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Global structure of four-way RNA junctions studied using fluorescence resonance energy transfer

Published online by Cambridge University Press:  12 December 2000

FRANK WALTER ,
ALASTAIR I.H. MURCHIE ,
DEREK R. DUCKETT  and
DAVID M.J. LILLEY
FRANK WALTER
Affiliation:
CRC Nucleic Acid Structure Research Group, Department of Biochemistry, The University of Dundee, Dundee DD14HN, United Kingdom
ALASTAIR I.H. MURCHIE
Affiliation:
CRC Nucleic Acid Structure Research Group, Department of Biochemistry, The University of Dundee, Dundee DD14HN, United Kingdom
DEREK R. DUCKETT
Affiliation:
CRC Nucleic Acid Structure Research Group, Department of Biochemistry, The University of Dundee, Dundee DD14HN, United Kingdom Present address: Department of Biochemistry, Box 3711, Duke University Medical Center, Durham, North Carolina 27710, USA.
DAVID M.J. LILLEY
Affiliation:
CRC Nucleic Acid Structure Research Group, Department of Biochemistry, The University of Dundee, Dundee DD14HN, United Kingdom
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Abstract

Four-way helical junctions are found widely in natural RNA species. In this study, we have studied the conformation of two junctions by fluorescence resonance energy transfer. We show that the junctions are folded by pairwise coaxial helical stacking, forming one predominant stacking conformer in both examples studied. At low magnesium ion concentrations, the helical axes of both junctions are approximately perpendicular. One junction undergoes a rotation into a distorted antiparallel structure induced by the binding of a single magnesium ion. By contrast, the axes of the four-way junction of the U1 snRNA remain approximately perpendicular under all conditions examined, and we have determined the stacking conformer adopted.

Keywords

branched RNAFRETmetal ionsRNA structureU1 snRNA
Type
Research Article
Information
RNA , Volume 4 , Issue 6 , June 1998 , pp. 719 - 728
Copyright
1998 RNA Society

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