Direct identification of NH{middle dot}{middle dot}{middle dot}N hydrogen bonds in non-canonical base pairs of RNA by NMR spectroscopy
- 1 August 1999
- journal article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 27 (15) , 3104-3110
- https://doi.org/10.1093/nar/27.15.3104
Abstract
It is shown that the recently developed quantitative J(NN)HNN-COSY experiment can be used for the direct identification of hydrogen bonds in non-canonical base pairs in RNA. Scalar(2h)J(NN)couplings across NH.N hydrogen bonds are observed in imino hydrogen bonded GA base pairs of the hpGA RNA molecule, which contains a tandem GA mismatch, and in the reverse Hoogsteen AU base pairs of the E-loop of Escherichia coli 5S rRNA. These scalar couplings correlate the imino donor(15)N nucleus of guanine or uridine with the acceptor N1 or N7 nucleus of adenine. The values of the corresponding(2h)J(NN)coupling constants are similar in size to those observed in Watson-Crick base pairs. The reverse Hoogsteen base pairs could be directly detected for the E-loop of E.coli 5S rRNA both in the free form and in a complex with the ribosomal protein L25. This supports the notion that the E-loop is a pre-folded RNA recognition site that is not subject to significant induced conformational changes. Since Watson-Crick GC and AU base pairs are also readily detected the HNN-COSY experiment provides a useful and sensitive tool for the rapid identification of RNA secondary structure elements.Keywords
This publication has 30 references indexed in Scilit:
- A common motif organizes the structure of multi-helix loops in 16 S and 23 S ribosomal RNAsJournal of Molecular Biology, 1998
- Solution Structure of (rGGCAGGCC)2 by Two-Dimensional NMR and the Iterative Relaxation Matrix Approach,Biochemistry, 1997
- Structural Change in Rev Responsive Element RNA of HIV-1 on Binding Rev PeptideJournal of Molecular Biology, 1996
- Molecular Recognition in the FMN – RNA Aptamer ComplexJournal of Molecular Biology, 1996
- Initial analysis of 750 MHz NMR spectra of selectively 15N‐G,U labelled E. coli 5S rRNAFEBS Letters, 1996
- A proposal for the conformation of loop E in Escherichia coli 5S rRNABiochemistry and Cell Biology, 1995
- NMRPipe: A multidimensional spectral processing system based on UNIX pipesJournal of Biomolecular NMR, 1995
- A common RNA loop motif as a docking module and its function in the hammerhead ribozymeNature Structural & Molecular Biology, 1994
- Bend and Helical Twist Associated with a Symmetric Internal Loop from 5S Ribosomal RNABiochemistry, 1994
- Crystal and molecular structure of r(CGCGAAUUAGCG): an RNA duplex containing two G(anti)· A(anti) base pairsStructure, 1994