Poster abstracts

Poster number 15 submitted by Alice Deckert

A kinetic approach to the mechanism for nucleic acid renaturation

Alice A. Deckert (Allegheny College), Brittany Rauzan, Rachel Cave, Lesley Sevcik, Kara Ostrofsky, Betsy Whitman (Allegheny College)

Abstract:
The activation parameters, &Delta^*H and &Delta^*S, for renaturation of two octamers (5'-CACAGCAC/GTGCTGTG-3' and 5'-CACGGCTC/GAGCCGTG-3') of DNA, the homomorphous RNA, and complementary hybrids were measured as a function of the sodium chloride concentration (0.01 to 1.0 M). The change in enthalpy of activation for the RNA renaturation reactions increased from approximately zero kcal/mol to 10-15 kcal/mol (depending on sequence) with increasing salt concentration whereas the activation parameters for the DNA renaturation reactions initially decreased from 5-10 kcal/mol to nearly zero kcal/mol before increasing slightly to 3-5 kcal/mol. The change in entropy of activation mirrored these trends. The &Delta^*S for the RNA renaturation reactions increased from -30 to -40 cal/mol K at 0.01 M [NaCl] to +10 to +20 cal/mol K at 1.0 M [NaCl]. In contrast, the value of &Delta^*S was negative (approximately -30 cal/mol K at the minimum) or nearly zero at all salt concentrations for the DNA renaturation reactions. The trends in activation parameters for the hybrids were intermediate to these two cases. The data are interpreted in terms of a reaction path that includes disruption of intrastrand stacking and hydration interactions, association of the two complementary strands, and rehydration of the transition state.

Keywords: kinetics, renaturation, mechanism