THERMODYNAMICS OF SINGLE-STRANDED RNA AND DNA INTERACTIONS WITH OLIGOLYSINES CONTAINING TRYPTOPHAN - EFFECTS OF BASE COMPOSITION

We have examined the thermodynamics of binding of a series of oligolysines (net charge z = +2 to +10) containing one, two, or three tryptophans to several single-stranded (ss) homo-polynucleotides [poly(A), poly(C), poly(I), poly(dU), poly(dT)] and duplex (ds) DNA in order to investigate the effects of peptide charge, tryptophan content, and polynucleotide base and sugar type. Equilibrium association constants, K(obs), were measured as a function of monovalent salt concentration (KCH3CO2) and temperature by monitoring the quenching of the peptide tryptophan fluorescence upon interaction with the polynucleotides, from which the dependence of DELTAG-degrees obs, DELTAH-degrees obs, and DELTAS-degrees obs on [KCH3CO2] was obtained. As observed previously with poly(U) [Mascotti, D. P., & Lohman, T. M. (1992) Biochemistry 31, 8932], the dependence of DELTAG-degrees obs on [K+] for peptide binding to each polynucleotide is entirely entropic in origin (i.e., DELTAH-degrees obs is independent of [K+]), consistent with the conclusion that K(obs) increases with decreasing salt concentration due to the favorable increase in entropy resulting from the displacement of bound cations (K+) from the nucleic acid upon formation of the complex. For each ss polynucleotide, we find that significantly less than one potassium ion is released thermodynamically per net positive peptide charge, as determined from the value of partial derivative log K(obs)/partial derivative log[K+]. Interestingly, (-partial derivative log K(obs)/partial derivative log[K+])/z decreases with increasing peptide charge for poly(A), poly(C), and poly(dT), contrary to the behavior observed with poly(U) and ds-DNA, which may reflect a significant release of bound water upon formation of peptide complexes with these ss homo-polynucleotides or an increased binding of K+ to the ss polynucleotide with increasing [K+]. Alternatively, there may be conformational differences between the bound states of oligolysines of low charge, relative to oligolysines of higher charge. However, in all cases, peptides with z < +4 display different thermodynamics of binding than peptides with z > +4. The presence of tryptophan (Trp) within these peptides does not influence the salt dependence of K(obs) for binding to poly(A), poly(C), or poly(dT). However, the Trp content of the peptide does contribute significantly to the thermodynamics of these interactions: Trp interactions result in a favorable contribution to DELTAH-degrees obs but an unfavorable contribution to DELTAS-degrees obs, with little effect on DELTAG-degrees obs due to entropy-enthalpy compensations. Oligolysines containing Trp also display a small, but significant, dependence of K(obs) on base composition, with K(obs) decreasing in the order poly(I) >> poly(dT) is similar to poly(U) is similar to poly(A) >> poly(C).