Thermodynamic and kinetic parameters of an oligonucleotide hairpin helix.

The thermodynamics of the hairpin helix-single strand transition of A(6)C(6)U(6) has been analyzed by a staggering zipper model with consideration of single strand stacking. This analysis yields an enthalpy change of +11 kcal/mole for the formation of a first, isolated base pair. The stability constant of a first (intramolecular) base pair in A(6)C(6)U(6) is around 2 × 1O(-5) at 25°C, whereas a first (intermoleciilar) base pair in an A(6) · U(6) helix is characterised by a stability constant of about 4 × 10(-3)M(-1) (25°C, extrapolated from A(n) · V(n) oligomer measurements). These data indicate a destabilizing effect of the C(6) loop. The rate constant of hairpin helix formation is 2 to 3 × 10(4) sec(-1) associated with an activation enthalpy of +2.5 kcal/mote. The rate of helix dissociation of the A(6)C(6)U(6) hairpin is in the range of 10(3) to lO(5) sec(-1) with an activation enthalpy of 21 kcal mole . A comparison with the kinetic parameters obtained for A · U oligomer helices shows a specific influence of the C(6) loop due to the stacking tendency of the cytosine residues. This intluence is preferentially reflected in the relatively low value of the rate constant of helix formation.