View source for 1yy0

[[Image:1yy0.gif|left|200px]]<br /><applet load="1yy0" size="350" color="white" frame="true" align="right" spinBox="true" 
caption="1yy0, resolution 3.20&Aring;" />
'''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'''<br />

==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==
1YY0 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YY0 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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16190727 16190727]
[[Category: Protein complex]]
[[Category: Gherghe, C M.]]
[[Category: Krahn, J M.]]
[[Category: Weeks, K M.]]
[[Category: CA]]
[[Category: 2'-amine]]
[[Category: 2-amide]]
[[Category: duplex]]
[[Category: in-crystal reaction]]
[[Category: mismatch]]
[[Category: rna]]

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:10:13 2008''