Computational insights into the interactions between DNA and siRNA with "rigid" and "flexible" triazine dendrimers.
Computational insights into the interactions between DNA and siRNA with "rigid" and "flexible" triazine dendrimers.
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DOI：
10.1021/bm901298t
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发表时间：
2010-03-08
影响因子：
6.2
通讯作者：
Danani, Andrea
中科院分区：
文献类型：
--
作者：
Pavan, Giovanni M.;Mintzer, Meredith A.;Simanek, Eric E.;Merkel, Olivia M.;Kissel, Thomas;Danani, Andrea
在这项研究中，模拟挑战直观的模型“灵活”和“刚性”代二嗪树枝状聚合物，因为它涉及到解决方案的构象和构象结合DNA或siRNA序列。这些结果来自结合事件的结构和能量分析。刚性结构的模拟加强了约束哌嗪接头在将外围基团定位在彼此和树枝状聚合物的核心的显著距离处的作用。相比之下，以三甘醇样连接体为特征的柔性树枝状聚合物在溶液中塌陷。在结合DNA和siRNA时，这些构象在很大程度上保留。刚性树枝状聚合物经历外围基团的重组以产生与核酸的大量接触。相比之下，最初设想与核酸产生多价相互作用的柔性树枝状聚合物仅产生少量接触并进一步塌陷。本文提供了独特的洞察力的作用所发挥的分子的灵活性的结合现象。
In this study, simulation challenges intuitive models of “flexible” and “rigid” generation two triazine dendrimers as it pertains to solution conformation and conformation on binding DNA or siRNA sequences. These results derive from structural and energetic analyses of the binding events. Simulations of the rigid structure reinforce the role of the constrained piperazine linker in positioning the peripheral groups at significant distance from each other and the core of the dendrimer. In contrast, the flexible dendrimer, characterized by triethyleneglycol-like linkers, collapses in solution. On binding DNA and siRNA, these conformations are largely retained. The rigid dendrimer undergoes reorganization of peripheral groups to generate a large number of contacts to the nucleic acid. In contrast, the flexible dendrimer, originally conceived to create multivalent interactions with nucleic acids, generates only a few contacts and collapses further. This paper provides unique insight in the role played by molecular flexibility in the binding phenomenon.
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