Structure, stability, and thermodynamics of a short intermolecular purine-purine-pyrimidine triple helix.
Structure, stability, and thermodynamics of a short intermolecular purine-purine-pyrimidine triple helix.
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短分子间嘌呤-嘌呤-嘧啶三螺旋的结构、稳定性和热力学。
DOI：
10.1021/bi00239a001
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发表时间：
1991
期刊：
影响因子：
2.9
通讯作者：
Shafer,RH
中科院分区：
文献类型：
--
作者：
Pilch,DS;Levenson,C;Shafer,RH
摘要：我们通过聚丙烯酰胺凝胶电泳（PAGE）、核磁共振氢谱和紫外吸收光谱研究了d（C3 T4 C3）-2 [d（G3 A4 G3）]三股螺旋的结构和物理化学。在中性pH下用MgCl 2稳定三链体。PAGE研究验证了包含三链体的链的化学计量，并表明嘌呤-嘌呤-嘧啶（pur-pur-pyr）三链体中第三链的取向相对于底层双链体的嘌呤链是反平行的。亚氨基质子核磁共振谱提供了证据，存在新的嘌呤嘌呤（pur-pur）氢键，除了沃森-克里克（WC）碱基对，在三链体结构。这些新的氢键可能对应于第三链鸟嘌呤NH 1亚氨基质子和基础双链体嘌呤链上鸟嘌呤残基的N7原子之间的相互作用。在本研究中使用的条件下，三链体的热变性在一个步骤中进行至单链。第三条链的结合似乎将双链体的热稳定性提高了1-3 C，具体取决于DNA浓度。三链体形成的自由能（-26.0 0. 5 kcal/mol）大约是双链体形成的自由能（-12.6 0. 7 kcal/mol）的两倍，这表明pur-pur碱基对的总体稳定性与WC碱基对相似。此外，在除pH（7.3对5.5）之外的相同溶液条件下，d（C3 T4 C3）-2 [d（G3 A4 G3）]三链体中第三链的稳定性约为相应d（C+3 T4 C + 3）-d（G3 A4 G3）-d（C3 T4 C3）三链体中第三链的稳定性的两倍（-6.4 ~0.5 kcal/mol）[Pilch，D.美国，布鲁索河& Shafer，R. H.（1990）Nucleic Acids Res. 18，5743-5750]。这种稳定性的显著增强，加上缺乏酸性pH要求，表明pur-pur-pyr三链体是用于涉及体外和体内双链体DNA的寡核苷酸靶向的应用的有吸引力的选择。近年来，核酸的结构多样性变得越来越明显。三螺旋是多种不寻常结构中的一种形式（威尔斯等人，（1988）
Revised Manuscript Received April 18, 1991 abstract: We have investigated the structure and physical chemistry of the d (C3T4C3)-2 [d (G3A4G3)] triple helix by polyacrylamide gel electrophoresis (PAGE),'H NMR, and ultraviolet (UV) absorption spectroscopy. The triplex was stabilized with MgCl2 at neutral pH. PAGE studies verify the stoichiometry of the strands comprising the triplex and indicate that the orientation of the third strand in purine-purine-pyrimidine (pur-pur-pyr) triplexes is antiparallel with respect to the purine strand of the underlying duplex. Imino proton NMR spectra provide evidence for the existence of new purine-purine (pur-pur) hydrogen bonds, in addition to those of the Watson-Crick (WC) base pairs, in the triplex structure. These new hydrogen bonds are likely to correspond to the interaction between third-strand guanine NH1 imino protons and the N7 atoms of guanine residues on the purine strand of the underlying duplex. Thermal denaturation of the triplex proceeds to single strands in one step, under the conditions used in this study. Binding of the third strand appears to enhance the thermal stability of the duplex by 1-3 C, depending on the DNA concentration. The free energy of triplex formation (-26.0±0.5 kcal/mol) is approximately twice that of duplex formation (-12.6±0.7 kcal/mol), suggesting that the overall stability of the pur-pur base pairs is similar to that of the WC base pairs. In addition, under identical solution conditions with the exception of pH (7.3 vs 5.5), the stability of the third strand in the d (C3T4C3)-2 [d (G3A4G3)] triplex is approximately twice that of the third strand in the corresponding d (C+ 3T4C+ 3)-d (G3A4G3)-d (C3T4C3) triplex (-6.4±0.5 kcal/mol)[Pilch, D. S., Brousseau, R., & Shafer, R. H.(1990) Nucleic Acids Res. 18, 5743-5750]. This marked enhancement in stability, coupled with the lack of an acidic pH requirement, suggests that pur-pur-pyr triplexes are appealing choices for use in applications involving oligonucleotide targeting of duplex DNA in vitro and in vivo. e structural diversity of nucleic acids has become in-creasingly evident in recent years. Thetriple helix is one form among a variety of unusual structures (Wells et al., 1988) that