BASE-PAIR EXCHANGE KINETICS OF THE IMINO AND AMINO PROTONS OF THE 3'-PHENAZINIUM TETHERED DNA-RNA DUPLEX, R((5')GAUUGAA(3'))-D((5')TCAATC(3')-PZN), AND THEIR COMPARISON WITH THOSE OF B-DNA DUPLEX

The dynamics of the opening-closing of the constituent base-pairs as w ell as of the exchange kinetics of the base-paired imino and amino pro tons with water in a DNA-RNA hybrid, ')]:(5')p[d(T(8)C(9)A(10)A(11)T(1 2)C-13)](3')-Pzn] duplex (I), are reported here in details for the fir st time. The exchange kinetics of amino and imino protons in the DNA-R NA hybrid (duplex I) have been compared with identical studies on the following B-D N A duplexes: d(C(1)G(2)T(3)A(4)C(5)G(6))(2) (II), d[p(( 5')T(1)G(2)T(3)T(4)T(5)G(6) ]:d[p((5')C(9)C(10)A(11)A(12)A(13)C(14)A(1 5))(3')] (III), (7)G(8)A(9)A(10)T(11)T(12)C(13)G(14)C(15)G(16))(2) (IV ) and )T(12)C(13)G(14)C(15)G(16)C(17)G(18)C(19)G(20))(2) (V). This com parative study shows that the life-times tau of various base-pairs in the DNA-RNA hybrid (I) varies in the range of similar to 1 ms, and the y are quite comparable to those of the shorter B-DNA duplexes (II) and (III), but very different from the tau(0) of the larger duplexes (IV) and (V): the tau(0) for the base pair of T-11 and T-12 residues in th e 20-mer (duplex V) are 2.9 +/- 2.3 ms and 23.2 +/- 8.9 ms, respective ly, while the corresponding tau(0) 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 e nergy of activation (E(a)) assessed from the exchange rates of both im ino and amino protons, representing energetic contributions from both base-pair and helix opening-closing as well as from the exchange proce ss of the imino protons from the open state with the bound water, is c lose to the E(a) of the short B-DNA duplex (E(a) approximate to 28-47 kcal/mol).