PROBING OF NUCLEIC ACID CONFORMATIONAL HETEROGENEITY: STARTING WITH DNA BULGES

这个子项目是许多研究子项目中的一个 由NIH/NCRR资助的中心赠款提供的资源。子项目和 研究者（PI）可能从另一个NIH来源获得了主要资金， 因此可以在其他CRISP条目中表示。列出的机构是 研究中心，而研究中心不一定是研究者所在的机构。 利用金标记物之间的小角度X射线散射干涉，Mathew-Fenn等人测量了溶液中一系列DNA双螺旋的端到端长度。这种新开发的基于Au-SAXS的X射线标尺确定了分子系综的距离概率分布，为大分子构象异质性提供了独特而强大的探针。为了建立这种X射线标尺技术测量分子系综的距离分布的能力，我们建议研究具有凸出核苷酸的DNA螺旋中的构象灵活性和异质性。A-凸起已被证明可以使DNA弯曲，这为这些研究提供了一个很好的起点，但潜在的构象异质性程度尚不清楚。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特性奠定基础。为此，我们将使用的初步结果，在一个完整的建议，核酸构象异质性的系统研究，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.