Chuprina V P, Sletten E
Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region.
J Biomol Struct Dyn. 1993 Feb;10(4):693-707. doi: 10.1080/07391102.1993.10508001.
1H NMR spectroscopy, restrained molecular mechanics and dynamics and refinements after back-calculation of the NOESY spectrum have been performed to study the structure of the d(GAATTTAAATTC)2 duplex and to determine whether it is bent or not. It is found that the duplex adopts a B-type conformation; all sugar conformations belong to the C2' endo region and purines have a larger pseudorotation angle as compared to pyrimidines. The cross-strand AH2(n)-AH1' (m + 1) distance (where (n) and (m) are complementary residues), crucial for an anomalous A/T tract structure, is large on the TA step and gradually decreases at the 3' and 5' ends of the TTTAAA tract and follows the rules proposed previously [Chuprina, V.P., Lipanov, A.A., Fedoroff, O.Yu, Kim, S.G., Kintanar, A., and Reid, B.R., Proc. Natl. Acad. Sci. U.S.A. 88, 9087 (1991)]. The changes in this distance correlate with those in the T1 value for AH2 protons which we measured for several oligonucleotide sequences. A total number of about 250 interproton distance constraints were determined from NOESY spectra and were used for structure determination by molecular mechanics, dynamics and refinement by back-calculations. It is shown that these data are not enough to determine whether the duplex is bent or not. The whole family of B-type conformations including bent and straight structures fit well with the available NMR data. In principle, additional non-NMR data could be used in order to reduce the number of the allowable structures. The refinement of the structures with additional different non-NMR constraints (used as a driving force) on P-P or H1'-H1' minor groove width distances in the TA region shows a very good correlation between these distances and the angle of bending of the dodecamer. The more the minor groove width increases in the TA region the more the duplex is bent at the major groove of this region. On the other hand, there is also a very good correlation between P-P, H1'-H1' and AH2-H1' cross-strand distances as follows from analysis of X-ray B-type structures. These two correlations, together with the increased AH2-H1' cross-strand NMR distance in the TA region of the dodecamer indicate that the duplex should be characterized by a wider minor groove in the TA region and be bent in the major groove in this region.
已采用1H NMR光谱、受限分子力学和动力学以及在对NOESY光谱进行反算后的结构优化，来研究d(GAATTTAAATTC)2双链体的结构，并确定其是否弯曲。结果发现，该双链体采用B型构象；所有糖的构象均属于C2'内型区域，与嘧啶相比，嘌呤具有更大的假旋转角。对于异常A/T序列结构至关重要的跨链AH2(n)-AH1'(m + 1)距离（其中(n)和(m)为互补残基），在TA步上较大，在TTTAAA序列的3'和5'端逐渐减小，并遵循先前提出的规则[Chuprina, V.P., Lipanov, A.A., Fedoroff, O.Yu, Kim, S.G., Kintanar, A., and Reid, B.R., Proc. Natl. Acad. Sci. U.S.A. 88, 9087 (1991)]。我们对几个寡核苷酸序列测量了该距离的变化与AH2质子的T1值变化相关。从NOESY光谱中确定了总共约250个质子间距离约束，并将其用于通过分子力学、动力学和反算优化来确定结构。结果表明，这些数据不足以确定双链体是否弯曲。包括弯曲和直线结构在内的整个B型构象家族都与现有的NMR数据吻合良好。原则上，可以使用额外的非NMR数据来减少允许结构的数量。在TA区域对P-P或H1'-H1'小沟宽度距离施加额外不同的非NMR约束（用作驱动力）对结构进行优化，结果表明这些距离与十二聚体的弯曲角度之间存在非常好的相关性。TA区域中小沟宽度增加得越多，双链体在该区域大沟处的弯曲就越明显。另一方面，从X射线B型结构分析可知，P-P、H1'-H1'和AH2-H1'跨链距离之间也存在非常好的相关性。这两种相关性，以及十二聚体TA区域中AH2-H1'跨链NMR距离的增加，表明双链体在TA区域应具有更宽的小沟，并在该区域的大沟处弯曲。
