An NMR relaxation study of polynucleotide - nucleotide interactions

Abstract

A study has been made of the influence of polyuridylic acid (poly U)-adenosine (A) interactions upon the NMR proton relaxation behavior of H 2O protons in aqueous solutions doped with Mn ++ ions. Factors investigated included the effect of adenine oligonucleotide chain length, nucleoside concentration, and temperature upon the relaxation behavior of H 2O. The results show that in all cases where solution and temperature conditions favor 2 poly U:A triple strand formation, a significant enhancement in H 2O relaxation rate occurs over that for poly U or nucleotide solutions alone. Moreover, plots of relaxation enhancement versus temperature show well-defined transition regions with the enhancement approaching values for free poly U above the transition temperature, T m . The data also show that T m increases with increasing adenosine concentration and oligomer chain length. No comparable changes were observed for poly U solutions containing guanosine or cytidine derivatives. The increased relaxation rate in 2 poly U:A solutions is consistent with a more rigid secondary structure in the complex than in poly U; melting of this structure leads to an increase in polymer segmental mobility and a corresponding decrease in relaxation rate. The “melting” transitions and variation of T m with concentration and chain length have been interpreted quantitatively in terms of recent statistical models and yield values of ΔH = −20 ± 3 kcal/mole (base triplet) and ΔS = −63 ± 10 cal/mole °K (base triplet) in satisfactory agreement with results of optical studies.