Abstract
In the framework of the ‘sugar’ coarse-grained DNA model [N.A. Kovaleva, I.P. Koroleva (Kikot), M.A. Mazo, Journal of Molecular Modeling 23(2):66 (2017), https://doi.org/10.1007/s00894-017-3209-z], we study the transition between B and A forms of a short DNA molecule (12 base pairs) when the concentration of salt changes. The model exploits the explicit ions and implicit water representation and allows to separately change the friction of the ions and of the DNA molecule. We compare the behavior of the system for different values of friction which proved to not affect the order of the transition, but allowed to determine the roles of the DNA and the ions in the behavior of the conglomerate. We find the order (the first) and the point of the transition (0.316 M) in the case of ‘inviscid’ water (zero friction for both the ions and the DNA, the NVE ensemble). The helix consisting of 12 bp (more than thousand atoms) proved to exhibit the features of small systems. Namely, even at low salt concentrations, one can observe the jumps from B-DNA to A-DNA and back. We analyse the structure of the A-DNA and find the reasons for such a behavior.
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References
Lebrun, A., Lavery, R.: Modeling DNA deformations induced by minor groove binding proteins. Biopolymers 49(5), 341–353 (1999). https://doi.org/10.1002/(sici)1097-0282(19990415)49:5%3C341::aid-bip1%3E3.0.co;2-c
Lu, X.J., Shakked, Z., Olson, W.: A-form conformational motifs in ligand-bound DNA structures. J. Mol. Biol. 300(4), 819–840 (2000). https://doi.org/10.1006/jmbi.2000.3690
Timsit, Y.: DNA structure and polymerase fidelity. J. Mol. Biol. 293(4), 835–853 (1999). https://doi.org/10.1006/jmbi.1999.3199
Ivanov, V., Minchenkova, L., Schyolkina, A., Poletayev, A.: Different conformations of double-stranded nucleic acid in solution as revealed by circular dichroism. Biopolymers 12(1), 89–110 (1973). https://doi.org/10.1002/bip.1973.360120109
Nishimura, Y., Torigoe, C., Tsuboi, M.: Salt induced B - A transition of poly(dG).poly(dC) and the stabilization of A form by its methylation. Nucl. Acids Res. 14, 2737–2748 (1986)
Feig, M., Pettitt, B.M.: Experiment versus force fields: DNA conformation from molecular dynamics simulations. J. Phys. Chem. B 101(38), 7361–7363 (1997). https://doi.org/10.1021/jp971180a
Pastor, N.: The B- to A-DNA transition and the reorganization of solvent at the DNA surface. Biophys. J. 88(5), 3262 (2005). https://doi.org/10.1529/biophysj.104.058339
Hart, K., Foloppe, N., Baker, C.M., Denning, E.J., Nilsson, L., MacKerell, A.D.: Optimization of the charmm additive force field for DNA: improved treatment of the BI/BII conformational equilibrium. J. Chem. Theory Comput. 8(1), 348–362 (2012). https://doi.org/10.1021/ct200723y
Waters, J.T., Lu, X.J., Galindo-Murillo, R., Gumbart, J.C., Kim, H.D., Cheatham, T.E., Harvey, S.C.: Transitions of double-stranded DNA between the A- and B-forms. J. Phys. Chem. B 120(33), 8449–8456 (2016). https://doi.org/10.1021/acs.jpcb.6b02155
Ivani, I., Dans, P.D., Noy, A., Pérez, A., Faustino, I., Hospital, A., Walther, J., Andrio, P., Goñi, R., Balaceanu, A., Portella, G., Battistini, F., Gelpí, J.L., González, C., Vendruscolo, M., Laughton, C.A., Harris, S.A., Case, D.A., Orozco, M.: Parmbsc1: a refined force field for DNA simulations. Nat. Methods 13(1), 55–58 (2015). https://doi.org/10.1038/nmeth.3658
Kovaleva, N., Koroleva (Kikot), I., Mazo, M., Zubova, E.: The sugar coarse-grained DNA model. J. Mol. Model. 23(2), 66 (2017). https://doi.org/10.1007/s00894-017-3209-z
Savin, A., Mazo, M., Kikot, I., Manevitch, L., Onufriev, A.: Heat conductivity of the DNA double helix. Phys. Rev. B 83(24), 245,406 (2011). https://doi.org/10.1103/physrevb.83.245406
Klinov, A.P., Zubova, E.A., Mazo, M.A.: Temperature and concentration dependence of effective potentials of Na+ and Cl-ions in aqueous solution. Phys. Chem. Asp. Study Clust. Nanostruct. Nanomater. (9), 230–235 (2017). https://doi.org/10.26456/pcascnn/2017.9.230
Acknowledgements
We thank Dr. I.A. Strelnikov for pointing out some errata in numerical values and in one formula in the tables in [11]. We appreciate financial support of the Russian Science Foundation (grant 16-13-10302). The simulations were carried out in the Joint Supercomputer Center of Russian Academy of Sciences.
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Appendix: The Sugar DNA CG Force Field: Potential Functions and Parameters
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Kovaleva, N.A., Zubova, E.A. (2019). B\(\leftrightarrow \)A Transition in a Short DNA Molecule. In: Andrianov, I., Manevich, A., Mikhlin, Y., Gendelman, O. (eds) Problems of Nonlinear Mechanics and Physics of Materials. Advanced Structured Materials, vol 94. Springer, Cham. https://doi.org/10.1007/978-3-319-92234-8_13
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