Thermodynamics and kinetics of the helix‐coil transition of oligomers containing GC base pairs

Abstract Absorbance‐temperature profiles have been determined for the following self‐complementary oligonucleotides or equimolar paris of complementary oligonucleotides containing GC base pairs: A 2 GCU 2 , A 3 GCU 3 , A 4 GCU 4 , A 6 CG + CGU 6 , A 8 CG + CGU 8 , A 4 G 2 + C 2 U 4 , A 5 G 2 + C 2 U 5 , A 4 G 3 + C 3 U 4 , and A 5 G 3 + C 3 U 5 . In all cases cooperative melting transitions indicate double‐helix formation. As was found previously, the stability of GC containing oligomer helices is much higher than that of AU helices of corresponding length. Moreover, helices with the same length and base composition but different sequences also have quite different stabilites. The melting curves were andlyzed using a zipper model and the thermodynamic parameters for the AU pairs determined previously. The effect of single‐strand stacking was considered separately. According to this model, the formation of a GC pair from unstacked single strands is associated with an ethalpy change of −15 kcal/mole. Due to the high degree of single‐strand stacking at room temperature the enthalpy change for the formation of GC pairs from unstacked single strands is only −5 to −6 kcal/mole. (The corresponding parameters for AU pairs are −10.7 kcal/mole and −5 to −6 kcal/mole.) The sequence dependence of helix stability seems to be primarily entropic since no differences in Δ H were seen among the sequence isomers. The kinetics of helix formation was investigated for the same molecules using the temperature jump technique. Recombination of strands is second order with rate constants in the range of 10 5 to 10 7 M −1 sec −1 depending on the chain length and the nucleotide sequence. Within a series of oligomers of a given type, the rates of recombination decrease with increasing chain length. Oligomers with the sequence A n GCU n recombine six to eight times slower than the other oligomers of corresponding chain length. The experimental enthalpies of activation of 6 to 9 kcal/mole suggest a nucleation length of one or two GC base pairs. The helix dissociation process has rate constants between 0.5 and 500 sec −1 and enthalpies of activation of 25 to 50 kcal/mole. An increase of chain length within a given nucleotide series leads to decreased rates of dissociation and increased enthalpies of activation. An investigation of the effect of ionic strength on A n GCU n helix formation showed that the rates of recombination increase considerably with increased ionic strength.