Stability and migration of metal ions in G4-wires by molecular dynamics simulations

Article Abstract:

A molecular dynamics investigation of guanine quadruple helices based on classical force fields is done by studying the dependence of the helical conformation on different compositional factors like lengths of the G4 wire, the incorporation into the helix channel of alkali ions of various species and in varying amount. The empirical outcomes indicate that monovalent alkali cations help the stability of the quadruplex arrangement against disruption on the few nanoseconds time scale in the order of increasing van der Waals radius.

Molecular dynamics, Metal ions, Van der Waals forces, Report

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Characterization of nucleobase-amino acid stacking interactions utilized by a DNA repair enzyme

Article Abstract:

The characterization of the gas-phase stacking interactions between four aromatic amino acid residues (histidine, phenylalanine, tyrosine, and tryptophan) and adenine or 3-methyladeninde due to the proposed utilization of these interactions by enzymes that repair DNA alkylation damage is presented. The results suggest that alkylation likely plays a more important role in substrate identification and removal than the nature of the aromatic amino acid that interacts with the substrate via stacking interactions.

DNA repair, Nucleobases

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Stabilization of the noncomplementary guanine-adenine base pairs by Zn (II) ions, an ab initio SCF-MI study

Article Abstract:

The structure and energy of the guanine (G)- adenine (A) base pairs in the G (anti)-A (anti) and G (anti)-A (syn) conformations as well as their complexes with hydrated zinc (II) ions was investigated by the self-consistent field for molecular interaction (SCF-MI) an initio method. The formation of covalent bonds between the Zn (II) ions and N7 site of the guanine bases resulted in an increase of the binding energy of the G-A pairs.

Ions, Chemical bonds

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