TY - JOUR
T1 - Stability and cooperativity of individual tertiary contacts in RNA revealed through chemical denaturation
AU - Ralston, Corie Y.
AU - He, Qin
AU - Brenowitz, Michael
AU - Chance, Mark R.
N1 - Funding Information:
We are grateful to S. Woodson for providing the DNA templates used for transcription of the Tetrahymena ribozyme and the P4-P6 subdomain of the ribozyme. We also thank M. Deras and J. Swisher for advice and help in the preparation and handling of RNA samples. This work was supported by grants from the NIH Institute for General Medical Sciences and the Biomedical Technology Program of the Division of Research Resources. The National Synchrotron Light Source at Brookhaven National Laboratory is supported by the Department of Energy.
PY - 2000/5
Y1 - 2000/5
N2 - For proteins, understanding tertiary interactions involved in local versus global unfolding has become increasingly important for understanding the nature of the native state ensemble, the mechanisms of unfolding, and the stability of both the native and intermediate states in folding. In this work we have addressed related questions with respect to RNA structure by combining chemical denaturation and hydroxyl radical foot-printing methods. We have determined unfolding isotherms for each of 26 discrete sites of protection located throughout the Tetrahymena thermophila group I ribozyme. The cooperativity of folding, m-value, and the free energy, ΔG°(N-U), associated with formation of each tertiary contact was determined by analysis of the isotherms. The ΔG°(N-U) values measured in this study vary from 1.7 ± 0.2 to 7.6 ± 1.2 kcal mol+1. Thus, the stability of these discrete tertiary contacts vary by almost 104. In addition, an intradomain contact and three interdomain contacts show high cooperativity (m-values of 1.1 ± 0.2 to 1.7 ± 0.3 kcal mol+1 M+1) indicating that these contacts exhibit global cooperatively in their folding behavior. This new approach to examining RNA stability provides an exciting comparison to our understanding of protein structure and folding mechanisms.
AB - For proteins, understanding tertiary interactions involved in local versus global unfolding has become increasingly important for understanding the nature of the native state ensemble, the mechanisms of unfolding, and the stability of both the native and intermediate states in folding. In this work we have addressed related questions with respect to RNA structure by combining chemical denaturation and hydroxyl radical foot-printing methods. We have determined unfolding isotherms for each of 26 discrete sites of protection located throughout the Tetrahymena thermophila group I ribozyme. The cooperativity of folding, m-value, and the free energy, ΔG°(N-U), associated with formation of each tertiary contact was determined by analysis of the isotherms. The ΔG°(N-U) values measured in this study vary from 1.7 ± 0.2 to 7.6 ± 1.2 kcal mol+1. Thus, the stability of these discrete tertiary contacts vary by almost 104. In addition, an intradomain contact and three interdomain contacts show high cooperativity (m-values of 1.1 ± 0.2 to 1.7 ± 0.3 kcal mol+1 M+1) indicating that these contacts exhibit global cooperatively in their folding behavior. This new approach to examining RNA stability provides an exciting comparison to our understanding of protein structure and folding mechanisms.
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U2 - 10.1038/75139
DO - 10.1038/75139
M3 - Article
C2 - 10802732
AN - SCOPUS:0034059197
SN - 1545-9993
VL - 7
SP - 371
EP - 374
JO - Nature Structural and Molecular Biology
JF - Nature Structural and Molecular Biology
IS - 5
ER -