Bandyopadhyay D, Bhattacharyya D
Biophysics Division, Saha Institute of Nuclear Physics, Calcutta, India.
J Biomol Struct Dyn. 2000 Aug;18(1):29-43. doi: 10.1080/07391102.2000.10506645.
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.
人们普遍认为，DNA双螺旋中的碱基对堆积相互作用是控制序列导向结构变异性的最强相互作用之一。然而，一些碱基对双峰序列的X射线晶体结构在两侧有不同碱基对时会呈现出不同的结构。然而，DNA晶体数据库仍然太小，无法对这种侧翼残基的影响做出良好的统计推断。本文利用分子动力学模拟研究了相邻残基对B-DNA中碱基对双峰局部螺旋几何结构的影响。我们通过改变中心双峰5'-或3'-位置的碱基，生成了位于d(CGCGCAAAGCG).d(CGCTTTGCGCG)和d(CGCGAAAACGCG).d(CGCGTTTTCGCG)序列中心的d(CA).d(TG)和d(AA).d(TT)碱基对双峰及其类似物的结构集合。结构集合的碱基对双峰参数比较表明，d(CA).d(TG)双峰的堆积几何结构取决于一些侧翼碱基对。另一方面，当侧翼残基改变时，d(AA).d(TT)双峰几乎不受干扰。
