Download MendeleyStructure of a 16-mer RNA duplex r(GCAGACUUAAAUCUGC)2 with wobble C.A+ mismatches.
Pan, B., Mitra, S.N., Sundaralingam, M.(1998) J Mol Biol 283: 977-984
- PubMed: 9799637
- DOI: https://doi.org/10.1006/jmbi.1998.2140
- Primary Citation of Related Structures:
405D - PubMed Abstract:
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.
Organizational Affiliation:
Biological Macromolecular Structure Center, Departments of Chemistry, Biochemistry and Biophysics Program, The Ohio State University, 1060 Carmack Road, Columbus, Ohio, 43210-1002, USA.
