Kinetics and Thermodynamics of Double Strand Formation in Selected Deoxyoligonucleotides

摘要

The thermodynamics and relaxation kinetics for the double strand-single strand transition in three deoxyoligonucleotide double helices was investigated. delta H exp 0 , delta S exp 0 for double helix formation and the rate constants for helix association and dissociation were measured for dATGCAT, dA sub 3 GCT sub 3 , and dA sub 8 + dT sub 8 in an effort to compare DNA double helices with similar RNA helices. No trends in these parameters due to base sequence or helix length were observed; however, from a calculation of the free energies for helix formation, it can be seen that double strand formation is less favored for each DNA oligomer than for its analogous RNA oligomer. This agrees with earlier measurements of melting temperatures for DNA and RNA double stranded polymers. The temperature jump technique was applied to the study of the relaxation kinetics of the deoxyoligomers. The association rates are the same as for the comparable RNAs in the case of the two oligomers containing GC base pairs. The association is an order of magnitude faster for dA sub 8 + dT sub 8 than for rA sub 8 + rU sub 8 . In contrast to RNA oligomers where those with GC base pairs have positive activation energies for association and those with only AU base pairs have negative activation energies, the deoxyoligomers all have small negative activation energies for helix association. This is indicative of a mechanistic change between DNA and RNA double strand formation. The formation of one GC base pair is rate-limiting in RNA oligomer association. If no GC base pairs are possible, the formation of a third AU base pair is rate-limiting. In DNA, helix propagation is favored after the formation of two adjacent base pairs. Dissociation activation energies are similar for both DNA and RNA helices. (ERA citation 05:009276)