The data-set of the crystallographic coordinates of the DNA oligonucleotides (naked, i.e. non-comlexed A-DNA, naked B-DNA, and protein–DNA complexes) is extracted from the Nucleic Acid Data Bank (June 2012)(Berman et al., 1992). The complete list of 226structures selected for further analysis is shown inSupplementary Table 1.The cutoff criteria used for the structure selection areas follows:•The resolution of structures solved by the X-ray crystallography is better than 1.9 Å. This resolution has been previously identified as the one that ensures accurate determination of the sugar puckers and backbone torsion angles as well as statistical analysis of their distribution (Schneideret al., 1997).•The DNA oligonucleotides are double-stranded and contain 4 and more nucleotides in each chain.•The bases are unmodified.•The set of structures is non-redundant, i.e. only one structure is selected from the group of complexes containing an identical protein or its mutants. Preference is given to the complexes with wild-type proteins and complexes with better resolution.The pre-calculation treatment of the structural data includes erasing of the terminal unpaired nucleotides and splitting the oligonucleotides containing ruptures or modified bases so that the modified bases or the base pairs on both sides of the break are eliminated. In order to avoid the end effects, the terminal base pairs on both ends of each DNA structure are not included into analysis.
All structural parameters was calculated with 3DNA analyzer (Lu &Olson, 2003).
The ASA of the DNA atoms is calculated using the modified software described in Tolstorukov et al.,2004, built on the basis of the Higo and Go algorithm (Higo & Go, 1989). The principle of the algorithm is as follows: (1) the volume under study is filled with cubes with the edge size 1.5625102Å; (2) for each cube it is calculated whether it is located inside, out-side, or on a surface of the macromolecule; and (3)the surface of cubes located on the surface of the macromolecule gives the value of ASA. The resulting values are insensitive to orientation of the molecule in space. The following atom radii are chosen for calculations: 1.85 Å for C, 1.5 Å for N, 1.4 Å for O,and 2.0 Å for P. Hydrogen atoms are not included into analysis. The values of the atom ASA exposed in the major or minor grooves are calculated separately.Distinguishing the ASA in the grooves is done accord-ing to the same procedure as for the atom–atom contacts. The total polar and hydrophobic ASA of each nucleotide in either of groove are calculated asthe sum of the ASA of the atoms O3′,O4′,O5′, O1P,O2P, N2, O2, N3, N4, N6, N7, O4, O6, and the atoms C1′,C2′,C3′,C4′,C5′, C4, C5, C6, C8,С7,and C2, correspondingly. The ratio of the total polar to the total hydrophobic ASA gives the polar/hydro-phobic ratio.
The calculation of electrostatic potentials was performed using the software package DelPhi (Li et al.,2012),which was based on the solution of the nonlinear Poisson–Boltzmann equation. All calculations were done at physiological salt concentration of 0.145 M. The charges and atomic radii were taken from the Amber force field(Cornell et al.,1995). The following dielectric parameters were used: internal molecular dielectric constant ε=2and the dielectric constant of the surrounding water ε= 80. Electrostatic potential was calculated at the reference point i located near‘bottom’of minor groove, approximately in the plane of the base pair i.Reference point i is defined as a geometric center between O4′atoms ofi+ 1 nucleotide in Strand I (5′-3′direction) and i-1 nucleotide in Strand II (3′-5′direction) of DNA double helix. This definition of reference point allows one to estimate the minor groove electrostatic potential for single complementary nucleotide pair (Joshiet al.,2007)
1. Tkachenko M.Yu., Boryskina O.P., Shestopalova А.V., Tolstorukov М.Y. (2009) ProtNA-ASA: Protein-Nucleic Acid Structural Database with Information on Accessible Surface Area. Int J Quantum Chem. 2010. V. 110, P. 230 – 232. (English)
2. Boryskina O.P., Tkachenko M.Yu., Shestopalova А.V. Variability of DNA structure and protein-nucleic acid recognition. Biopolymers & Cell. Accepted for publication, September 2010. V. 26, N. 5. (Russian) 2010. - № 5, Т.26. - С.360-372.
3. Boryskina O.P., Tkachenko M.Yu., Shestopalova А.V. Specificity of protein-nucleic acid complexes and DNA readout mechanisms. Biopolymers & Cell. Submitted, May 2010. 2011. - № 1, Т.27. - С.3-16. (Russian)
4. Zhitnikova M.Yu., Boryskina O.P., Shestopalova A.V. Sequence-specific transitions of the torsion angle gamma change the polar-hydrophobic profile of the DNA grooves: implication for indirect protein-DNA recognition. J. Biomol. Struct. Dyn. - 2014. - V.32. – N 10. – pp. 1670-1685. (English)
5. Shestopalova A.V., Zhitnikova M.Yu., Boryskina O.P. DNA Polymorphism and the Problem of Protein-Nucleic Recognition. Monography. LAP: Lambert Academic Publishing, Saarbrucken, Germany, 2014-03-25, p. 112, ISBN 978-3-659-30140-7. (Russian)
6. Zhitnikova M.Yu., Boryskina O.P., Shestopalova A.V. Nucleosome as an example of a nanosystem formation: structural dynamics of nucleosomal DNA. Chapter 4. In book: “Nanobiophysics: Fundamentals and Applications”, Pan Stanford Publishing, CRC press, Taylor & Francis Group, NY. – 2015. – P. 95-128. (English)
7. Zhitnikova M.Yu., Shestopalova A.V. Influence of sequence-specific transitions of the torsion angle gamma and deoxyribose conformations on DNA minor groove electrostatic potential. J. Biomol.Struct. Dyn. – 2017. – V.35, N 15. – pp. 3384-3397. (English)
8. Zhitnikova M.Yu., Shestopalova A.V. DNA-protein complexation: contact profiles in DNA grooves. Biophysical Bulletin. – 2017. – V. 37(2). – P. 54-65.