Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA.
Nucleic Acids Res. 2011 Dec;39(22):9649-58. doi: 10.1093/nar/gkr699. Epub 2011 Sep 3.
Structural results with minor groove binding agents, such as netropsin, have provided detailed, atomic level views of DNA molecular recognition. Solution studies, however, indicate that there is complexity in the binding of minor groove agents to a single site. Netropsin, for example, has two DNA binding enthalpies in isothermal titration calorimetry (ITC) experiments that indicate the compound simultaneously forms two thermodynamically different complexes at a single AATT site. Two proposals for the origin of this unusual observation have been developed: (i) two different bound species of netropsin at single binding sites and (ii) a netropsin induced DNA hairpin to duplex transition. To develop a better understanding of DNA recognition complexity, the two proposals have been tested with several DNAs and the methods of mass spectrometry (MS), polyacrylamide gel electrophoresis (PAGE) and nuclear magnetic resonance spectroscopy in addition to ITC. All of the methods with all of the DNAs investigated clearly shows that netropsin forms two different complexes at AATT sites, and that the proposal for an induced hairpin to duplex transition in this system is incorrect.
结构研究表明，与小沟结合的试剂（如 netropsin）可以提供详细的、原子水平的 DNA 分子识别视图。然而，溶液研究表明，小沟结合物与单个位点的结合存在复杂性。例如，在等温滴定量热法（ITC）实验中，netropsin 具有两个 DNA 结合焓，表明该化合物同时在单个 AATT 位点形成两种热力学上不同的复合物。对于这种不寻常观察结果的起源，已经提出了两种建议：（i）在单个结合位点上存在两种不同的结合态 netropsin，（ii）netropsin 诱导的 DNA 发夹到双链的转变。为了更好地理解 DNA 识别的复杂性，已经使用几种 DNA 以及质谱（MS）、聚丙烯酰胺凝胶电泳（PAGE）和核磁共振波谱学等方法对这两种建议进行了测试，除了 ITC 之外。所有方法和所有研究的 DNA 都清楚地表明，netropsin 在 AATT 位点形成两种不同的复合物，并且该系统中诱导发夹到双链的转变的建议是不正确的。
