Conformational dynamics in mixed alpha/beta-oligonucleotides containing polarity reversals: a molecular dynamics study using time-averaged restraints.
Conformational dynamics in mixed alpha/beta-oligonucleotides containing polarity reversals: a molecular dynamics study using time-averaged restraints.
复制标题
包含极性反转的混合 α/β 寡核苷酸的构象动力学：使用时间平均约束的分子动力学研究。
DOI：
10.1023/a:1026798010342
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发表时间：
2000
影响因子：
2.7
通讯作者：
Germann,MW
中科院分区：
文献类型：
--
作者：
Aramini,JM;Mujeeb,A;Ulyanov,NB;Germann,MW
Nucleic acid duplexes featuring a single alpha-anomeric thymidine inserted into each DNA strand via 3′-3′ and 5′-5′ phosphodiester linkages exhibit local conformational dynamics that are not adequately depicted by conventional restrained molecular dynamics (rMD) methods. We have used molecular dynamics with time-averaged NMR restraints (MDtar) to explore its applicability to describing the conformational dynamics of two α-containing duplexes – d(GCGAAT-3′-3′-αT-5′-5′-CGC)2and d(ATGG-3′-3′-αT-5′-5′-GCTC)•r(gagcaccau). In contrast to rMD, enforcing NOE-based distance restraints over a period of time in MDtar rather than instantaneously results in better agreement with the experimental NOE andJ-data. This conclusion is based on the dramatic decreases in average distance and coupling constant violations (Δdav,Jrms, and ΔJav) and improvements in sixth-rootR-factors (Rx). In both duplexes, the deoxyribose ring puckering behavior predicted independently by pseudorotation analysis is portrayed remarkably well using this approach compared to rMD. This indicates that the local dynamic behavior is encoded within the NOE data, although this is not obvious from the localRxvalues. In both systems, the backbone torsion angles comprising the 3′-3′ linkage as well as the (high S-) sugars of the α-nucleotide and preceding residue (α−1) are relatively static, while the conformations of the 5′-5′ linkage and the sugar in the neighboring β-nucleotide (α+1) show enhanced flexibility. To reduce the large ensembles generated by MDtar to more manageable clusters we utilized the PDQPRO program. The resulting PDQPRO clusters (in both cases, 13 structures and associated probabilities extracted from a pool of 300 structures) adequately represent the structural and dynamic characteristics predicted by the experimental data.
