2IRO

The NMR Structures of (rGCUGAGGCU)2 and (rGCGGAUGCU)2

Summary for 2IRO

• Entry DOI: 10.2210/pdb2iro/pdb
• Related: 2IRN
• Descriptor: 5'-R(P*GP*CP*GP*GP*AP*UP*GP*CP*U)-3' (1 entity in total)
• Functional Keywords: rna internal loops, sheared ga pairs, sheared gu pairs, non canonical pairs, thermodynamics, rna
• Total number of polymer chains: 2
• Total formula weight: 5775.53

Authors

Tolbert, B.S. (deposition date: 2006-10-16, release date: 2007-02-20, Last modification date: 2024-05-29)

Primary citation

Tolbert, B.S.,Kennedy, S.D.,Schroeder, S.J.,Krugh, T.R.,Turner, D.H.
NMR Structures of (rGCUGAGGCU)(2) and (rGCGGAUGCU)(2): Probing the Structural Features That Shape the Thermodynamic Stability of GA Pairs(,).
Biochemistry, 46:1511-1522, 2007

PubMed Abstract: The NMR structures of [see text] and [see text] are reported. The internal loop, [see text], is about 2 kcal/mol more stable than [see text] at 37 degrees C. The duplexes assemble into similar global folds characterized by the formation of tandem sheared GA pairs. The different stabilities of the loops are accompanied by differences in the local structure of the closing GU pairs. In the [see text] internal loop, the GU pairs form canonical wobble configurations with two hydrogen bonds, whereas in [see text], the GU pairs form a single hydrogen bond involving the amino group, GH22, and the carbonyl group, UO4. This pairing is similar to the GU closing pair of the 690 hairpin loop found in E. coli 16S rRNA. The [see text] and [see text] structures reveal how the subtle interplay between stacking and hydrogen bonding determines sequence dependent conformation and thermodynamic stability. Thus, this work provides structural and thermodynamic benchmarks for theoreticians in the ongoing effort to understand the sequence dependence of RNA physicochemical properties.

PubMed: 17279616
DOI: 10.1021/bi061350m

Experimental method

SOLUTION NMR