The crystal structure of an RNA oligomer incorporating tandem adenosine-inosine mismatches.
The X-ray crystallographic structure of the RNA duplex [r(CGCAIGCG)]2 has been refined to 2.5 A. It shows a symmetric internal loop of two non-Watson-Crick base pairs which form in the middle of the duplex. The tandem A-I/I-A pairs are related by a crystallographic two-fold axis. Both A(anti)-I(anti) mismatches are in a head-to-head conformation forming hydrogen bonds using the Watson-Crick positions. The octamer duplexes stack above one another in the cell forming a pseudo-infinite helix throughout the crystal. A hydrated calcium ion bridges between the 3'-terminal of one molecule and the backbone of another. The tandem A-I mismatches are incorporated with only minor distortion to the backbone. This is in contrast to the large helical perturbations often produced by sheared G-A pairs in RNA oligonucleotides.
Carter
R J
RJ
Structural Biology Division, Lawrence Berkeley Laboratory, Berkeley, CA 94720, USA.
Baeyens
K J
KJ
SantaLucia
J
J
Turner
D H
DH
Holbrook
S R
SR
D000241:Adenosine / Q000737:chemistry*; D001482:Base Composition; D001483:Base Sequence; D001665:Binding Sites; D002118:Calcium / Q000378:metabolism; D003460:Crystallization; D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D007288:Inosine / Q000737:chemistry*; D008958:Models, Molecular; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes; D009843:Oligoribonucleotides / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*; D014867:Water / Q000737:chemistry
D009692:Nucleic Acid Heteroduplexes; D009843:Oligoribonucleotides; D014867:Water; D007288:Inosine; D012313:RNA; D000241:Adenosine; D002118:Calcium