Ivanova Anela, Jezierski Grzegorz, Rösch Notker
Department Chemie, Theoretische Chemie, Technische Universität München, 85747, Garching, Germany.
Phys Chem Chem Phys. 2008 Jan 21;10(3):414-21. doi: 10.1039/b712506b. Epub 2007 Nov 8.
We calculated ab initio electronic coupling elements between neighboring base-pair dimers in a set of LNA:DNA oligomers with different numbers of locked nucleotides and compared them by averaging the values over ensembles of snapshots from molecular dynamics trajectories. Averaging was based on coupling elements for various ensembles comprising of 33,000 structures. The known pronounced variations of coupling elements on the nanosecond timescale due to thermal fluctuations of the DNA structure were confirmed. We found significant differences in electronic coupling at the dimer level between a non-modified DNA:DNA duplex and the corresponding duplex containing one fully LNA-substituted strand. We rationalized these differences by very dissimilar overlap in the pi-stack as a consequence of the LNA-modified system approximating an A-DNA-type helix. The calculated coupling elements for the non-modified reference duplex were similar to those of standard B-DNA and those for the fully modified oligomer resembled the matrix elements estimated for standard A-DNA.
我们计算了一组具有不同数量锁定核苷酸的锁核酸（LNA）：DNA寡聚物中相邻碱基对二聚体之间的从头算电子耦合元件，并通过对分子动力学轨迹的快照集合中的值进行平均来比较它们。平均是基于由33,000个结构组成的各种集合的耦合元件。由于DNA结构的热波动，耦合元件在纳秒时间尺度上已知的明显变化得到了证实。我们发现未修饰的DNA：DNA双链体与包含一条完全LNA取代链的相应双链体在二聚体水平上的电子耦合存在显著差异。由于LNA修饰系统近似于A-DNA型螺旋，我们通过π堆积中非常不同的重叠来解释这些差异。未修饰参考双链体的计算耦合元件与标准B-DNA的相似，而完全修饰寡聚物的耦合元件类似于为标准A-DNA估计的矩阵元件。
