Metal Ion Dependence, Thermodynamics, and Kinetics for Intramolecular Docking of a GAAA Tetraloop and Receptor Connected by a Flexible Linker
The GAAA tetraloop−receptor motif is a commonly occurring tertiary interaction in RNA. This motif usually occurs in combination with other tertiary interactions in complex RNA structures. Thus, it is difficult to measure directly the contribution that a single GAAA tetraloop−receptor interaction mak...
Saved in:
Published in | Biochemistry (Easton) Vol. 45; no. 11; pp. 3664 - 3673 |
---|---|
Main Authors | , , , , , |
Format | Journal Article |
Language | English |
Published |
United States
American Chemical Society
21.03.2006
|
Subjects | |
Online Access | Get full text |
Cover
Loading…
Summary: | The GAAA tetraloop−receptor motif is a commonly occurring tertiary interaction in RNA. This motif usually occurs in combination with other tertiary interactions in complex RNA structures. Thus, it is difficult to measure directly the contribution that a single GAAA tetraloop−receptor interaction makes to the folding properties of a RNA. To investigate the kinetics and thermodynamics for the isolated interaction, a GAAA tetraloop domain and receptor domain were connected by a single-stranded A7 linker. Fluorescence resonance energy transfer (FRET) experiments were used to probe intramolecular docking of the GAAA tetraloop and receptor. Docking was induced using a variety of metal ions, where the charge of the ion was the most important factor in determining the concentration of the ion required to promote docking {[Co(NH3)6 3+] ≪ [Ca2+], [Mg2+], [Mn2+] ≪ [Na+], [K+]}. Analysis of metal ion cooperativity yielded Hill coefficients of ≈2 for Na+- or K+-dependent docking versus ≈1 for the divalent ions and Co(NH3)6 3+. Ensemble stopped-flow FRET kinetic measurements yielded an apparent activation energy of 12.7 kcal/mol for GAAA tetraloop−receptor docking. RNA constructs with U7 and A14 single-stranded linkers were investigated by single-molecule and ensemble FRET techniques to determine how linker length and composition affect docking. These studies showed that the single-stranded region functions primarily as a flexible tether. Inhibition of docking by oligonucleotides complementary to the linker was also investigated. The influence of flexible versus rigid linkers on GAAA tetraloop−receptor docking is discussed. |
---|---|
Bibliography: | ark:/67375/TPS-292JN7N4-T This work was supported in part by grants from NIH (AI 33098), NSF, NIST, and the W. M. Keck Foundation initiative in RNA science at the University of Colorado, Boulder. C.D.D. was also supported in part by NIH Biophysics Training Grant GM 65103. istex:AAF310BED1666A4B392C38C6D7D15EB15E6D7AC3 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Department of Chemistry and Biochemistry JILA, NIST |
ISSN: | 0006-2960 1520-4995 |
DOI: | 10.1021/bi0520941 |