The proposed research has three principal objectives: (I) a more quantitative understanding of the sequence-dependence and origins of nucleic acid helix rigidity; (ii)characterization of the conformational changes induced in DNA (or RNA) by three site- specific nucleic acid binding proteins; (iii) further development of two solution-based methods, namely, transient electric birefringence (TEB) and luminescence resonance energy transfer (LRET), for studying the long-range conformations of nucleic acids. Used in combination, these two methods should complement one another to reduce the experimental and theoretical uncertainties associated with either method alone. Each of the three protein-nucleic acid interactions is designed to examine a somewhat different issue: The TATA-box protein (TBP) is a critical component of the eukaryotic transcriptional machinery; its complex with DNA provides an excellent test system for examining large bends in solution, and for laying the groundwork for a more comprehensive study of the specific interactions that give rise to DNA bending. The basic region- leucine zipper protein (bZIP) family is extremely important in the process of tissue-specific transcriptional regulation; examination of the bZIP-DNA interaction will hopefully resolve the question of how much (or whether) those proteins bend their DNA targets. The third study will focus on the nature of the conformational change induced in a plant viral RNA genome (alfalfa mosaic virus) by site-specific binding of the viral coat protein. The RNA target is likely to possess a significant degree of flexibility prior to protein binding, thus providing a test of the TEB/LRET approach to assess flexibility.
Showing the most recent 10 out of 35 publications
