Kondo N S, Danyluk S S
Biochemistry. 1976 Feb 24;15(4):756-68. doi: 10.1021/bi00649a006.
A detailed 220-MHz NMR study has been made of the conformational properties for the homodinucleotide adenylyl-3' leads to 5'-adenosine, ApA, in D2O. Unambiguous signal assignments of all proton signals were made with the aid of selectively deuterated nucleotidyl units, ApA, ApA, and D-8ApA, and complete, accurate sets of NMR parameters were derived by simulation-iteration methods. Sets of limiting chemical shifts and coupling values were also obtained for ApA and constituent monomers 3'-AMP and 5'-AMP at infinite dilution and at identical ionization states for assessment of dimerization effects. Conformational properties were evaluated quantitatively for most of the conformational bonds of ApA and these are consistent with two compact folded dynamically averaged structures, a base-stacked right helical structure, I, characterized as anti, C3'-endo, g-, w,w' (320,330 degrees), g'g', gg, C3'-endo, anti, and a more loosely base-stacked loop structure, II, with anti, C3'-endo, g-, w,w' (80 degrees, 50 degrees), g'g', gg, C3'-endo, anti orientations. Dimerization produces a number of nucleotidyl conformational changes including a shift in ribose equilibrium C2'-endo (S) in equilibrium C3'-endo (N) in favor of C3'-endo in both Ap- and -pA (60:40 vs. 35:65 in monomers), a change in glycosidic torsion angle chiCN toward 0 degrees, and a greater locking-in of rotamers along bonds involved in the phosphodiester backbone. Moreover, there is clear evidence that the transitions from S leads to N forms and chiCN leads to 0 degrees are directly related to base stacking in ApA. Finally, ApA exists in solution as an equilibrium between I, II and an unstacked form(s) with as yet undetermined conformational features. Since C4'-C5', C5'-O5', and C3'-O3' bonds possess exceptional conformational stabilities, it is proposed that destacking occurs primarily by rotation about P-O5' and/or O3'-P. Predominant factors influencing the overall ApA conformation are thus base-base interaction and flexibility about P-O5' and O3'-P, with change of ribose conformation occurring in consequence of an alteration of chiCN, the latter in turn being governed by the need for maximum eta overlap of stacked adenine rings.
已对重水（D₂O）中同型二核苷酸腺苷酰-3′→5′-腺苷（ApA）的构象性质进行了详细的220兆赫兹核磁共振（NMR）研究。借助选择性氘代的核苷酸单元ApA、ApA和D-8ApA对所有质子信号进行了明确的信号归属，并通过模拟迭代方法得出了完整、准确的NMR参数集。还获得了ApA及其组成单体3′-AMP和5′-AMP在无限稀释和相同电离状态下的极限化学位移和耦合值集，以评估二聚化效应。对ApA的大多数构象键的构象性质进行了定量评估，这些性质与两种紧密折叠的动态平均结构一致，一种是碱基堆积的右螺旋结构I，其特征为反式、C3′-内型、g-、ω、ω′（320°、330°）、g′g′、gg、C3′-内型、反式；另一种是碱基堆积较松散的环结构II，具有反式、C3′-内型、g-、ω、ω′（80°、50°）、g′g′、gg、C3′-内型、反式取向。二聚化产生了许多核苷酸构象变化，包括核糖平衡从C2′-内型（S）向C3′-内型（N）的转变，在Ap-和-pA中均有利于C3′-内型（单体中为60:40，而不是35:65），糖苷扭转角χCN向0°的变化，以及沿磷酸二酯主链相关键的旋转异构体锁定增强。此外，有明确证据表明，从S型向N型的转变以及χCN向0°的转变与ApA中的碱基堆积直接相关。最后，ApA在溶液中以I、II和一种尚未确定构象特征的未堆积形式之间的平衡存在。由于C₄′-C₅′、C₅′-O₅′和C₃′-O₃′键具有特殊的构象稳定性，因此提出解堆积主要通过围绕P-O₅′和/或O₃′-P的旋转发生。因此，影响整体ApA构象的主要因素是碱基-碱基相互作用以及围绕P-O₅′和O₃′-P的灵活性，核糖构象的变化是由于χCN的改变而发生的，而χCN的改变又受堆积腺嘌呤环最大η重叠需求的支配。
