Structure of a 16-mer RNA duplex r(GCAGACUUAAAUCUGC)2 with wobble C•A+ mismatches

被引:47
作者
Pan, BC
Mitra, SN
Sundaralingam, M
机构
[1] Ohio State Univ, Biol Macromol Struct Ctr, Dept Chem, Columbus, OH 43210 USA
[2] Ohio State Univ, Biol Macromol Struct Ctr, Dept Biochem & Biophys, Columbus, OH 43210 USA
[3] Ohio State Univ, Biophys Program, Columbus, OH 43210 USA
关键词
crystal structure; wobble A(+)center dot C mismatches; bent RNA; major groove widening; protein interactions;
D O I
10.1006/jmbi.1998.2140
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The crystal structure of a 16-mer, the longest known RNA duplex, has been determined at 2.5 Angstrom 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 basepair 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 Angstrom/7.3 Angstrom. The duplexes form helical columns and are tightly packed around the 3(1)-screw axis. The minor grooves of adjacent columns in juxtaposition interact through the O2' atoms and the anionic phosphate oxygen atoms. (C) 1998 Academic Press.
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页码:977 / 984
页数:8
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