PROBING OF NUCLEIC ACID CONFORMATIONAL HETEROGENEITY: STARTING WITH DNA BULGES

这个子项目是许多研究子项目中利用 资源由NIH/NCRR资助的中心拨款提供。子项目和 调查员(PI)可能从NIH的另一个来源获得了主要资金， 并因此可以在其他清晰的条目中表示。列出的机构是 该中心不一定是调查人员的机构。 利用金纳米晶体标记之间的小角x射线散射干涉，Mathew-Fenn等人。测量了一系列DNA双螺旋在溶液中的端到端长度。这一新开发的基于Au-SAXS的X射线标尺确定了一组分子的距离概率分布，为大分子构象异质性提供了一个独特而强大的探测器。为了建立这种X射线标尺技术测量分子系综距离分布的能力，我们建议研究DNA螺旋中膨胀核苷酸的构象灵活性和异质性。A-凸起已经被证明可以弯曲DNA，为这些研究提供了一个很好的起点，但潜在的构象异质性的程度尚不清楚。我们将比较长度为1-5的A和U凸起对DNA弯曲和异质性的影响。这些研究将为深入研究RNA分子及其结构和动力学性质奠定基础。为此，我们将使用初步结果在一个完整的提案中系统地研究核酸构象的异质性，包括DNA A-道和RNA凸起。

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Using small-angle x-ray scattering interference between gold nanocrystal labels, Mathew-Fenn et al. measured the end-to-end length for a series of DNA double helices in solution. This newly developed Au-SAXS-based x-ray ruler determines the distance probability distribution of an ensemble of molecules, providing a unique and powerful probe of macromolecular conformational heterogeneity. To establish the ability of this x-ray ruler technique to measure the distance distribution of molecular ensembles, we propose to study the conformational flexibility and heterogeneity in DNA helices with bulged nucleotides. A-bulges have been shown to bend DNA, giving a good starting point for these studies, but the degree of underlying conformational heterogeneity is unknown. We will compare the effect of A and U bulges of length 1-5 on DNA bending and heterogeneity. These studies would set the stage for incisive investigation of RNA molecules and their structural and dynamic properties. Toward this end, we will use the initial results in a full proposal for the systematic study of nucleic acid conformational heterogeneity, including DNA A-tract, and RNA bulges.