31P NMR investigation of backbone dynamics in DNA binding sites.
31P NMR investigation of backbone dynamics in DNA binding sites.
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DNA 结合位点主链动力学的 31P NMR 研究。
DOI：
10.1021/jp711203m
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发表时间：
2009
期刊：
影响因子：
--
通讯作者：
Hatcher,MaryE
中科院分区：
文献类型：
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作者：
Tian,Ye;Kayatta,Michael;Shultis,Katharine;Gonzalez,Alejandro;Mueller,LeonardJ;Hatcher,MaryE
DNA的主干构象在蛋白质- DNA识别事件的间接读出机制中起着重要作用。因此，研究DNA结合序列中每个步骤的主干动力学为这些相互作用的表征提供了必要的有用信息。在这里，我们使用31p动态核磁共振来表征Dickerson十二聚体（一个包含ecori结合位点的序列）的主链构象和动力学，并证实固态2h核磁共振结果表明，C3pG4和C9pG10步骤经历了独特的动力学，这些动力学在胞嘧啶甲基化时被猝灭。此外，我们发现胞嘧啶甲基化影响邻近核苷酸步骤的构象和动力学，但这种影响仅局限于邻近的邻居和碱基配对伙伴。最后，我们已经能够表征每个主链步骤中BII的百分比，并说明C3pG4和C9pG10即使在低温下也有利于非规范BII构象。我们的研究结果表明，31p动态核磁共振提供了一种强大而有效的方法来表征DNA中的主链动力学。这允许简单，快速确定序列依赖的动态信息，为研究蛋白质- DNA识别事件的趋势提供了一种有用的方法。
The backbone conformation of DNA plays an important role in the indirect readout mechanisms for protein−DNA recognition events. Thus, investigating the backbone dynamics of each step in DNA binding sequences provides useful information necessary for the characterization of these interactions. Here, we use31P dynamic NMR to characterize the backbone conformation and dynamics in the Dickerson dodecamer, a sequence containing theEcoRI binding site, and confirm solid-state2H NMR results showing that the C3pG4 and C9pG10 steps experience unique dynamics and that these dynamics are quenched upon cytosine methylation. In addition, we show that cytosine methylation affects the conformation and dynamics of neighboring nucleotide steps, but this effect is localized to only near neighbors and base-pairing partners. Last, we have been able to characterize the percent BII in each backbone step and illustrate that the C3pG4 and C9pG10 favor the noncanonical BII conformation, even at low temperatures. Our results demonstrate that31P dynamic NMR provides a robust and efficient method for characterizing the backbone dynamics in DNA. This allows simple, rapid determination of sequence-dependent dynamical information, providing a useful method for studying trends in protein−DNA recognition events.