Concerted folding of a Candida ribozyme into the catalytically active structure posterior to a rapid RNA compaction

Mu Xiao, Michael J Leibowitz, Yi Zhang

Research output: Contribution to journalArticle

23 Citations (Scopus)

Abstract

Folding of the major population of Tetrahymena intron RNA into the catalytically active structure is trapped in a slow pathway. In this report, folding of Candida albicans intron was investigated using the trans-acting Ca.L-11 ribozyme as a model. We demonstrated that both the catalytic activity (kobs) and compact folding equilibrium of Ca.L-11 are strongly dependent on Mg2+ at physiological concentrations, with both showing an Mg2+ Hill coefficient of 3. Formation of the compact structure of Ca.L-11 is shown to occur very rapidly, on a subsecond time scale similar to that of RNase T1 cleavage. Most of the ribozyme RNA population folds into the catalytically active structure with a rate constant of 2 min-1 at 10 mM Mg2+; neither slower kinetics nor obvious Mg2+ inhibition is observed. These results suggest that folding of the Ca.L-11 ribozyme is initiated by a rapid magnesium-dependent RNA compaction, which is followed by a slower searching for the native contacts to form the catalytically active structure without interference from the long-lived trapped states. This model thus provides an ideal system to address a range of interesting aspects of RNA folding, such as conformational searching, ion binding and the role of productive intermediates.

Original languageEnglish (US)
Pages (from-to)3901-3908
Number of pages8
JournalNucleic Acids Research
Volume31
Issue number14
DOIs
StatePublished - Jul 15 2003
Externally publishedYes

Fingerprint

Catalytic RNA
Candida
RNA
Introns
RNA Folding
Ribonuclease T1
Tetrahymena
Candida albicans
Magnesium
Population
Ions

ASJC Scopus subject areas

  • Genetics

Cite this

Concerted folding of a Candida ribozyme into the catalytically active structure posterior to a rapid RNA compaction. / Xiao, Mu; Leibowitz, Michael J; Zhang, Yi.

In: Nucleic Acids Research, Vol. 31, No. 14, 15.07.2003, p. 3901-3908.

Research output: Contribution to journalArticle

@article{eed67ed4a0164a3d96053498058b9142,
title = "Concerted folding of a Candida ribozyme into the catalytically active structure posterior to a rapid RNA compaction",
abstract = "Folding of the major population of Tetrahymena intron RNA into the catalytically active structure is trapped in a slow pathway. In this report, folding of Candida albicans intron was investigated using the trans-acting Ca.L-11 ribozyme as a model. We demonstrated that both the catalytic activity (kobs) and compact folding equilibrium of Ca.L-11 are strongly dependent on Mg2+ at physiological concentrations, with both showing an Mg2+ Hill coefficient of 3. Formation of the compact structure of Ca.L-11 is shown to occur very rapidly, on a subsecond time scale similar to that of RNase T1 cleavage. Most of the ribozyme RNA population folds into the catalytically active structure with a rate constant of 2 min-1 at 10 mM Mg2+; neither slower kinetics nor obvious Mg2+ inhibition is observed. These results suggest that folding of the Ca.L-11 ribozyme is initiated by a rapid magnesium-dependent RNA compaction, which is followed by a slower searching for the native contacts to form the catalytically active structure without interference from the long-lived trapped states. This model thus provides an ideal system to address a range of interesting aspects of RNA folding, such as conformational searching, ion binding and the role of productive intermediates.",
author = "Mu Xiao and Leibowitz, {Michael J} and Yi Zhang",
year = "2003",
month = "7",
day = "15",
doi = "10.1093/nar/gkg455",
language = "English (US)",
volume = "31",
pages = "3901--3908",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "14",

}

TY - JOUR

T1 - Concerted folding of a Candida ribozyme into the catalytically active structure posterior to a rapid RNA compaction

AU - Xiao, Mu

AU - Leibowitz, Michael J

AU - Zhang, Yi

PY - 2003/7/15

Y1 - 2003/7/15

N2 - Folding of the major population of Tetrahymena intron RNA into the catalytically active structure is trapped in a slow pathway. In this report, folding of Candida albicans intron was investigated using the trans-acting Ca.L-11 ribozyme as a model. We demonstrated that both the catalytic activity (kobs) and compact folding equilibrium of Ca.L-11 are strongly dependent on Mg2+ at physiological concentrations, with both showing an Mg2+ Hill coefficient of 3. Formation of the compact structure of Ca.L-11 is shown to occur very rapidly, on a subsecond time scale similar to that of RNase T1 cleavage. Most of the ribozyme RNA population folds into the catalytically active structure with a rate constant of 2 min-1 at 10 mM Mg2+; neither slower kinetics nor obvious Mg2+ inhibition is observed. These results suggest that folding of the Ca.L-11 ribozyme is initiated by a rapid magnesium-dependent RNA compaction, which is followed by a slower searching for the native contacts to form the catalytically active structure without interference from the long-lived trapped states. This model thus provides an ideal system to address a range of interesting aspects of RNA folding, such as conformational searching, ion binding and the role of productive intermediates.

AB - Folding of the major population of Tetrahymena intron RNA into the catalytically active structure is trapped in a slow pathway. In this report, folding of Candida albicans intron was investigated using the trans-acting Ca.L-11 ribozyme as a model. We demonstrated that both the catalytic activity (kobs) and compact folding equilibrium of Ca.L-11 are strongly dependent on Mg2+ at physiological concentrations, with both showing an Mg2+ Hill coefficient of 3. Formation of the compact structure of Ca.L-11 is shown to occur very rapidly, on a subsecond time scale similar to that of RNase T1 cleavage. Most of the ribozyme RNA population folds into the catalytically active structure with a rate constant of 2 min-1 at 10 mM Mg2+; neither slower kinetics nor obvious Mg2+ inhibition is observed. These results suggest that folding of the Ca.L-11 ribozyme is initiated by a rapid magnesium-dependent RNA compaction, which is followed by a slower searching for the native contacts to form the catalytically active structure without interference from the long-lived trapped states. This model thus provides an ideal system to address a range of interesting aspects of RNA folding, such as conformational searching, ion binding and the role of productive intermediates.

UR - http://www.scopus.com/inward/record.url?scp=0242317691&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0242317691&partnerID=8YFLogxK

U2 - 10.1093/nar/gkg455

DO - 10.1093/nar/gkg455

M3 - Article

C2 - 12853605

AN - SCOPUS:0242317691

VL - 31

SP - 3901

EP - 3908

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 14

ER -