Base-pair exchange kinetics of the imino and amino protons of the 3'-phenazinium tethered DNA-RNA duplex, r(5'GAUUGAA3'):d(5'TCAATC3'-Pzn), and their comparison with those of B-DNA duplex

Abstract

The dynamics of the opening-closing of the constituent base-pairs as well as of the exchange kinetics of the base-paired imino and amino protons with water in a DNA-RNA hybrid, [5'r(G1A2U3U4G5A6A7)3']:5'p[d(T8C9A10A11T12C13)]3'-Pzn ] duplex (I), are reported here in details for the first time. The exchange kinetics of amino and imino protons in the DNA-RNA hybrid (duplex I) have been compared with identical studies on the following B-DNA duplexes: d(C1G2T3A4C5G6)2 (II), d[p(5'T1G2T3T4T5G6G7C8)3']:d[p(5'C9C10A11A12A13C14A15)3'] (III), d(C5G6C7G8A9A10T11T12C13G14C15G16)2 (IV) and d(C1G2C3G4C5G6C7G8A9A10T11T12C13G14C15G16C17G18C19G20)2 (V). This comparative study shows that the life-times tau o of various base-pairs in the DNA-RNA hybrid (I) varies in the range of approximately 1 ms, and they are quite comparable to those of the shorter B-DNA duplexes (II) and (III), but very different from the tau o of the larger duplexes (IV) and (V): the tau o for the base pair of T11 and T12 residues in the 20-mer (duplex V) are 2.9 +/- 2.3 ms and 23.2 +/- 8.9 ms, respectively, while the corresponding tau o in the 12-mer (duplex IV) are 2.8 +/- 2.2 ms and 17.4 +/- 5.4 ms. It has also been shown that the total energy of activation (Ea) assessed from the exchange rates of both imino and amino protons, representing energetic contributions from both base-pair and helix opening-closing as well as from the exchange process of the imino protons from the open state with the bound water, is close to the Ea of the short B-DNA duplex (Ea approximately 28-47 kcal/mol).