d(A)3d(T)3 and d(G)3d(C)3 B-DNA mini-helixes: the DFT/M06-2x and DFT/B97-D3 comparison of geometrical and energetic characteristics

  • Leonid Gorb
  • Tatiana A. Zubatiuk
  • Roman Zubatyuk
  • Dmytro Hovorun
  • Jerzy Leszczynski
Original Paper

Abstract

We report the comprehensive DFT based comparison of geometrical and energetic parameters of the d(A)3·d(T)3 and d(G)3·d(C)3 nucleic acid mini-helixes performed at B97-D3 and M06-2× levels of theory. We studied the ability of mini-helixes to retain the conformation of B-DNA in the gas phase and under the influence of water bulk, uncompensated charges, and counter-ions. The def2-SV(P) and 6-31G(d,p) basis sets have been used for B97-D3 and M06-2× calculations, correspondently. To estimate basis set superposition error, the recently developed semi-empirical procedure that calls geometrical counterpoise type correction for inter- and intra—molecular basis set superposition error (gcp) has been used in the case of def2-SV(P) basis set. We found that both considered DFT functionals predict very similar results for geometrical ad energetic characteristics. We also found that in contrast to average classical molecular dynamics and data of simple geometrical models, both considered DFT functionals predict the existence of duplex specific geometries. A prediction of interaction energies of d(A)3d(T)3 and d(G)3d(C)3 duplexes accomplished in this study also verifies the applied models and confirms reliability of the new computational gcp technique.

Keywords

DNA mini helixes Geometrical counterpoise type correction DNA geometrical and energetic characteristics 

Supplementary material

894_2017_3449_MOESM1_ESM.docx (20 kb)
ESM 1 (DOCX 20.1 kb)
894_2017_3449_MOESM2_ESM.docx (24 kb)
ESM 2 (DOCX 24.3 kb)
894_2017_3449_MOESM3_ESM.docx (20 kb)
ESM 3 (DOCX 20.1 kb)
894_2017_3449_MOESM4_ESM.docx (20 kb)
ESM 4 (DOCX 20.3 kb)
894_2017_3449_MOESM5_ESM.docx (20 kb)
ESM 5 (DOCX 20.1 kb)
894_2017_3449_MOESM6_ESM.docx (20 kb)
ESM 6 (DOCX 20.1 kb)
894_2017_3449_MOESM7_ESM.docx (20 kb)
ESM 7 (DOCX 20.1 kb)
894_2017_3449_MOESM8_ESM.docx (20 kb)
ESM 8 (DOCX 20.1 kb)
894_2017_3449_MOESM9_ESM.docx (21 kb)
ESM 9 (DOCX 20.7 kb)
894_2017_3449_MOESM10_ESM.docx (21 kb)
ESM 10 (DOCX 21 kb)
894_2017_3449_MOESM11_ESM.docx (21 kb)
ESM 11 (DOCX 20.5 kb)
894_2017_3449_MOESM12_ESM.docx (21 kb)
ESM 12 (DOCX 20.8 kb)
894_2017_3449_MOESM13_ESM.docx (21 kb)
ESM 13 (DOCX 20.7 kb)
894_2017_3449_MOESM14_ESM.docx (21 kb)
ESM 14 (DOCX 20.8 kb)
894_2017_3449_MOESM15_ESM.docx (20 kb)
ESM 15 (DOCX 20.4 kb)
894_2017_3449_MOESM16_ESM.docx (21 kb)
ESM 16 (DOCX 20.5 kb)

References

  1. 1.
    Rosenberg JM, Seeman NC, Day RO, Rich A (1976) RNA double-helical fragments at atomic resolution: II. The crystal structure of sodium guanylyl-3′,5′-cytidine nonahydrate. J Mol Biol 104:145–167CrossRefGoogle Scholar
  2. 2.
    Frankline RE, Gossling RG (1953) Molecular configuration in sodium thymonucleate. Nature 171:740–741CrossRefGoogle Scholar
  3. 3.
    Dršata T et al. (2013) Structure, stiffness and substates of the Dickerson-Drew dodecamer. J Chem Theory Comput 9:707–721Google Scholar
  4. 4.
    Lavery R, Lebrun A (1999) Modelling DNA stretching for physics and biology. Genetica 106:75–84CrossRefGoogle Scholar
  5. 5.
    Lavery R et al. (2010) A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. Nucleic Acids Res 38:299–313CrossRefGoogle Scholar
  6. 6.
    Hobza P, Šponer J (1999) Structure, energetics, and dynamics of the nucleic Acid Base pairs: nonempirical ab initio calculations. Chem Rev 99:3247–3276CrossRefGoogle Scholar
  7. 7.
    Leszczyński J (1992) Are the amino groups in the nucleic acid bases coplanar with the molecular rings? Ab initioHF/6-31G* andMP2/6-31G* studies. Int J Quantum Chem 44:43–55Google Scholar
  8. 8.
    Sponer J, Florián J, Hobza P, Leszczynski J (1996) Nonplanar DNA base pairs. J Biomol Struct Dyn 13:827–833CrossRefGoogle Scholar
  9. 9.
    Šponer Leszczynski J, Hobza PJ (1996) Structures and energies of hydrogen-bonded DNA base pairs. A nonempirical study with inclusion of electron correlation. J Phys Chem 100:1965–1974CrossRefGoogle Scholar
  10. 10.
    Gorb L, Kaczmarek A, Gorb A, Sadlej AJ, Leszczynski J (2005) Thermodynamics and kinetics of intramolecular proton transfer in guanine. Post Hartree-Fock study. J Phys Chem B 109:13770–13776CrossRefGoogle Scholar
  11. 11.
    Shishkin, O. V, Gorb, L. & Leszczynski, J. Conformational flexibility of pyrimidine rings of nucleic acid bases in polar environment: PCM study. Struct Chem 20, 743–749 (2009)Google Scholar
  12. 12.
    Shishkin OV, Gorb L, Zhikol OA, Leszczynski J (2004) Conformational analysis of canonical 2-Deoxyribonucleotides. 2. Purine nucleotides. J Biomol Struct Dyn 22:227–243CrossRefGoogle Scholar
  13. 13.
    Zubatiuk T, Shishkin O, Gorb L, Hovorun DM, Leszczynski J (2013) B-DNA characteristics are preserved in double stranded d(a)3•d(T)3 and d(G)3•d(C)3 mini-helixes: conclusions from DFT/M06-2X study. Phys Chem Chem Phys. https://doi.org/10.1039/c3cp51584b
  14. 14.
    Perdew JP, Burke K, Ernzerhof M (1997) Generalized gradient approximation made simple [Phys. Rev. Lett. 77, 3865 (1996)]. Phys Rev Lett 78:1396–1396CrossRefGoogle Scholar
  15. 15.
    Gill PMW (1996) A new gradient-corrected exchange functional. Mol Phys 89:433–445CrossRefGoogle Scholar
  16. 16.
    Grimme S (2006) Semiempirical GGA-type density functional constructed with a long-range dispersion correction. J Comput Chem 27:1787–1799CrossRefGoogle Scholar
  17. 17.
    Lu X-J (2003) 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res 31:5108–5121Google Scholar
  18. 18.
    Ahlrichs R, Bär M, Häser M, Horn H, Kölmel C (1989) Electronic structure calculations on workstation computers: the program system turbomole. Chem Phys Lett 162:165–169CrossRefGoogle Scholar
  19. 19.
    Barone V, Cossi M (1998) Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model. J Phys Chem A 102:1995–2001CrossRefGoogle Scholar
  20. 20.
    Kruse H, Grimme S (2012) A geometrical correction for the inter- and intra-molecular basis set superposition error in Hartree-Fock and density functional theory calculations for large systems. J Chem Phys 136:154101CrossRefGoogle Scholar
  21. 21.
    Řezáč J, Riley KE, Hobza P (2011) S66: a well-balanced database of benchmark interaction energies relevant to biomolecular structures. J Chem Theory Comput 7:2427–2438Google Scholar
  22. 22.
    El Hassan MA, Calladine CR (1997) Conformational characteristics of DNA: empirical classifications and a hypothesis for the conformational behaviour of dinucleotide steps. Philos Trans R Soc A Math Phys Eng Sci 355:43–100CrossRefGoogle Scholar
  23. 23.
    Schneider B, Neidle S, Berman HM (1997) Conformations of the sugar-phosphate backbone in helical DNA crystal structures. Biopolymers 42:113–124CrossRefGoogle Scholar
  24. 24.
    Klyne W, Prelog V (1960) Description of steric relationships across single bonds. Experientia 16:521–523CrossRefGoogle Scholar
  25. 25.
    Saenger W (1984) Principles of nucleic acid structure. Springer, HeidelbergGoogle Scholar
  26. 26.
    Šponer J, Burda JV, Sabat M, Leszczynski J, Hobza P (1998) Interaction between the guanine−cytosine Watson−crick DNA Base pair and hydrated group IIa (mg 2+ , ca 2+ , Sr 2+ , Ba 2+ ) and group IIb (Zn 2+ , cd 2+ , hg 2+ ) metal cations. J Phys Chem A 102:5951–5957Google Scholar
  27. 27.
    Shishkin OV et al. (2003) Structure and conformational flexibility of uracil: a comprehensive study of performance of the MP2, B3LYP and SCC-DFTB methods. J Mol Struct THEOCHEM 625:295–303CrossRefGoogle Scholar
  28. 28.
    Shishkin OV, Gorb L, Leszczynski J (2000) Does the hydrated cytosine molecule retain the canonical structure? A DFT study. J Phys Chem B 104:5357–5361CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  1. 1.Interdisciplinary Center for Nanotoxicity, Department of Chemistry and BiochemistryJackson State UniversityJacksonUSA
  2. 2.Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and GeneticsNational Academy of Sciences of UkraineKyivUkraine

Personalised recommendations