RNA molecules play a number of critical roles in the expression of genetic information, yet very little is known about the tertiary structures of these molecules, or how such structures relate to the diverse functions of RNA. We have recently applied the method of transient electric birefringence (TEB) to the study of a branched DNA structure, and as a result, have obtained a geometry of the branch in solution. This result suggests that TEB may be quite useful as a means of characterizing certain elements of RNA structure. Therefore, the major focus of the proposed research is to apply TEB to several well-studied RNA structures whose global conformations in solution have resisted characterization. The second focus of the proposed research builds on our observation, during the previous period of funding, that the prokaryotic histone-like protein, HU, is capable of facilitating the formation of very small DNA circles upon the addition of DNA ligase. This observation may explain the roles played by HU in a number of recombination systems. Our objective with the HU work is a better understanding as to the means by which HU facilitates DNA loop formation.
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