1z79

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{{STRUCTURE_1z79| PDB=1z79 | SCENE= }}
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'''Crystal structure of an RNA duplex containing site specific 2'-amine substitution at a C-A mismatch (at pH 5)'''
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===Crystal structure of an RNA duplex containing site specific 2'-amine substitution at a C-A mismatch (at pH 5)===
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==Overview==
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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.
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(as it appears on PubMed at http://www.pubmed.gov), where 16190727 is the PubMed ID number.
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{{ABSTRACT_PUBMED_16190727}}
==About this Structure==
==About this Structure==
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[[Category: Mismatch]]
[[Category: Mismatch]]
[[Category: Rna]]
[[Category: Rna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 17:15:58 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 04:07:18 2008''

Revision as of 01:07, 29 July 2008

Image:1z79.png

Template:STRUCTURE 1z79

Crystal structure of an RNA duplex containing site specific 2'-amine substitution at a C-A mismatch (at pH 5)

Template:ABSTRACT PUBMED 16190727

About this Structure

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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