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DFT study of the interaction of cytidine and 2′-deoxycytidine with Li+, Na+, and K+: effects of metal cationization on sugar puckering and stability of the N-glycosidic bond

Aliakbar Tehrani, Z ; Sharif University of Technology | 2009

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  1. Type of Document: Article
  2. DOI: 10.1016/j.carres.2009.02.007
  3. Publisher: 2009
  4. Abstract:
  5. Density functional theory (DFT) calculations were performed at the B3LYP level with a 6-311++G(d,p) basis set to systematically explore the geometrical multiplicity and binding strength for complexes formed by Li+, Na+, and K+ with cytidine and 2′-deoxycytidine. All computational studies indicate that the metal ion affinity (MIA) decreases from Li+ to Na+ and K+ for cytosine nucleosides. For example, for cytidine the affinity for the above metal ions are 79.5, 55.2, and 41.8 and for 2′-deoxycytidine, 82.8, 57.4, and 42.2 kcal/mol, respectively. It is also interesting to mention that linear correlations between calculated MIA values and the atomic numbers (Z) of the above metal ions were found. The influence of metal cationization on the coordination modes and the strength of the N-glycosidic bond in cytosine nucleosides have been studied. In all cases, the N1-C1′ bond distance changes upon introducing a positive charge in the nucleosides. It has been found that metal binding significantly changes the values of the phase angle of pseudorotation P in the sugar unit of these nucleosides. With respect to the sugar ring, metal binding changes the values of the glycosyl torsion angle and sugar ring conformation. The present calculations in the gas phase provide the first clues on the intrinsic chemistry of these systems and may be of value for studies of the influence of metal cations on the conformational behavior and function of nucleic acids. © 2009 Elsevier Ltd. All rights reserved
  6. Keywords:
  7. 2′-Deoxyribonucleoside ; Metal complexation ; N-Glycosidic bond ; Ribonucleoside ; Atomic numbers ; Basis sets ; Binding strengths ; Bond distances ; Computational studies ; Conformational behaviors ; Coordination modes ; Cytidine ; Density functional theory calculations ; DFT study ; Gas-phase ; Glycosyl ; Linear correlations ; Metal bindings ; Metal cationization ; Metal cations ; Metal complexation ; Metal ion ; Phase angles ; Positive charges ; Pseudorotation ; Sugar ring conformations ; Sugar rings ; Sugar units ; Torsion angles ; Atoms ; Conformations ; Coordination reactions ; Density functional theory ; Metal ions ; Nucleic acids ; Nucleotides ; Probability density function ; Sugar (sucrose) ; Sugars ; Trace analysis ; Metals ; Nucleoside ; Potassium ; Chemical bond ; Chemical interaction ; Conformation ; Mathematical computing ; Metal binding ; Molecular stability ; Nucleic acid analysis ; Priority journal ; Cations ; Computers, Molecular ; Deoxycytidine ; Glycosylation ; Lithium ; Molecular Structure ; Sodium
  8. Source: Carbohydrate Research ; Volume 344, Issue 6 , 2009 , Pages 771-778 ; 00086215 (ISSN)
  9. URL: https://www.sciencedirect.com/science/article/abs/pii/S0008621509000408