APPARENT HEAT-CAPACITY CHANGE ACCOMPANYING A NONSPECIFIC PROTEIN-DNA INTERACTION. ESCHERICHIA-COLI SSB TETRAMER BINDING TO OLIGODEOXYADENYLATES

We have examined the effects of temperature on the equilibrium constan t, K-obs, for Escherichia coli SSB tetramer binding to a series of sin gle-stranded (ss) oligodeoxyribonucleotides, dT(pT)(n), dC(pC)(n), and dA(pA)(n) (n = 34, 55, and 69) in order to investigate the thermodyna mic basis for the strong preference of E. coli SSB (and other SSB prot eins) for binding polypyrimidine stretches of ss-DNA. In addition to t he expected base-dependent differences in the magnitude of K-obs, we a lso observe qualitatively different temperature dependencies for the b inding of the SSB tetramer to oligodeoxyadenylates. Linear van't Hoff plots are obtained for SSB tetramer binding to dT(pT)(n) and dC(pC)(n) , with Delta H degrees(obs) ranging from -50 to -100 kcal/mol dependin g on the oligodeoxynucleotide length and salt concentration. In contra st, all van't Hoff plots for SSB tetramer binding to dA(pA)(N) are dis tinctly nonlinear with maxima in K-obs occurring near 25 degrees C, in dicative of an apparent large negative change in molar heat capacity ( Delta C degrees(P,obs) < 0). Thus for the SSB-dA(pA)(n) interaction, D elta H degrees(obs) and Delta S degrees(obs) are both highly temperatu re dependent, but compensate such that Delta G degrees(obs) is relativ ely insensitive to temperature. These nonlinear van't Hoff plots are n ot due to coupling of SSB assembly to dA(pA)(n) binding or to temperat ure-dependent shifts in the formation of other SSB-PNA binding modes. The nonlinear van't Hoff plots for SSB tetramer binding to dA(pA)(n) a ppear to result from the coupling of two processes: (1) the unstacking of the dA(pA)(n) bases (occurring with Delta H degrees > 0 and Delta C degrees(P) = 0) and (2) the binding of SSB to the unstacked DNA (occ urring with Delta H degrees < 0 and Delta C degrees(P) = 0). Therefore , although each isolated equilibrium occurs with Delta C degrees(P) ap proximate to 0, the overall equilibrium displays an apparent Delta C d egrees(P,obs) < 0 due to the coupled equilibrium. The binding of SSB t o dT(pT)(n) and dC(pC)(n) occurs with Delta H degrees < 0 and Delta C degrees(P,obs) = 0, since the bases in these ss-DNA moleculesdo not st ack appreciably. These results indicate that a nonspecific protein-DNA interaction can display a large negative apparent Delta C degrees(P); however, this effect appears not to be due to the hydrophobic effect, but rather to a temperature-dependent conformational transition in th e DNA that is coupled to protein binding. Implications of these observ ations for other protein-nucleic acid systems are discussed.