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.
journal_name
J Biomol Struct Dynjournal_title
Journal of biomolecular structure & dynamicsauthors
Bandyopadhyay D,Bhattacharyya Ddoi
10.1080/07391102.2000.10506645subject
Has Abstractpub_date
2000-08-01 00:00:00pages
29-43issue
1eissn
0739-1102issn
1538-0254journal_volume
18pub_type
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