title: Effect of neighboring bases on base-pair stacking orientation: a molecular dynamics study.
abstract: It is generally believed that base-pair stacking interaction in DNA double helix is one of the strongest interactions that governs sequence directed structural variability. However, X-ray crystal structures of some base-paired doublet sequences have been seen to adopt different structures when flanked by different base-pairs. DNA crystal database, however, is still too small to make good statistical inference about effect of such flanking residues. Influence of neighboring residue on the local helical geometry of a base-paired doublet in B-DNA has been investigated here using molecular dynamics simulation. We have generated ensembles of structures for d(CA).d(TG) and d(AA).d(TT) base-paired doublets located at the centers of d(CGCGCAAAGCG).d(CGCTTTGCGCG) and d(CGCGAAAACGCG).d(CGCGTTTTCGCG) sequences along with their analogs by varying the bases either at 5'- or 3'- position to the central doublet. Comparison of base paired doublet parameters for the ensembles of structures show that stacking geometry of d(CA).d(TG) doublet depends on some of the flanking base-pairs. On the other hand d(AA).d(TT) doublet remains nearly unperturbed when the flanking residues are altered.
authors.affiliation: Biophysics Division, Saha Institute of Nuclear Physics, Calcutta, India.
authors.forename: D
authors.initials: D
authors.lastname: Bandyopadhyay
authors.forename: D
authors.initials: D
authors.lastname: Bhattacharyya
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D009838:Oligodeoxyribonucleotides; D004247:DNA