This subproject is one of many research subprojects utilizing theresources provided by a Center grant funded by NIH/NCRR. The subproject andinvestigator (PI) may have received primary funding from another NIH source,and thus could be represented in other CRISP entries. The institution listed isfor the Center, which is not necessarily the institution for the investigator.As a parallel effort to our protein interaction studies, we have begun solution x-ray scattering studies on duplex oligonucleotides. The electrostatic properties of duplex oligonucleotides are the key factors that determine the conformations of DNA and RNA and nature of interactions with binding proteins. Our research focuses on electrostatic properties of dodecamer oligonucleotides, the minimum-length oligomer that maintains a specific duplex conformation in solution, in A- and B-form duplex. They exhibit different affinities with specific DNA-binding proteins, thus are involved in different biological functions, likely due to different electrostatic properties. Initial results on the Dickerson DNA (B-form dodecamer, BDL001) and an A-form dodecamer ADL045 are very encouraging. Initial measurements on SSRL BL4-2 indicate the ability to record x-ray scattering accurately from very small proteins of comparable molecular weights as these, or lower, at sub 1mg/ml concentrations. In the non-interactive regime (lowest nucleotide concentration), we obtained the electron pair distance distribution function consistent with the crystal structures of the duplex oligonucleotides and the low-resolution models we obtained by an ab initio modeling approach have the appearance of two twisted ribbons. We are currently fine tuning our annealing protocol to obtain reproducible results, and will investigate the effects of added salt in very near future. Our initial goal is to examine commonly used electrostatic potential models such as Derjaguin-Landau-Verwey-Overbeek theory to interpret the intermolecular structure factor. We intend to utilize the high-resolution structures of the duplex oligonulceotides by crystallography or NMR to further our understanding of their electrostatic properties. We also plan on using anomalous scattering effects of heavy anions such as Rb and Sr to locate counterion distribution on duplex nucleic acids to correlate it with electrostatic properties.
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