Znosko Brent M, Burkard Mark E, Krugh Thomas R, Turner Douglas H
Department of Chemistry, University of Rochester, New York 14627-0216, USA.
Biochemistry. 2002 Dec 17;41(50):14978-87. doi: 10.1021/bi0203278.
The contribution of amino groups to the thermodynamics, structure, and dynamics of tandem A.A mismatches is investigated by substitution of purine (P) for adenine (A) within the RNA duplex, 5'(rGGCAAGCCU)(2), to give 5'(rGGCPAGCCU)(2), 5'(rGGCAPGCCU)(2), and 5'(rGGCPPGCCU)(2). The 5'(rGGCAAGCCU)(2) duplex has sheared A(anti).A(anti) (A.A trans Hoogsteen/Sugar-edge) pairs in which the A5 amino group is involved in hydrogen bonds but the A4 amino group is not [Znosko, B. M., Burkard, M. E., Schroeder, S. J., Krugh, T. R., and Turner, D. H. (2002) Biochemistry 41, 14969-14977]. In comparison to 5'(rGGCAAGCCU)(2), replacing the amino group of A4 with a hydrogen stabilizes the duplex by 1.3 kcal/mol, replacement of the A5 amino group destabilizes the duplex by 0.6 kcal/mol, and replacement of both A4 and A5 amino groups destabilizes the duplex by 0.8 kcal/mol. In NMR structures, the P.A noncanonical pairs of the 5'(rGGCPAGCCU)(2) duplex have a sheared anti-anti structure (P.A trans Hoogsteen/Sugar-edge) with P4.A5 interstrand hydrogen bonding and A5 bases that interstrand stack, similar to the structure of 5'(rGGCAAGCCU)(2). In contrast, the A.P pairs of the 5'(rGGCAPGCCU)(2) duplex have a face-to-face conformation (A.P trans Watson-Crick/Watson-Crick) with intrastrand stacking resembling typical A-form geometry. Although the P5 bases in 5'(rGGCPPGCCU)(2) are involved in an interstrand stack, the loop region is largely undefined. The results illustrate that both hydrogen-bonded and non-hydrogen-bonded amino groups play important roles in determining the thermodynamic, structural, and dynamic characteristics of purine rich internal loops.
通过将RNA双链体5'(rGGCAAGCCU)(2)中的腺嘌呤（A）替换为嘌呤（P），得到5'(rGGCPAGCCU)(2)、5'(rGGCAPGCCU)(2)和5'(rGGCPPGCCU)(2)，研究了氨基对串联A.A错配的热力学、结构和动力学的贡献。5'(rGGCAAGCCU)(2)双链体具有剪切的A(反式).A(反式)（A.A反式Hoogsteen/糖边缘）对，其中A5氨基参与氢键形成，但A4氨基不参与[Znosko, B. M., Burkard, M. E., Schroeder, S. J., Krugh, T. R., and Turner, D. H. (2002) Biochemistry 41, 14969 - 14977]。与5'(rGGCAAGCCU)(2)相比，用氢取代A4的氨基使双链体稳定1.3千卡/摩尔，取代A5氨基使双链体不稳定0.6千卡/摩尔，同时取代A4和A5氨基使双链体不稳定0.8千卡/摩尔。在NMR结构中，5'(rGGCPAGCCU)(2)双链体的P.A非经典对具有剪切的反-反结构（P.A反式Hoogsteen/糖边缘），P4.A5链间氢键形成且A5碱基链间堆积，类似于5'(rGGCAAGCCU)(2)的结构。相比之下，5'(rGGCAPGCCU)(2)双链体的A.P对具有面对面构象（A.P反式Watson-Crick/Watson-Crick），链内堆积类似于典型的A-型几何结构。虽然5'(rGGCPPGCCU)(2)中的P5碱基参与链间堆积，但环区域在很大程度上不明确。结果表明，氢键结合和非氢键结合的氨基在决定富含嘌呤的内部环的热力学, 结构和动力学特征方面都起着重要作用。
