Pieters J M, de Vroom E, van der Marel G A, van Boom J H, Koning T M, Kaptein R, Altona C
Gorlaeus Laboratories, University of Leiden, The Netherlands.
Biochemistry. 1990 Jan 23;29(3):788-99. doi: 10.1021/bi00455a029.
Nuclear magnetic resonance (NMR) and model-building studies were carried out on the hairpin form of the octamer d(CGaCTAGCG) (aC = arabinofuranosylcytosine), referred to as the TA compound. The nonexchangeable protons of the TA compound were assigned by means of nuclear Overhauser effect spectroscopy (NOESY) and correlated spectroscopy (COSY). From a detailed analysis of the coupling data and of the NOESY spectra the following conclusions are reached: (i) The hairpin consists of a stem of three Watson-Crick type base pairs, and the two remaining residues, T(4) and dA(5), participate in a loop. (ii) All sugar rings show conformational flexibility although a strong preference for the S-type (C2'-endo) conformer is observed. (iii) The thymine does not stack upon the 3' side of the stem as expected, but swings into the minor groove. (This folding principle of the loop involves an unusual alpha t conformer in residue T(4).) (iv) At the 5'-3' loop-stem junction a stacking discontinuity occurs as a consequence of a sharp turn in that part of the backbone, caused by the unusual beta + and gamma t torsion angles in residue dG(6). (v) The A base slides over the 5' side of the stem to stack upon the aC(3) residue at the 3' side of the stem in an antiparallel fashion. On the basis of J couplings and a set of approximate proton-proton distances from NOE cross peaks, a model for the hairpin was constructed. This model was then refined by using an iterative relaxation matrix approach (IRMA) in combination with restrained molecular dynamics calculations. The resulting final model satisfactorily explains all the distance constraints.
对八聚体d（CGaCTAGCG）（aC = 阿拉伯呋喃糖基胞嘧啶）的发夹形式（称为TA化合物）进行了核磁共振（NMR）和模型构建研究。通过核Overhauser效应光谱（NOESY）和相关光谱（COSY）对TA化合物的非交换质子进行了归属。通过对耦合数据和NOESY光谱的详细分析，得出以下结论：（i）发夹由三个沃森-克里克型碱基对组成的茎以及其余两个残基T（4）和dA（5）参与形成的环组成。（ii）所有糖环均表现出构象灵活性，尽管观察到强烈偏好S型（C2'-内型）构象异构体。（iii）胸腺嘧啶不像预期的那样堆积在茎的3'侧，而是摆动到小沟中。（环的这种折叠原理涉及残基T（4）中不寻常的αt构象异构体。）（iv）在5'-3'环-茎连接处，由于主链该部分的急剧转弯，发生了堆积不连续，这是由残基dG（6）中不寻常的β +和γt扭转角引起的。（v）A碱基在茎的5'侧滑动，以反平行方式堆积在茎3'侧的aC（3）残基上。基于J耦合和来自NOE交叉峰的一组近似质子-质子距离，构建了发夹的模型。然后使用迭代弛豫矩阵方法（IRMA）结合受限分子动力学计算对该模型进行了优化。所得的最终模型令人满意地解释了所有距离限制。
