Winters-Hilt Stephen, Davis Amanda, Amin Iftekhar, Morales Eric
Department of Computer Science, University of New Orleans, New Orleans, LA 70148, USA.
BMC Bioinformatics. 2007 Nov 1;8 Suppl 7(Suppl 7):S10. doi: 10.1186/1471-2105-8-S7-S10.
Synthetic transcription factors (STFs) promise to offer a powerful new therapeutic against Cancer, AIDS, and genetic disease. Currently, 10% of drugs are of this type, including salicylate and tamoxifen. STFs that can appropriately target (and release) their transcription factor binding sites on native genomic DNA provide a means to directly influence cellular mRNA production. An effective mechanism for screening amongst transcription factor (TF) candidates would itself be highly valued, and such may be possible with nanopore cheminformatics methods.
It is hypothesized that binding targets on channel-captured molecules, that are well away from the channel-captured region, can be monitored insofar as their binding status, or history, is concerned. The first set of experiments we perform to explore this "transduction" hypothesis involve non-terminal dsDNA binding to protein (DNA TATA box receptor binding to TBP), where we show new experimental results and application of a new cheminformatics data analysis method. In the second series of experiments to explore the transduction hypothesis we examine terminal (blunt-ended) dsDNA binding to protein. We show experimental results before and after introduction of HIV's DNA integrase to a solution of bifunctional "Y" shaped aptamers that have an HIV consensus terminus exposed for interaction.
X-ray crystallographic studies have guided our understanding of DNA structure for almost a century. It is still difficult, however, to translate the sequence-directed curvature information obtained through these tools to actual systems found in solution. With a nanopore detector the sequence-dependent conformation kinetics of DNA, especially at the DNA terminus, can be studied in a new way while still in solution and on a single molecule basis.
合成转录因子有望成为对抗癌症、艾滋病和遗传疾病的强大新型疗法。目前，10%的药物属于此类，包括水杨酸盐和他莫昔芬。能够在天然基因组DNA上适当靶向（并释放）其转录因子结合位点的合成转录因子提供了一种直接影响细胞mRNA产生的方法。一种用于筛选转录因子（TF）候选物的有效机制本身将具有很高的价值，而通过纳米孔化学信息学方法可能实现这一点。
据推测，就通道捕获分子上远离通道捕获区域的结合靶点的结合状态或历史而言，可以对其进行监测。我们进行的第一组探索这种“转导”假设的实验涉及非末端双链DNA与蛋白质的结合（DNA TATA盒受体与TBP的结合），在此我们展示了新的实验结果以及一种新的化学信息学数据分析方法的应用。在探索转导假设的第二系列实验中，我们研究了末端（平端）双链DNA与蛋白质的结合。我们展示了在将HIV的DNA整合酶引入具有暴露的HIV共有末端以进行相互作用的双功能“Y”形适体溶液前后的实验结果。
近一个世纪以来，X射线晶体学研究一直指导着我们对DNA结构的理解。然而，仍然难以将通过这些工具获得的序列导向的曲率信息转化为溶液中实际存在的系统。使用纳米孔检测器，可以在溶液中且基于单分子的基础上以一种新的方式研究DNA的序列依赖性构象动力学，尤其是在DNA末端。
