Conformation of an RNA molecule that models the P4/P6 junction for group I introns

Biochemistry
J Nowakowski, I Tinoco

Abstract

We present a three-dimensional structure of a 34-nucleotide RNA molecule determined by NMR spectroscopy. The molecule was designed to form a junction between two double-helical stems whose sequence was based on the P4/P6 domain from group I introns. There are 5' and 3' single-strand overhangs at the junctions of the stems. Contrary to our expectations, we found that the 3' end of the molecule is placed in the minor and not the major groove of the P4 helix. As a result of tertiary contacts and stacking interactions from nucleotides in the 3' end, the junction helices are rotated in a left-handed fashion and do not stack coaxially. This conformation is highly dependent on the presence of single-stranded nucleotides at the 3' overhang. When the 3' end is removed, the molecule assumes a radically different structure with 5' end in the minor groove of the P6 helix and overall right-handed rotation between the stems. Only one nucleotide at the 3' end is sufficient to change the geometry of the junction.

References

Jul 3, 1992·Science·J D PuglisiJ R Williamson
Oct 5, 1990·Journal of Molecular Biology·S CoutureJ W Szostak
Nov 11, 1991·Quarterly Reviews of Biophysics·G Varani, I Tinoco
Jan 1, 1984·Annual Review of Biochemistry·H F Noller

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Citations

Jan 1, 1997·Annual Review of Biochemistry·G J Narlikar, D Herschlag
Nov 1, 2005·Critical Reviews in Biochemistry and Molecular Biology·Norbert Polacek, Alexander S Mankin
Feb 5, 2013·Wiley Interdisciplinary Reviews. RNA·Wade W GrabowLuc Jaeger
May 23, 2007·Nucleic Acids Research·Stefan L AmeresKatharina Semrad

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