1YY0: Crystal Structure Of An Rna Duplex Containing A 2'-Amine Substitution And A 2'-Amide Product Produced By In-Crystal Acylation At A C-A Mismatch

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.
PDB ID: 1YY0Download
MMDB ID: 52174
PDB Deposition Date: 2005/2/23
Updated in MMDB: 2011/11
Experimental Method:
x-ray diffraction
Resolution: 3.2  Å
Source Organism:
Biological Unit for 1YY0: dimeric; determined by author
Molecular Components in 1YY0
Label Count Molecule
Nucleotides(2 molecules)
5'-r(*gp*cp*ap*gp*ap*(a5m)p*up*up*ap*ap*ap*up*cp*up*gp*c)- 3'
Molecule annotation
5'-r(*gp*cp*ap*gp*ap*(m5m)p*up*up*ap*ap*ap*up*cp*up*gp*c)- 3'
Molecule annotation
Chemical (1 molecule)
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