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Effects of counterions and solvents on the geometrical and vibrational features of dinucleoside-monophosphate (dNMP): case of 3',5'-dideoxycytidine-monophosphate (dDCMP)

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Abstract

The effects of the interaction of the monovalent (Li+, Na+, K+) and divalent (Mg2+) counterions hexahydrated (6H2O), with the PO2− group, on the geometrical and vibrational characteristics of 3', 5'-dDCMP, were studied using the DFT/B3LYP/6-31++G(d) method. These calculations were performed using the explicit (6H2O) and hybrid (6H2O/Continuum) solvation models. The optimizations reveal that in the conformation g−g− and in the explicit model of solvation, the small ions (Li+, Na+) deviate from the bisector plane of the angle O1-P-O2 and the large ions (K+ and Mg2+) remain in this plane, whereas in the hybrid model of solvation, the counterions deviate from this plane. However, when the conformer is g+g+, the monovalent counterions deviate and divide the remainder of the plane regardless of the type of solvation model. In addition, the g−g− conformer is the most stable in the presence of the explicit solvent, while the g+g+ conformer is the most stable in the presence of the hybrid solvent. Finally, the normal modes of the conformers g−g− and g+g+ in the presence of the counterions in the hybrid model show a better agreement with the available experimental data of the DNA forms A, B (g−g−), and Z (g+g+) relatively to the explicit model. This very good agreement is illustrated by the very small deviations ≤ 0.08% (g−g−) and ≤ 0.41% (g+g+) observed between the calculated and experimental data for the PO2− (asymmetric) stretching mode in the presence of the counterion K+ in the hybrid model.

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References

  1. Hartmann B, Lavery R (1996) DNA structural forms. Q Rev Biophys 29:309–368

    CAS  PubMed  Google Scholar 

  2. Watson JD, Crick FHC (1953) Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature 171:737–738

    CAS  PubMed  Google Scholar 

  3. Wang AHJ, Quigley GJ, Kolpak FJ, Rawford JLC, van Boom JH, van der Marel G, Rich A (1979) Molecular structure of a left handed double helical DNA fragment at atomic resolution. Nature 282:680–686

    CAS  PubMed  Google Scholar 

  4. Drew HE, Wing RM, Takano T, Broka C, Tanaka S, Itakura K, Dickerson RE (1981) Structure of a B-DNA dodecamer: conformation and dynamics. Proc Natl Acad Sci U S A 78:2179–2183

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Dickerson RE (1983) The DNA helix and how it is read. Sci Am 249(6):94–111

    CAS  Google Scholar 

  6. Kopka ML, Fratini AV, Drew HR, Dickerson RE (1983) Ordered water structure around a B- DNA dodecamer. A quantitative study. J Mol Biol 163:129–146

    CAS  PubMed  Google Scholar 

  7. Dickerson RE, Drew HR, Conner BN, Kopka ML, Pjura PE (1983) Helix geometry and hydration in A-DNA, B-DNA, and Z-DNA. Cold Spring HarbSymp Quant Biol 47(Pt1):13–24

    Google Scholar 

  8. Coll MI, Fita J, Lloveras JA, Subirana F, Bardella T, Huynh-Dinh, Igolen Structure of d(CACGTG), a Z-DNA hexamer containing AT base pairs. Nucleic Acids Res 16(17):8695–8705

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Schneider B, Patel K, Berman HM (1998) Hydration of the phosphate group in double helical DNA. J Biophys 75(5):2422–2434

    CAS  Google Scholar 

  10. Gao YG, Robinson H, Wang AHJ (1999) High-resolution A-DNA crystal structures of D(AGGGGCCCCT), An A-DNA model of poly(dG) X poly(dC. Eur J Biochem 261:413–420

  11. Soler-López M, Malinina L, Subirana JA (2000) Solvent organization in an oligonucleotide crystal the structure of d(GCGAATTC G)2 at atomic resolution 210. J Biol Chem 275:23034–23044

    PubMed  Google Scholar 

  12. Ng HL, Dickerson RE (2002) Mediation of the a/B DNA helix transition by G-tracts in the crystal structure of duplex CATGGGCCCATG. Nucleic Acids Res 30(18):4061–4067

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Egli M (2002) DNA-cation interactions: quo Vadis? Biol Chem 9:277–286

    CAS  Google Scholar 

  14. Draper DE (2004) A guide to ions and RNA structure. RNA 10:335–343

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Chen SJ (2008) RNA folding: conformational statistics, folding kinetics, and ion electrostatics. Annu Rev Biophys 37:197–214

    CAS  PubMed  PubMed Central  Google Scholar 

  16. Kennard O, Cruse WB, Nachman J, Prange T, Shakked Z, Rabinovich D (1986) Ordered water structure in an A-DNA octamer at 1.7 Å resolution. J Biomol Struct Dyn 3:623

    CAS  PubMed  Google Scholar 

  17. Packer MJ, Hunter CA (1998) Sequence-dependent DNA structure: the role of the sugar- phosphate backbone. J Mol Biol 280:407–420

    CAS  PubMed  Google Scholar 

  18. Thomas Jr G, Tsuboi M (1993) Raman spectroscopy of nucleic acids and their complexes. Adv Biophys Chem 3:1–70

    CAS  Google Scholar 

  19. Peticolas WL, Evertsz E (1992) Conformation of DNA in vitro and in vivo from laser Raman scattering. Methods Enzymol 211:335–352

    CAS  PubMed  Google Scholar 

  20. Taillandier E, Liquier J (1992) Infrared spectroscopy of DNA. Methods Enzymol 211:307–335

    CAS  PubMed  Google Scholar 

  21. Leulliot N, Ghomi M, Scalmani G, Berthier G (1999) Ground state properties of the nucleic acid constituents studied by density functional calculations I: conformational features of ribose, dimethyl phosphate, cytidine, 5’-methyl phosphate-uridine, and 3’-methyl phosphate uridine. J Phys Chem A 103:8716

    CAS  Google Scholar 

  22. Foloppe N, MacKerell Jr AD (1998) Conformational properties of the deoxyribose and ribose moieties of nucleic acids: a quantum mechanical study. J Phys Chem B 102:6669–6678

    CAS  Google Scholar 

  23. Leulliot N, Ghomi M, Jobic H, Bouloussa O, Baumruk V, Coulombeau C (1999) Ground state properties of the nucleic acid constituents studied by density functional calculations, 2: comparison between calculated and experimental vibrational spectra of uridine and Cytidine. J Phys Chem B 103:10934

    CAS  Google Scholar 

  24. Louit G, Hocquet A, Ghomi M (2002) Intramolecular hydrogen bonding in ribonucleosides: an AIM topological study of the electronic density. Phys Chem Chem Phys 4:3835

    Google Scholar 

  25. Arnott S, Hukins DWL (1973) Refinement of the structure of B-DNA and implication for the analysis of X-ray diffraction data from fiber of biopolymers. J Mol Biol 81:93–105

    CAS  PubMed  Google Scholar 

  26. Dhaouadi Z, Nsangou M, Hernández B, Pflüger F, Liquier J, Ghomi M (2009) Geometrical and vibrational features of phosphate, phosphorothioate and phosphorodithioate linkages interacting with hydrated cations: a DFT study. Spectrochim Acta A 73:805–814

    Google Scholar 

  27. Minguirbara A, Nsangou M (2018) DFT study of geometrical and vibrational features of a 3′,5′-deoxydisugar-monophosphate (dDSMP) DNA model in the presence of counterions and solvent. J Mol Model 24:88

    PubMed  Google Scholar 

  28. Lee C, Yang W, Parr RP (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B 37:785–789

    CAS  Google Scholar 

  29. Becke AD (1993) Density-functional thermochemistry III: the role of exact exchange. J Phys Chem 98:5648–5652

    CAS  Google Scholar 

  30. Arnott S, Hukins DWL (1972) Optimized parameters for A-DNA and B-DNA. BioChem Biophys Res Com 47:1504–1509

    CAS  PubMed  Google Scholar 

  31. Yurenko YP, Zhurakivsky RO, Ghomi M, Samijlenko SP, Hovorun DM (2007) How many conformers determine the thymidine low-temperature matrix infrared spectrum? DFT and MP2 quantum chemical study. J Phys Chem B 111:9655–9663

    CAS  PubMed  Google Scholar 

  32. Rich A, Norheim A, Wang AHJ (1984) The chemistry and biology of left-handed Z-DNA. Annu Rev Biochem 53:791–846

    CAS  PubMed  Google Scholar 

  33. M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G.A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H.P. Hratchian, A.F. Izmaylov, J. Bloino, G. Zheng, J.L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J.A. Montgomery Jr., J.E. Peralta, F. Ogliaro, M. Bearpark, J.J. Heyd, E. Brothers, K.N. Kudin, V.N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J.C. Burant, S.S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J.M. Millam, M. Klene, J.E. Knox, J.B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, R.L. Martin, K. Morokuma, V.G. Zakrzewski, G.A. Voth, P. Salvador, J.J. Dannenberg, S. Dapprich, A.D. Daniels, O. Farkas, J.B. Foresman, J.V. Ortiz, J. Cioslowski, D.J. Fox, Gaussian Inc. Wallingford (2009)

  34. Andrushchenko V, Benda L, Păv O, Dračínsky M, Bouř P (2015) Vibrational properties of the phosphate group investigated by molecular dynamics and density functional theory. J Phys Chem B 119:10682–10692

    CAS  PubMed  Google Scholar 

  35. Small EW, Peticolas WL (1971) Conformational dependence of the Raman scattering intensities from polynucleotides, 3. Orderdisorder changes in helical structures. Biopolymers 10:1377–1416

    CAS  PubMed  Google Scholar 

  36. Erfurth SC, Kiser EJ, Peticolas WL (1972) Determination of the backbone structure of nucleic acids and nucleic acid oligomers by laser Raman scattering. Proc Natl Acad Sci U S A 69:938–941

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Taboury JA, Liquier J, Taillandier E (1984) Characterization of DNA structures by infrared spectroscopy: double helical forms of poly(dG-dC) poly(dG-dC), poly(dD8G-dC poly(dD8G-dC), and poly(dG-dm5C) poly(dG-dm5C). Can J Chem 63:1904–1909

    CAS  Google Scholar 

  38. Erfurth SC, Peticolas WL (1975) Melting and premelting phenomena in DNA by laser Raman scattering. Biopolymers 14:247–264

    CAS  PubMed  Google Scholar 

Download references

Acknowledgments

The authors are grateful to the Higher Teachers’ Training College Maroua (University of Maroua) for their support to this project.

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Authors and Affiliations

  1. Department of Physics, Faculty of Science, University of Maroua, Maroua, P.O.Box 814, Cameroon

    Alain Minguirbara & Berthelot Saïd Duvalier Ramlina Vamhindi

  2. Department of Physics, Faculty of Science, University of Bangui, Bangui, Central African Republic

    Stève Jonathan Koyambo-Konzapa

  3. CERDISFA, Department of Physics, Higher Teacher’s Training College, University of Maroua, Maroua, P.O.Box 46, Cameroon

    Mama Nsangou

  4. Department of Physics, Faculty of Science, University of Ngaoundere, Ngaoundere, P.O.Box 454, Cameroon

    Mama Nsangou

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  1. Alain Minguirbara
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  2. Berthelot Saïd Duvalier Ramlina Vamhindi
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Correspondence to Mama Nsangou.

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Minguirbara, A., Vamhindi, B.D.R., Koyambo-Konzapa, S.J. et al. Effects of counterions and solvents on the geometrical and vibrational features of dinucleoside-monophosphate (dNMP): case of 3',5'-dideoxycytidine-monophosphate (dDCMP). J Mol Model 26, 99 (2020). https://doi.org/10.1007/s00894-020-04369-6

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