Pan B, Mitra S N, Sundaralingam M
Biological Macromolecular Structure Center, Departments of Chemistry, Biochemistry and Biophysics Program, The Ohio State University, 1060 Carmack Road, Columbus, Ohio, 43210-1002, USA.
J Mol Biol. 1998 Nov 13;283(5):977-84. doi: 10.1006/jmbi.1998.2140.
The crystal structure of a 16-mer, the longest known RNA duplex, has been determined at 2.5 A resolution. The hexadecamer r(GCAGACUUAAAUCUGC) contains isolated C.A/A.C mismatches with two hydrogen bonds. The two hydrogen bonds in the mismatches suggests that N1 of A is protonated even though the crystallization was done at neutral pH. Therefore, the C.A mismatch is a C.A+ wobble similar to the G.U wobble. The two C.A+ pairs are isolated by four Watson-Crick pairs and flanked by five Watson-Crick base-pairs on either sides. Kinks/bends of 20 degrees are observed at the wobble sites. The Watson-Crick base-pair A5.U26 on the 5'-side of the first C6.A27(+) wobble has a twist angle of 27 degrees compared to the 3'-side U7.A28 pair of 36 degrees. The twist angles are reversed (37 degrees and 26 degrees) in the second A11(+).C22 wobble because of the approximate dyad in the molecule, the flanking base-pair sequences are A.U pairs. The wobbles expand the major groove to 7.1 A/7.3 A. The duplexes form helical columns and are tightly packed around the 31-screw axis. The minor grooves of adjacent columns in juxtaposition interact through the O2' atoms and the anionic phosphate oxygen atoms.
已确定一种16聚体（已知最长的RNA双链体）的晶体结构，分辨率为2.5埃。十六聚体r(GCAGACUUAAAUCUGC)包含具有两个氢键的孤立C.A/A.C错配。错配中的两个氢键表明，即使结晶是在中性pH下进行的，A的N1也是质子化的。因此，C.A错配是一种类似于G.U摆动的C.A+摆动。两个C.A+对被四个沃森-克里克对隔开，两侧各有五个沃森-克里克碱基对。在摆动位点观察到20度的扭结/弯曲。第一个C6.A27(+)摆动5'侧的沃森-克里克碱基对A5.U26的扭转角为27度，而3'侧的U7.A28对为36度。由于分子中的近似二分体，第二个A11(+).C22摆动中的扭转角相反（37度和26度），侧翼碱基对序列为A.U对。摆动将大沟扩展到7.1埃/7.3埃。双链体形成螺旋柱，并围绕31螺旋轴紧密堆积。并列相邻柱的小沟通过O2'原子和阴离子磷酸氧原子相互作用。
