Maltseva T V, Zarytova V F, Chattopadhyaya J
Department of Bioorganic Chemistry, University of Uppsala, Sweden.
J Biochem Biophys Methods. 1995 Jun;30(2-3):163-77. doi: 10.1016/0165-022x(94)00075-o.
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).
本文首次详细报道了DNA - RNA杂交体[5'r(G1A2U3U4G5A6A7)3']:5'p[d(T8C9A10A11T12C13)]3'-Pzn双链体（I）中组成碱基对的开闭动力学以及碱基对中亚氨基和氨基质子与水的交换动力学。已将DNA - RNA杂交体（双链体I）中氨基和亚氨基质子的交换动力学与以下B - DNA双链体的相同研究进行了比较：d(C1G2T3A4C5G6)2（II）、d[p(5'T1G2T3T4T5G6G7C8)3']:d[p(5'C9C10A11A12A13C14A15)3']（III）、d(C5G6C7G8A9A10T11T12C13G14C15G16)2（IV）和d(C1G2C3G4C5G6C7G8A9A10T11T12C13G14C15G16C17G18C19G20)2（V）。这项比较研究表明，DNA - RNA杂交体（I）中各种碱基对的寿命τo在约1毫秒范围内变化，它们与较短的B - DNA双链体（II）和（III）的寿命相当，但与较大双链体（IV）和（V）的τo非常不同：20聚体（双链体V）中T11和T12残基碱基对的τo分别为2.9±2.3毫秒和23.2±8.9毫秒，而12聚体（双链体IV）中相应的τo为2.8±2.2毫秒和17.4±5.4毫秒。还表明，根据亚氨基和氨基质子的交换速率评估的总活化能（Ea），代表了碱基对和螺旋开闭以及亚氨基质子从开放状态与结合水的交换过程的能量贡献，接近短B - DNA双链体的Ea（Ea约为28 - 47千卡/摩尔）。
