Book of Abstracts: Albany 2007
June 19-23 2007
Spectroscopic Investigations of DNA Dynamics and Relationship to HU DNA Interactions
The structure and dynamics of DNA can be observed at the nucleic acid level using fluorescent nucleoside analogs. Fluorescent nucleoside analogs that minimally distort the structure and function of nucleic acids are effective for studying the structure, the dynamics and the interactions of nucleic acids with their molecular targets. In this study, the fluorescent guanosine analog 6-methylisoxanthopterin (6MI), is used to study DNA dynamics because it minimally distorts the geometry of double stranded DNA due to its ability to hydrogen bond with cytosine. HU, a heterodimeric DNA binding protein, exhibits high binding affinity to discontinuous DNA substrates and we are interested in probing whether the dynamics of these substrates correlate with binding. The 6MI was systematically incorporated into a series of DNA overhang substrates. The probes were located close to the ends of the single strand regions and close to the single strand double strand junction. The dependence of 6MI motion upon location in the overhangs were observed by time-resolved fluorescence and anisotropy decay and were compared with the control single strand and double strand substrate. Our preliminary results show that as predicted the dynamics of the probe are slower in the duplex than in the single strand oligomers. The relative distribution of 6.5 ns and 0.5 ns populations were dependent on the location of the probe in the oligomer. The binding affinity of the HU protein will be discussed in terms of the local dynamics of the DNA substrates.
Funding: Patrick and Catherine Weldon Donaghue Medical Research Foundation a grant from NSF (MCB 03-16625) and NIH training grant in Molecular Biophysics (GM 08271-11)
1Department of Chemistry