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.