The DOI matches its Crossref record; 24 of the 24 references it cites were found in a registry or an index.
Correlating Structural Dynamics and Function in Single Ribozyme Molecules
Abstract
We have studied the correlation between structural dynamics and function of the hairpin ribozyme. The enzyme-substrate complex exists in either docked (active) or undocked (inactive) conformations. Using single-molecule fluorescence methods, we found complex structural dynamics with four docked states of distinct stabilities and a strong memory effect where each molecule rarely switches between different docked states. We also found substrate cleavage to be rate-limited by a combination of conformational transitions and reversible chemistry equilibrium. The complex structural dynamics quantitatively explain the heterogeneous cleavage kinetics common to many catalytic RNAs. The intimate coupling of structural dynamics and function is likely a general phenomenon for RNA.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
The Structural Basis of Ribosome Activity in Peptide Bond Synthesis
Nissen, P., Hansen, J., Ban, N., Moore, P. B., & Steitz, T. A. (2000) · Science · doi:10.1126/science.289.5481.920 · Cited by 2,269
Single-Molecule Enzymatic Dynamics
Lu, H. P. (1998) · Science · doi:10.1126/science.282.5395.1877 · Cited by 1,470
A Single-Molecule Study of RNA Catalysis and Folding
Zhuang, X., Bartley, L. E., Babcock, H. P., Russell, R., Ha, T., Herschlag, D., & Chu, S. (2000) · Science · doi:10.1126/science.288.5473.2048 · Cited by 732
Self-citationEnzyme Dynamics During Catalysis
Eisenmesser, E. Z., Bosco, D. A., Akke, M., & Kern, D. (2002) · Science · doi:10.1126/science.1066176 · Cited by 731
Single-molecule fluorescence spectroscopy of enzyme conformational dynamics and cleavage mechanism
Ha, T., Ting, A. Y., Liang, J., Caldwell, W. B., Deniz, A. A., Chemla, D. S., Schultz, P. G., & Weiss, S. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.3.893 · Cited by 520
Noller, H. F. (1991) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.60.070191.001203 · Cited by 500
Crystal structure of a hairpin ribozyme–inhibitor complex with implications for catalysis
Rupert, P. B., & Ferré-D'Amaré, A. R. (2001) · Nature · doi:10.1038/35071009 · Cited by 447
Ligand-induced conformational changes observed in single RNA molecules
Ha, T., Zhuang, X., Kim, H. D., Orr, J. W., Williamson, J. R., & Chu, S. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.16.9077 · Cited by 261
Self-citationStructure and function of the hairpin ribozyme
Fedor, M. J. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3560 · Cited by 244
Splicing-related catalysis by protein-free snRNAs
Valadkhan, S., & Manley, J. L. (2001) · Nature · doi:10.1038/35099500 · Cited by 221
Cited by
Functional Aptamers and Aptazymes in Biotechnology, Diagnostics, and Therapy
Famulok, M., Hartig, J. S., & Mayer, G. (2007) · Chemical Reviews · doi:10.1021/cr0306743 · Cited by 887
Analysis of Single-Molecule FRET Trajectories Using Hidden Markov Modeling
McKinney, S. A., Joo, C., & Ha, T. (2006) · Biophysical Journal · doi:10.1529/biophysj.106.082487 · Cited by 760
Probing Protein Folding and Conformational Transitions with Fluorescence
Royer, C. A. (2006) · Chemical Reviews · doi:10.1021/cr0404390 · Cited by 731
Kapanidis, A. N., Lee, N. K., Laurence, T. A., Doose, S., Margeat, E., & Weiss, S. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0401690101 · Cited by 630
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview
Šponer, J., Bussi, G., Krepl, M., Banáš, P., Bottaro, S., Cunha, R. A., Gil-Ley, A., Pinamonti, G., Poblete, S., Jurečka, P., et al. (2018) · Chemical Reviews · doi:10.1021/acs.chemrev.7b00427 · Cited by 599
Self-citationHigh-Resolution, Single-Molecule Measurements of Biomolecular Motion
Greenleaf, W. J., Woodside, M. T., & Block, S. M. (2007) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.36.101106.101451 · Cited by 462
Carbocyanine Dyes as Efficient Reversible Single-Molecule Optical Switch
Heilemann, M., Margeat, E., Kasper, R., Sauer, M., & Tinnefeld, P. (2005) · Journal of the American Chemical Society · doi:10.1021/ja044686x · Cited by 406
Single-Molecule Measurement of Protein Folding Kinetics
Lipman, E. A., Schuler, B., Bakajin, O., & Eaton, W. A. (2003) · Science · doi:10.1126/science.1085399 · Cited by 401
Short-Range Spectroscopic Ruler Based on a Single-Molecule Optical Switch
Bates, M., Blosser, T. R., & Zhuang, X. (2005) · Physical Review Letters · doi:10.1103/physrevlett.94.108101 · Cited by 364
Self-citationSingle-molecule biophysics: at the interface of biology, physics and chemistry
Deniz, A. A., Mukhopadhyay, S., & Lemke, E. A. (2008) · Journal of The Royal Society Interface · doi:10.1098/rsif.2007.1021 · Cited by 306
Margittai, M., Widengren, J., Schweinberger, E., Schröder, G. F., Felekyan, S., Haustein, E., König, M., Fasshauer, D., Grubmüller, H., Jahn, R., et al. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2331232100 · Cited by 290
Freeze-thaw cycles as drivers of complex ribozyme assembly
Mutschler, H., Wochner, A., & Holliger, P. (2015) · Nature Chemistry · doi:10.1038/nchem.2251 · Cited by 154
Mn2+-Sensing Mechanisms of yybP-ykoY Orphan Riboswitches
Price, I. R., Gaballa, A., Ding, F., Helmann, J. D., & Ke, A. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.02.016 · Cited by 136
RNA self-processing: formation of cyclic species and concatemers from a small engineered RNA
Petkovic, S., & Müller, S. (2013) · FEBS Letters · doi:10.1016/j.febslet.2013.06.013 · Cited by 41
Can DyeCycling break the photobleaching limit in single-molecule FRET?
Vermeer, B., & Schmid, S. (2022) · Nano Research · doi:10.1007/s12274-022-4420-5 · Cited by 25
Metadata
- Authors
- Zhuang, X., Kim, H., Pereira, M. J. B., Babcock, H. P., Walter, N. G., & Chu, S.
- Venue
- Science
- Published
- 2002-05-24
- Volume
- 296
- Issue
- 5572
- Pages
- 1473-1476
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2102032812
- Cited by
- 512
- References
- 24
- FWCI
- 13.18
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
