1Z7F

Crystal structure of 16 base pair RNA duplex containing a C-A mismatch

Summary for 1Z7F

• Entry DOI: 10.2210/pdb1z7f/pdb
• Related: 1YRM 1YY0 1YZD 1Z7F
• Descriptor: 5'-R(*GP*CP*AP*GP*AP*CP*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3', STRONTIUM ION (3 entities in total)
• Functional Keywords: rna, duplex, mismatch
• Total number of polymer chains: 3
• Total formula weight: 15421.48

Authors

Gherghe, C.M.,Krahn, J.M.,Weeks, K.M. (deposition date: 2005-03-24, release date: 2005-10-18, Last modification date: 2023-08-23)

Primary citation

Gherghe, C.M.,Krahn, J.M.,Weeks, K.M.
Crystal structures, reactivity and inferred acylation transition States for 2'-amine substituted RNA.
J.Am.Chem.Soc., 127:13622-13628, 2005

PubMed Abstract: 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.

PubMed: 16190727
DOI: 10.1021/ja053647y

Experimental method

X-RAY DIFFRACTION (2.1 Å)