19th-banner-rev.gif

Book of Abstracts: Albany 2003

category image Albany 2003
Conversation 13
Abstract Book
June 17-21 2003

Experimental Characterization of ACCGAAAACGGT Dynamics by 15N NMR Relaxation Measurements

The E2 protein of papillomaviruses is central to viral replication and the regulation of transcription of all viral genes. The E2 proteins from all viral strains bind a common palindromic DNA sequence ACCGnnnnCGGT. Crystal structures have shown that the spacer (nnnn) region makes no specific contacts with the E2 protein, yet changes in the spacer sequence alter the binding affinity of the E2-DNA interaction. In the absence of specific interactions with E2, changes in the structure of the spacer would seem to be an unlikely source for the observed changes in affinity. Hence, it is likely that the dynamics are contributing significantly to the differences in binding affinity.

We will present the results of NMR measurements of 15N dynamics for the sequence ACCGAAAACGGT. Predictions based on crystallographic and molecular biology data suggest that the A-tract sequence in the spacer region will be rigid. The validity of this hypothesis will be tested by characterization of the dynamic properties of the oligonucleotide on both fast (ps-ns) and slow (μs-ms) time-scales. These results represent the first step in a comprehensive characterization of the role of DNA dynamics in protein-DNA interactions.

Norma H. Pawley*
Ryszard Michalczyk

Bioscience Division
B-3, MS G758
Los Alamos National Laboratory
Los Alamos, New Mexico 87545
*npawley@lanl.gov