Modeling of recognition sites of nucleic acid bases and amide side chains of amino acids. Combination of experimental and theoretical approaches

V. S. Shelkovsky, S. G. Stepanian, I. K. Galetich, M. V. Kosevich, Ludwik Adamowicz

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

A combined experimental-theoretical approach to modeling of building blocks of recognition complexes formed by nucleic acid bases and the amino-acids side-chain amino group is reviewed. The approach includes the temperature dependent field-ionization mass spectrometry and ab initio quantum chemical calculations. The mass spectrometric technique allows determination of interaction enthalpies of biomolecules in the gas phase, and the results it produces are directly comparable to the results obtained through theoretical modeling. In our works we have analyzed both thermodynamic and structural aspects of the recognition complexes of four canonical nucleic acid bases and acrylamide, which models the side chain of asparagine and glutamine. It has been shown that all bases can interact with amide group of the amino acids via their Watson-Crick sites when being incorporated into a single strand DNA or RNA. Stability of the complexes studied, expressed as -Δ?H (kJ mole-1) decreases as: m9Gua (-59.5) ≥ m1Cyt (-57.0) ≥ m9Ade (-52.0) ≫ m1Ura (-40.6). We have determined that in the double stranded DNA only purine bases can be recognized.

Original languageEnglish (US)
Pages (from-to)421-430
Number of pages10
JournalEuropean Physical Journal D
Volume20
Issue number3
DOIs
StatePublished - Sep 2002

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nucleic acids
amides
amino acids
deoxyribonucleic acid
glutamine
purines
strands
mass spectroscopy
enthalpy
vapor phases
ionization
thermodynamics
interactions
temperature

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Atomic and Molecular Physics, and Optics

Cite this

Modeling of recognition sites of nucleic acid bases and amide side chains of amino acids. Combination of experimental and theoretical approaches. / Shelkovsky, V. S.; Stepanian, S. G.; Galetich, I. K.; Kosevich, M. V.; Adamowicz, Ludwik.

In: European Physical Journal D, Vol. 20, No. 3, 09.2002, p. 421-430.

Research output: Contribution to journalArticle

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