title: DNA minor groove electrostatic potential: influence of sequence-specific transitions of the torsion angle gamma and deoxyribose conformations.
abstract: The structural adjustments of the sugar-phosphate DNA backbone (switching of the γ angle (O5'-C5'-C4'-C3') from canonical to alternative conformations and/or C2'-endo → C3'-endo transition of deoxyribose) lead to the sequence-specific changes in accessible surface area of both polar and non-polar atoms of the grooves and the polar/hydrophobic profile of the latter ones. The distribution of the minor groove electrostatic potential is likely to be changing as a result of such conformational rearrangements in sugar-phosphate DNA backbone. Our analysis of the crystal structures of the short free DNA fragments and calculation of their electrostatic potentials allowed us to determine: (1) the number of classical and alternative γ angle conformations in the free B-DNA; (2) changes in the minor groove electrostatic potential, depending on the conformation of the sugar-phosphate DNA backbone; (3) the effect of the DNA sequence on the minor groove electrostatic potential. We have demonstrated that the structural adjustments of the DNA double helix (the conformations of the sugar-phosphate backbone and the minor groove dimensions) induce changes in the distribution of the minor groove electrostatic potential and are sequence-specific. Therefore, these features of the minor groove sizes and distribution of minor groove electrostatic potential can be used as a signal for recognition of the target DNA sequence by protein in the implementation of the indirect readout mechanism.
authors: a O. Ya. Usikov Institute for Radiophysics and Electronics , National Academy of Sciences of Ukraine , Acad. Proskury Street, 12 Kharkiv 61085 , Ukraine.
authors: M Y
authors: MY
authors: Zhitnikova
authors: a O. Ya. Usikov Institute for Radiophysics and Electronics , National Academy of Sciences of Ukraine , Acad. Proskury Street, 12 Kharkiv 61085 , Ukraine.
authors: A V
authors: AV
authors: Shestopalova
mesh_terms: D001483:Base Sequence; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D003855:Deoxyribose / Q000737:chemistry; D005092:Exonucleases / Q000737:chemistry; D009690:Nucleic Acid Conformation; D011485:Protein Binding
chemical_list: D003855:Deoxyribose; D004247:DNA; D005092:Exonucleases
keywords: DNA conformation; electrostatic potential; minor groove recognition