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spinqualitylabelsall models 1z7f, resolution 2.10Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

Crystal structure of 16 base pair RNA duplex containing a C-A mismatch

Overview

Ribose 2'-amine substitutions are broadly useful as structural probes in, nucleic acids. In addition, structure-selective chemical reaction at, 2'-amine groups is a robust technology for interrogating local nucleotide, flexibility and conformational changes in RNA and DNA. We analyzed crystal, structures for several RNA duplexes containing 2'-amino cytidine (C(N)), residues that form either C(N)-G base pairs or C(N)-A mismatches. The, 2'-amine substitution is readily accommodated in an A-form RNA helix and, thus differs from the C2'-endo conformation observed for free nucleosides., The 2'-amide product structure was visualized directly by acylating a, C(N)-A mismatch in intact crystals and is also compatible with A-form, geometry. To visualize conformations able to facilitate formation of the, amide-forming transition state, in which the amine nucleophile carries a, positive partial charge, we analyzed crystals of the C(N)-A duplex at pH, 5, where the 2'-amine is protonated. The protonated amine moves to form a, strong electrostatic interaction with the 3'-phosphodiester. Taken, together with solution-phase experiments, 2'-amine acylation is likely, facilitated by either of two transition states, both involving precise, positioning of the adjacent 3'-phosphodiester group.

About this Structure

1Z7F is a Protein complex structure of sequences from [1] with SR as ligand. Full crystallographic information is available from OCA.

Reference

Crystal structures, reactivity and inferred acylation transition states for 2'-amine substituted RNA., Gherghe CM, Krahn JM, Weeks KM, J Am Chem Soc. 2005 Oct 5;127(39):13622-8. PMID:16190727

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