Kinetics for exchange of imino protons in deoxyribonucleic acid, ribonucleic acid, and hybrid oligonucleotide helices

Abstract

The lifetime for opening of individual base pairs in a DNA (dCA5G + dCT5G), and RNA (rCA5G + rCU5G), and a hybrid DNA-RNA (rCA5G + dCT5G) helix have been measured by proton nuclear magnetic resonance. The lifetimes were obtained by saturation recovery experiments performed on the hydrogen-bonding imino protons of the Watson-Crick base pairs. In these oligonucleotide helices the observed relaxation rates were dominated by exchange with water, with the magnetic spin-lattice relaxation time of the imino protons possibly being important only at the lowest temperatures in the DNA helix. It was shown that three interior base pairs in the DNA heptamer dCA5G + dCT5G were in the open-limited region, which means that these imino protons exchange every time the base pair opens. The lifetime of the terminal G X C base pairs in the DNA helix are much shorter than the interior A X T base pairs. The pH dependence of the terminal base pairs indicated that the ends of the helix open and close many times before exchange of the imino protons with water takes place. The temperature dependence of the lifetimes of the interior A X T imino protons in the DNA helix showed that these protons exchange only when the double helix has dissociated into single strands. Thus, these lifetimes measure the rate for dissociation of the double helix. The activation energy for this process was found to be 47 kcal/mol. Comparison of the lifetimes of the interior protons in the DNA, RNA, and hybrid helices showed that the rates of dissociation of the RNA and hybrid helices are very similar at 5 degrees C, whereas the rate for the DNA helix was approximately 1 order of magnitude smaller than that for the other two helices. The reasons for the differences in the kinetics of the three helices are discussed, as are the general dynamics of oligonucleotide helices in solution.