Summary information and primary citation

PDB-id
2lx1; DSSR-derived features in text and JSON formats
Class
RNA
Method
NMR
Summary
Major conformation of the internal loop 5'gagu-3'ugag
Reference
Kennedy, S.D., Kierzek, R., Turner, D.H.: (2012) "Novel conformation of an RNA structural switch." Biochemistry, 51, 9257-9259.
Abstract
The RNA duplex, (5'GACGAGUGUCA)(2), has two conformations in equilibrium. The nuclear magnetic resonance solution structure reveals that the major conformation of the loop, 5'GAGU/3'UGAG, is novel and contains two unusual Watson-Crick/Hoogsteen GG pairs with G residues in the syn conformation, two A residues stacked on each other in the center of the helix with inverted sugars, and two bulged-out U residues. The structure provides a benchmark for testing approaches for predicting local RNA structure and a sequence that allows the design of a unique arrangement of functional groups and/or a conformational switch into nucleic acids.

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