DFT investigation of the vibrational properties of GC Watson-Crick and Hoogsteen base pairs in the presence of Mg2+, Ca2+, and Cu2+ ions

  • Cristian Morari
  • Cristina M. Muntean
  • Carmen Tripon
  • Luiza Buimaga-Iarinca
  • Adrian Calborean
Original Paper

DOI: 10.1007/s00894-014-2220-x

Cite this article as:
Morari, C., Muntean, C.M., Tripon, C. et al. J Mol Model (2014) 20: 2220. doi:10.1007/s00894-014-2220-x

Abstract

The binding effects of Mg2+, Ca2+, and Cu2+ ions on the vibrational properties of guanine-cytosine base pairs have been performed using density functional theory investigations. Both Watson-Crick and Hoogsteen configurations of the base pairs were investigated. In Watson-Crick configuration, the metal was coordinated at N7 atom of guanine, while in the case of Hoogsteen configuration, the coordination is at N3 atom of guanine. We have pointed out the geometric properties of the metal-GC base pairs structure, as well as the vibrational bands that can be used to detect the presence of metallic ions in the Watson-Crick and Hoogsteen GC structures. For the geometric models used by us, the vibrational amplitudes of metallic atoms were stronger for wavenumbers lower than 500 cm−1. This suggests that in the experimental studies on DNA the presence of the three metallic atoms (Mg, Ca, and Cu) can be explicitly detected at low frequencies.

Keywords

DFT Guanine-cytosine Hoogsteen base pair Hydrated metal cations Watson-Crick base pair 

Supplementary material

894_2014_2220_MOESM1_ESM.pdf (213 kb)
ESM 1(PDF 212 kb)

Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Cristian Morari
    • 1
  • Cristina M. Muntean
    • 1
  • Carmen Tripon
    • 1
  • Luiza Buimaga-Iarinca
    • 1
  • Adrian Calborean
    • 1
  1. 1.Department of Molecular and Biomolecular PhysicsNational Institute for Research and Development of Isotopic and Molecular TechnologiesCluj-NapocaRomania