FLUORESCENCE ANISOTROPY AS PROBE OF OLIGONUCLEOTIDE STRUCTURE &DYNAMICS

$545P41FY2000RRNIH

University Of Pennsylvania, Philadelphia PA

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Abstract

We are using fluorescence depolarization as an independent technique to ask why the solution NMR and X-ray diffraction structures of a RNA dodecamer grossly disagree (single-stranded loop vs. double helix). We have demonstrated that this RNA tetraloop and several analogs maintain single-strand hairpin conformations in solution in the conditions used to grow the crystal. We have also used this fluorescence depolarization to study base pair twisting in short DNA duplexes. These duplexes were modeled as cylinders, and rotational diffusion coefficients were determined in earlier studies.

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