1z7f
From Proteopedia
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'''Crystal structure of 16 base pair RNA duplex containing a C-A mismatch''' | '''Crystal structure of 16 base pair RNA duplex containing a C-A mismatch''' | ||
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==About this Structure== | ==About this Structure== | ||
| - | + | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Z7F OCA]. | |
==Reference== | ==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://www.ncbi.nlm.nih.gov/pubmed/16190727 16190727] | 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://www.ncbi.nlm.nih.gov/pubmed/16190727 16190727] | ||
| - | [[Category: Protein complex]] | ||
[[Category: Gherghe, C M.]] | [[Category: Gherghe, C M.]] | ||
[[Category: Krahn, J M.]] | [[Category: Krahn, J M.]] | ||
[[Category: Weeks, K M.]] | [[Category: Weeks, K M.]] | ||
| - | [[Category: | + | [[Category: Duplex]] |
| - | [[Category: | + | [[Category: Mismatch]] |
| - | [[Category: | + | [[Category: Rna]] |
| - | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 17:16:22 2008'' | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | |
Revision as of 14:16, 3 May 2008
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
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 Page seeded by OCA on Sat May 3 17:16:22 2008
Categories: Gherghe, C M. | Krahn, J M. | Weeks, K M. | Duplex | Mismatch | Rna
