van den Hoogen Y T, Erkelens C, de Vroom E, van der Marel G A, van Boom J H, Altona C
Gorlaeus Laboratories, Leiden University, The Netherlands.
Eur J Biochem. 1988 Apr 15;173(2):295-303. doi: 10.1111/j.1432-1033.1988.tb13998.x.
NMR studies were carried out on some alternating pyrimidine-purine sequences: the single-stranded tetramers CACA and UGUG and the self-complementary octamer CACAUGUG. Assignments, based upon COSY, homonuclear Hartmann-Hahn, and NOESY experiments, are given for the resonances of all base protons and of several sugar protons. Chemical shift vs temperature profiles were used to obtain thermodynamic parameters for the single-stranded stack in equilibrium with random coil and the duplex in equilibrium with random coil equilibria. The populations of N-type conformer of the ribose rings were estimated from the observed J1'2'. Comparisons with another alternating pyrimidine-purine sequence Um2(6)AUm2(6)A and with the deoxyribose counterparts d(CACA), d(TGTG) and d(CACATGTG) are given. Previous 1H-NMR investigations of Um2(6)AUm2(6)A revealed that the population of bulge-out structure diminishes compared to m2(6)AUm2(6)A due to the U(1)-m2(6)A(2) stacking interaction. In CACA a strong stacking proclivity (Tm = 310 K) together with a clear preference for N-type ribose is observed. However, the stacking interactions in UGUG are relatively less stable (Tm = 288 K) and a bias towards S-type sugar is present. Besides a small amount of stack, a significant contribution of bulge out structure is proposed for UGUG. We conclude that the nature of the pyrimidine base mainly determines the formation of bulge-out structures. The poor stacking properties of uracil now appear to be mainly responsible for this phenomenon. Comparison with the deoxyribose counterparts shows a reasonable agreement between the Tm values of CACA and d(CACA), whereas the Tm of UGUG (288 K) is much lower than the Tm of d(TGTG) (315 K). It is suggested that the absence of bulge-out structures in DNA purine-pyrimidine-purine sequences is related to the relatively strong stacking proclivity of dT residues compared to that of U residues. The Tm values (average 341 K) for the duplex in equilibrium with random coil transition obtained for each residue of CACAUGUG appear very similar. All ribose rings, except the G(8), adopt a pure N conformer in the duplex. This is taken to mean that the differences in conformational behaviour of the constituent tetramers disappear upon duplex formation.
对一些嘧啶 - 嘌呤交替序列进行了核磁共振（NMR）研究：单链四聚体CACA和UGUG以及自互补八聚体CACAUGUG。基于COSY、同核Hartmann - Hahn和NOESY实验，给出了所有碱基质子和几个糖质子的共振归属。利用化学位移随温度变化曲线获得了单链堆积体与无规卷曲处于平衡状态以及双链体与无规卷曲处于平衡状态时的热力学参数。根据观察到的J1'2'估计核糖环N型构象体的比例。给出了与另一个嘧啶 - 嘌呤交替序列Um2(6)AUm2(6)A以及脱氧核糖对应物d(CACA)、d(TGTG)和d(CACATGTG)的比较。先前对Um2(6)AUm2(6)A的1H - NMR研究表明，由于U(1) - m2(6)A(2)堆积相互作用，与m2(6)AUm2(6)A相比，凸起结构的比例降低。在CACA中观察到强烈的堆积倾向（Tm = 310 K）以及对N型核糖的明显偏好。然而，UGUG中的堆积相互作用相对不太稳定（Tm = 288 K），并且存在对S型糖的偏向。除了少量的堆积外，对于UGUG还提出了凸起结构的显著贡献。我们得出结论，嘧啶碱基的性质主要决定了凸起结构的形成。尿嘧啶较差的堆积性质现在似乎是造成这种现象的主要原因。与脱氧核糖对应物的比较表明，CACA和d(CACA)的Tm值之间有合理的一致性，而UGUG的Tm（288 K）远低于d(TGTG)的Tm（315 K）。有人认为，DNA嘌呤 - 嘧啶 - 嘌呤序列中不存在凸起结构与dT残基相比U残基相对较强的堆积倾向有关。对于CACAUGUG的每个残基与无规卷曲转变处于平衡状态的双链体，获得的Tm值（平均341 K）看起来非常相似。除了G(8)之外，所有核糖环在双链体中都采用纯N型构象体。这意味着在双链体形成时，组成四聚体的构象行为差异消失。
