cdDMPs [6, 7]. This error may be explained by underestimation of dispersion attraction between the aromatic rings in the DFT level of theory. This limitation of the DFT method however additionally strengthened our conclusion about the critical contribution of SPB to the formation of dDMP structure reproducing the conformational characteristics of WCD and to the nucleoside sequence dependence of 3D structure. This conclusion has been validated by exploring the local energy minima of SPB corresponding to BI, BII, AI, and AII families of DNA. This analysis demonstrated that the conformations of SPB in these DNA structures correspond to those of the local energy minima of the free SPB.

The MP2 computations of dDMPs and cdDMPs produce structures with shortened distances (up to 2.9 Å) between the stacked bases in comparison to the NDB data for

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