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| {{STRUCTURE_1yzd| PDB=1yzd | SCENE= }} | | {{STRUCTURE_1yzd| PDB=1yzd | SCENE= }} |
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| '''Crystal structure of an RNA duplex containing a site specific 2'-amine substitution at a C-G Watson-Crick base pair'''
| | ===Crystal structure of an RNA duplex containing a site specific 2'-amine substitution at a C-G Watson-Crick base pair=== |
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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.
| | The line below this paragraph, {{ABSTRACT_PUBMED_16190727}}, adds the Publication Abstract to the page |
| | (as it appears on PubMed at http://www.pubmed.gov), where 16190727 is the PubMed ID number. |
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| | {{ABSTRACT_PUBMED_16190727}} |
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| ==About this Structure== | | ==About this Structure== |
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| [[Category: Duplex]] | | [[Category: Duplex]] |
| [[Category: Rna]] | | [[Category: Rna]] |
| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 16:59:49 2008'' | | |
| | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 15:51:09 2008'' |
