Proton transfer involving nucleic acids: A temperature-jump study of the systems sulphonephthaleins-double stranded poly(A) and sulphonephthaleins-double stranded poly(C)

The kinetics of proton transfer between poly(A-AH) (partially protonated double-stranded polyadenylic acid) and CPR (chlorophenol red), and between poly(C-H-C) (partially protonated double-stranded polycytidylic acid) and the indicators CPR, BCP (bromocresol purple), and BCG (bromocresol green) have been investigated at 25 degrees C and ionic strength 0.1 M (NaClO4) by the temperature-jump method. The acidic proton of poly(C-H-C) is engaged in a hydrogen bond (N3H+----N-3) which is believed to contribute to stabilizing the double-strand conformation, whereas the acidic proton of poly(A-A-H) does not form hydrogen bonds. The analysis of the dependence of the relaxation times on the concentrations of the reactants has enabled the evaluation of the rate constants for the direct proton transfer and for the protolysis paths. The rate constants for proton recombination with the deprotonated forms of the polynucleotides and the indicators are of the order of magnitude expected for diffusion controlled processes involving oppositely charged ions (k(2) = (0.2 - 1.6) x 10(10) M(-1)s(-1)). The direct proton transfer from poly(C-H-C) to BCG is thermodynamically disfavored and its rate constant, k(1), is lower than k(2) by about three orders of magnitude. The (thermodynamically favored) proton transfers from poly(A-A-H) to CPR and from poly(C-H-C) to CPR and BCP are characterized by similar values of k(1). This result indicates that the hydrogen bonds in poly(C-H-C) are very weak and suggests that the stabilization of the double-stranded conformation of this polynucleotide could be ascribed to the large number of hydrogen bonds rather than to their specific strength. (C) 1998 John Wiley & Sons, Inc.