Howard F B, Miles H T, Liu K, Frazier J, Raghunathan G, Sasisekharan V
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892.
Biochemistry. 1992 Nov 10;31(44):10671-7. doi: 10.1021/bi00159a005.
The polynucleotide helix d(T)n.d(A)n.d(T)n is the only deoxypolynucleotide triple helix for which a structure has been published, and it is generally assumed as the structural basis for studies of DNA triplexes. The helix has been assigned to an A-form conformation with C3'-endo sugar pucker by Arnott and Selsing [1974; cf. Arnott et al. (1976)]. We show here by infrared spectroscopy in D2O solution that the helix is instead B-form and that the sugar pucker is in the C2'-endo region. Distamycin A, which binds only to B-form and not to A-form helices, binds to the triple helix without displacement of the third strand, as demonstrated by CD spectroscopy and gel electrophoresis. Molecular modeling shows that a stereochemically satisfactory structure can be build using C2'-endo sugars and a displacement of the Watson-Crick base-pair center from the helix axis of 2.5 A. Helical constraints of rise per residue (h = 3.26 A) and residues per turn (n = 12) were taken from fiber diffraction experiments of Arnott and Selsing (1974). The conformational torsion angles are in the standard B-form range, and there are no short contacts. In contrast, we were unable to construct a stereochemically allowed model with A-form geometry and C3'-endo sugars. Arnott et al. (1976) observed that their model had short contacts (e.g., 2.3 A between the phosphate-dependent oxygen on the A strand and O2 in the Hoogsteen-paired thymine strand) which are generally known to be outside the allowed range.(ABSTRACT TRUNCATED AT 250 WORDS)
多聚核苷酸螺旋d(T)n.d(A)n.d(T)n是唯一已发表结构的脱氧多聚核苷酸三链螺旋，通常被认为是DNA三链体研究的结构基础。阿诺特和塞尔辛[1974年；参见阿诺特等人（1976年）]已将该螺旋指定为具有C3'-内向型糖环构象的A-型构象。我们在此通过D2O溶液中的红外光谱表明，该螺旋实际上是B-型，且糖环构象处于C2'-内向型区域。仅与B-型而非A-型螺旋结合的Distamycin A与该三链螺旋结合且不使第三条链移位，这通过圆二色光谱和凝胶电泳得以证明。分子建模表明，使用C2'-内向型糖以及将沃森-克里克碱基对中心从螺旋轴位移2.5 Å可以构建出一个立体化学上令人满意的结构。每个残基的上升螺旋参数（h = 3.26 Å）和每圈的残基数（n = 12）的螺旋约束取自阿诺特和塞尔辛（1974年）的纤维衍射实验。构象扭转角处于标准B-型范围内，且不存在短接触。相比之下，我们无法构建出具有A-型几何结构和C3'-内向型糖的立体化学允许模型。阿诺特等人（1976年）观察到他们的模型存在短接触（例如，A链上依赖磷酸的氧与Hoogsteen配对的胸腺嘧啶链中的O2之间距离为2.3 Å），而这些短接触通常已知超出了允许范围。（摘要截短于250字）
