Enthalpy and heat capacity changes for formation of an oligomeric DNA duplex: Interpretation in terms of coupled processes of formation and association of single-stranded helices

The thermodynamics of self-assembly of a 14 base pair DNA double helix from complementary strands have been investigated by titration (ITC) and differ ential scanning (DSC) calorimetry, in conjunction with van't Hoff analysis of UV thermal scans of individual strands. These studies demonstrate that t hermodynamic characterization of the temperature-dependent contributions of coupled conformational equilibria in the individual "denatured" strands an d in the duplex is essential to understand the origins of duplex stability and to derive stability prediction schemes of general applicability. ITC st udies of strand association at 293 K and 120 mM Na+ yield an enthalpy chang e of -73 +/- 2 kcal (mol of duplex)(-1). ITC studies between 282 and 312 K at 20, 50, and 120 mM Na+ show that the enthalpy of duplex formation is onl y weakly salt concentration-dependent but is very strongly temperature-depe ndent, decreasing approximately linearly with increasing temperature with a heat capacity change (282-312 K) of -1.3 +/- 0.1 kcal K-1 (mol of duplex)( -1). From DSC denaturation studies in 120 mM Na+, we obtain an enthalpy of duplex formation of -120 +/- 5 kcal (mol of duplex)(-1) and an estimate of the corresponding heat capacity change of -0.8 +/- 0.4 kcal K-1 (mol of dup lex)(-1) at the T-m of 339 K. van't Hoff analysis of UV thermal scans on th e individual strands indicates that single helix formation is noncooperativ e with a temperature-independent enthalpy change of -5.5 +/- 0.5 kcal at 12 0 mM Na+. From these observed enthalpy and heat capacity changes, we obtain the corresponding thermodynamic quantities for two fundamental processes: (i) formation of single helices from disordered strands, involving only int rastrand (vertical) interactions between neighboring bases; and (ii) format ion of double helices by association (docking) of single helical strands, i nvolving interstrand (horizontal and vertical) interactions. At 293 K and 1 20 mM Naf, we calculate that the enthalpy change for association of single helical strands is approximately -64 kcal (mol of duplex)(-1) as compared t o -210 kcal (mol of duplex)(-1) calculated for duplex formation from comple tely unstructured single strands and to the experimental ITC value of -73 k cal (mol of duplex)(-1), The intrinsic heat capacity change for association of single helical strands to form the duplex is found to be small and posi tive [similar to 0.1 kcal K-1 (mol of duplex)(-1)], in agreement with the r esult of a surface area analysis, which also predicts an undetectably small heat capacity change for single helix formation.