Mg2+-dependent folding of a Diels-Alderase ribozyme probed by single-molecule FRET analysis
- Publication type:
- Journal article
- Metadata:
-
- Autoren
- Andrei Yu Kobitski
- Alexander Nierth
- Mark Helm
- Andres Jaeschke
- G Ulrich Nienhaus
- Autoren-URL
- https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000246123600036&DestLinkType=FullRecord&DestApp=WOS_CPL
- DOI
- 10.1093/nar/gkm072
- eISSN
- 1362-4962
- Externe Identifier
- Clarivate Analytics Document Solution ID: 162XU
- PubMed Identifier: 17344321
- ISSN
- 0305-1048
- Ausgabe der Veröffentlichung
- 6
- Zeitschrift
- NUCLEIC ACIDS RESEARCH
- Paginierung
- 2047 - 2059
- Datum der Veröffentlichung
- 2007
- Status
- Published
- Titel
- Mg<SUP>2+</SUP>-dependent folding of a Diels-Alderase ribozyme probed by single-molecule FRET analysis
- Sub types
- Article
- Ausgabe der Zeitschrift
- 35
Data source: Web of Science (Lite)
- Other metadata sources:
-
- Autoren
- Andrei Yu Kobitski
- Alexander Nierth
- Mark Helm
- Andres Jäschke
- G Ulrich Nienhaus
- DOI
- 10.1093/nar/gkm072
- eISSN
- 1362-4962
- ISSN
- 0305-1048
- Ausgabe der Veröffentlichung
- 6
- Zeitschrift
- Nucleic Acids Research
- Sprache
- en
- Online publication date
- 2007
- Paginierung
- 2047 - 2059
- Datum der Veröffentlichung
- 2007
- Status
- Published
- Herausgeber
- Oxford University Press (OUP)
- Herausgeber URL
- http://dx.doi.org/10.1093/nar/gkm072
- Datum der Datenerfassung
- 2019
- Titel
- Mg2+-dependent folding of a Diels-Alderase ribozyme probed by single-molecule FRET analysis
- Ausgabe der Zeitschrift
- 35
Data source: Crossref
- Abstract
- Here, we report a single-molecule fluorescence resonance energy transfer (FRET) study of a Diels-Alderase (DAse) ribozyme, a 49-mer RNA with true catalytic properties. The DAse ribozyme was labeled with Cy3 and Cy5 as a FRET pair of dyes to observe intramolecular folding, which is a prerequisite for its recognition and turnover of two organic substrate molecules. FRET efficiency histograms and kinetic data were taken on a large number of surface-immobilized ribozyme molecules as a function of the Mg(2+) concentration in the buffer solution. From these data, three separate states of the DAse ribozyme can be distinguished, the unfolded (U), intermediate (I) and folded (F) states. A thermodynamic model was developed to quantitatively analyze the dependence of these states on the Mg(2+) concentration. The FRET data also provide information on structural properties. The I state shows a strongly cooperative compaction with increasing Mg(2+) concentration that arises from association with several Mg(2+) ions. This transition is followed by a second Mg(2+)-dependent cooperative transition to the F state. The observation of conformational heterogeneity and continuous fluctuations between the I and F states on the approximately 100 ms timescale offers insight into the folding dynamics of this ribozyme.
- Addresses
- Institute of Biophysics, University of Ulm, 89069 Ulm, Germany.
- Autoren
- Andrei Yu Kobitski
- Alexander Nierth
- Mark Helm
- Andres Jäschke
- G Ulrich Nienhaus
- DOI
- 10.1093/nar/gkm072
- eISSN
- 1362-4962
- Externe Identifier
- PubMed Identifier: 17344321
- PubMed Central ID: PMC1874616
- Open access
- true
- ISSN
- 0305-1048
- Ausgabe der Veröffentlichung
- 6
- Zeitschrift
- Nucleic acids research
- Schlüsselwörter
- Cations, Divalent
- Magnesium
- RNA, Catalytic
- Fluorescence Resonance Energy Transfer
- Nucleic Acid Conformation
- Thermodynamics
- Models, Molecular
- Sprache
- eng
- Medium
- Print-Electronic
- Online publication date
- 2007
- Open access status
- Open Access
- Paginierung
- 2047 - 2059
- Datum der Veröffentlichung
- 2007
- Status
- Published
- Publisher licence
- CC BY-NC
- Datum der Datenerfassung
- 2007
- Titel
- Mg2+-dependent folding of a Diels-Alderase ribozyme probed by single-molecule FRET analysis.
- Sub types
- Research Support, Non-U.S. Gov't
- research-article
- Journal Article
- Ausgabe der Zeitschrift
- 35
Files
https://academic.oup.com/nar/article-pdf/35/6/2047/18781264/gkm072.pdf https://europepmc.org/articles/PMC1874616?pdf=render
Data source: Europe PubMed Central
- Abstract
- Here, we report a single-molecule fluorescence resonance energy transfer (FRET) study of a Diels-Alderase (DAse) ribozyme, a 49-mer RNA with true catalytic properties. The DAse ribozyme was labeled with Cy3 and Cy5 as a FRET pair of dyes to observe intramolecular folding, which is a prerequisite for its recognition and turnover of two organic substrate molecules. FRET efficiency histograms and kinetic data were taken on a large number of surface-immobilized ribozyme molecules as a function of the Mg(2+) concentration in the buffer solution. From these data, three separate states of the DAse ribozyme can be distinguished, the unfolded (U), intermediate (I) and folded (F) states. A thermodynamic model was developed to quantitatively analyze the dependence of these states on the Mg(2+) concentration. The FRET data also provide information on structural properties. The I state shows a strongly cooperative compaction with increasing Mg(2+) concentration that arises from association with several Mg(2+) ions. This transition is followed by a second Mg(2+)-dependent cooperative transition to the F state. The observation of conformational heterogeneity and continuous fluctuations between the I and F states on the approximately 100 ms timescale offers insight into the folding dynamics of this ribozyme.
- Autoren
- Andrei Yu Kobitski
- Alexander Nierth
- Mark Helm
- Andres Jäschke
- G Ulrich Nienhaus
- Autoren-URL
- https://www.ncbi.nlm.nih.gov/pubmed/17344321
- DOI
- 10.1093/nar/gkm072
- eISSN
- 1362-4962
- Externe Identifier
- PubMed Central ID: PMC1874616
- Ausgabe der Veröffentlichung
- 6
- Zeitschrift
- Nucleic Acids Res
- Schlüsselwörter
- Cations, Divalent
- Fluorescence Resonance Energy Transfer
- Magnesium
- Models, Molecular
- Nucleic Acid Conformation
- RNA, Catalytic
- Thermodynamics
- Sprache
- eng
- Country
- England
- Paginierung
- 2047 - 2059
- PII
- gkm072
- Datum der Veröffentlichung
- 2007
- Status
- Published
- Datum, an dem der Datensatz öffentlich gemacht wurde
- 2007
- Titel
- Mg2+-dependent folding of a Diels-Alderase ribozyme probed by single-molecule FRET analysis.
- Sub types
- Journal Article
- Research Support, Non-U.S. Gov't
- Ausgabe der Zeitschrift
- 35
Data source: PubMed
- Beziehungen:
- Property of