THE THERMODYNAMICS OF FORMATION OF A 3-STRAND, DNA 3-WAY JUNCTION COMPLEX

Isothermal titration calorimetry (ITC) is used to study the thermodyna mics of assembly of the three DNA oligonucleotides S1 (5'GCCTGCCACCGC) , S2 (5'-GCGGTGCGTCCG), and S3AA (5'-CGGACGAAGCAGGC) to form a three-w ay junction (TWJ) complex consisting of three double-helical arms radi ating from a junction region having two unpaired adenosines in one str and (S3AA). The thermodynamics of assembly were measured for three dif ferent orders of addition of the component oligonucleotides at four te mperatures between 10 and 25 degrees C. At each temperature studied, t he overall values of Delta H, Delta S degrees, and Delta G degrees for assembly of the complex from the component single strands were found to be independent of the order of addition. The enthalpy of binding, D elta H, was found to be linearly dependent on temperature. From the te mperature dependence of Delta H, the change in heat capacity Delta C-p , for the overall assembly of three strands to form the junction compl ex was calculated and found to be-1.6 kcal mol(-1) K-1. This work repr esents the first attempt to evaluate the thermodynamics of DNA TWJ for mation by ITC.