Biologically important conformational features of DNA as interpreted by quantum mechanics and molecular mechanics computations of its simple fragments
| Autor: | Victor M. Anisimov, V.I. Poltev, N. A. Polteva, E. Gonzalez, Francisco Rivas, V. Dominguez, Alexandra Deriabina, Dolores Garcia |
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| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Models Molecular Work (thermodynamics) Dihedral angle 01 natural sciences Catalysis Inorganic Chemistry 03 medical and health sciences chemistry.chemical_compound 0103 physical sciences Directionality Computer Simulation Physical and Theoretical Chemistry Physics 010304 chemical physics Internal energy Organic Chemistry DNA Computer Science Applications Maxima and minima 030104 developmental biology Computational Theory and Mathematics chemistry Chemical physics Pairing Nucleic Acid Conformation Quantum Theory Density functional theory |
| Zdroj: | Journal of molecular modeling. 24(2) |
| ISSN: | 0948-5023 |
| Popis: | Deciphering the mechanism of functioning of DNA as the carrier of genetic information requires identifying inherent factors determining its structure and function. Following this path, our previous DFT studies attributed the origin of unique conformational characteristics of right-handed Watson-Crick duplexes (WCDs) to the conformational profile of deoxydinucleoside monophosphates (dDMPs) serving as the minimal repeating units of DNA strand. According to those findings, the directionality of the sugar-phosphate chain and the characteristic ranges of dihedral angles of energy minima combined with the geometric differences between purines and pyrimidines determine the dependence on base sequence of the three-dimensional (3D) structure of WCDs. This work extends our computational study to complementary deoxydinucleotide-monophosphates (cdDMPs) of non-standard conformation, including those of Z-family, Hoogsteen duplexes, parallel-stranded structures, and duplexes with mispaired bases. For most of these systems, except Z-conformation, computations closely reproduce experimental data within the tolerance of characteristic limits of dihedral parameters for each conformation family. Computation of cdDMPs with Z-conformation reveals that their experimental structures do not correspond to the internal energy minimum. This finding establishes the leading role of external factors in formation of the Z-conformation. Energy minima of cdDMPs of non-Watson-Crick duplexes demonstrate different sequence-dependence features than those known for WCDs. The obtained results provide evidence that the biologically important regularities of 3D structure distinguish WCDs from duplexes having non-Watson-Crick nucleotide pairing. |
| Databáze: | OpenAIRE |
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