Improved polymerase ribozyme efficiency on hydrophobic assemblies
Open accessAbstract
During an early step in the evolution of life, RNA served both as genome and as catalyst, according to the RNA world hypothesis. For self-replication, the RNA organisms must have contained an RNA that catalyzes RNA polymerization. As a first step toward recapitulating an RNA world in the laboratory, a polymerase ribozyme was generated previously by in vitro evolution and design. However, the efficiency of this ribozyme is about 100-fold too low for self-replication because of a low affinity of the ribozyme to its primer/template substrate. To improve the substrate interactions by colocalizing ribozyme and substrate on micelles, we attached hydrophobic anchors to both RNAs. We show here that the hydrophobic anchors led to aggregates with the expected size of the corresponding micelles. The micelle formation increased the polymerization yield of full-length products by 3- to 20-fold, depending on substrates and reaction conditions. With the best-characterized substrate, the improvement in polymerization efficiency was primarily due to reduced sequence-specific stalling on partially extended substrates. We discuss how, during the origin of life, micellar ribozyme aggregates could have acted as precursors to membrane-encapsulated life forms.
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
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.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Y exceeded R18 by about fourfold at 17°C, by more than 15-fold at −7°C in ice, and by more than 30-fold in supercooled solution.
“While Y outperformed R18 by fourfold at 17°C (as judged by gel densitometry of average extension per primer15,22), at −7°C the differential rose to more than 15-fold in ice, and more than 30-fold in a supercooled solution.”
From In-ice evolution of RNA polymerase ribozyme activity (2013) · cites this paper as [22]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Dominant forces in protein folding
Dill, K. A. (1990) · Biochemistry · doi:10.1021/bi00483a001 · Cited by 3,824 · see citing works
Kalyanasundaram, K., & Thomas, J. K. (1977) · Journal of the American Chemical Society · doi:10.1021/ja00449a004 · Cited by 3,471 · see citing works
Kruger, K., Grabowski, P. J., Zaug, A. J., Sands, J., Gottschling, D. E., & Cech, T. R. (1982) · Cell · doi:10.1016/0092-8674(82)90414-7 · Cited by 2,331 · see citing works
Szostak, J. W., Bartel, D. P., & Luisi, P. L. (2001) · Nature · doi:10.1038/35053176 · Cited by 1,681 · see citing works
Self-citationMouvement brownien d'un ellipsoide - I. Dispersion diélectrique pour des molécules ellipsoidales
Perrin, F. (1934) · Journal de physique · doi:10.1051/jphysrad:01934005010049700 · Cited by 1,632 · see citing works
Asymmetric synthesis of bicyclic intermediates of natural product chemistry
Hajos, Z. G., & Parrish, D. R. (1974) · The Journal of Organic Chemistry · doi:10.1021/jo00925a003 · Cited by 1,253 · see citing works
Prebiotic chemistry and the origin of the RNA world.
Leslie E., O. (2004) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409230490460765 · Cited by 1,124 · see citing works
Tanford, C. (1972) · The Journal of Physical Chemistry · doi:10.1021/j100665a018 · Cited by 1,113 · see citing works
Isolation of New Ribozymes from a Large Pool of Random Sequences
Bartel, D. P., & Szostak, J. W. (1993) · Science · doi:10.1126/science.7690155 · Cited by 900 · see citing works
Self-citationExperimental Models of Primitive Cellular Compartments: Encapsulation, Growth, and Division
Hanczyc, M. M., Fujikawa, S. M., & Szostak, J. W. (2003) · Science · doi:10.1126/science.1089904 · Cited by 848 · see citing works
RNA-catalyzed RNA polymerization: Accurate and general RNA-templated primer extension.
Johnston, W. K., Unrau, P. J., Lawrence, M. S., Glasner, M. E., & Bartel, D. P. (2001) · Science · doi:10.1126/science.1060786 · Cited by 768 · see citing works
Self-citationOrganocatalytic Direct Asymmetric Aldol Reactions in Water
Mase, N., Nakai, Y., Ohara, N., Yoda, H., Takabe, K., Tanaka, F., & Barbas, C. F. (2005) · Journal of the American Chemical Society · doi:10.1021/ja0573312 · Cited by 653 · see citing works
An extracellular Darwinian experiment with a self-duplicating nucleic acid molecule.
Mills, D. R., Peterson, R. L., & Spiegelman, S. (1967) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.58.1.217 · Cited by 648 · see citing works
Liposomes from ionic, single-chain amphiphiles
Hargreaves, W. R., & Deamer, D. W. (1978) · Biochemistry · doi:10.1021/bi00611a014 · Cited by 576 · see citing works
Organocatalytic Direct Asymmetric Aldol Reactions in Water.
Mase, N., Nakai, Y., Ohara, N., Yoda, H., Takabe, K., Tanaka, F., & Barbas, C. F. (2006) · ChemInform · doi:10.1002/chin.200624079 · Cited by 557 · see citing works
117. Alkyl sulphates. Part I. Critical micelle concentrations of the sodium salts
Evans, H. C. (1956) · Journal of the Chemical Society (Resumed) · doi:10.1039/jr9560000579 · Cited by 398 · see citing works
Micellar solutions as reaction media
Ta§cioǧlu, S. (1996) · Tetrahedron · doi:10.1016/0040-4020(96)00669-2 · Cited by 398 · see citing works
The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone
Murray, J. B., Seyhan, A. A., Walter, N. G., Burke, J. M., & Scott, W. G. (1998) · Chemistry & Biology · doi:10.1016/s1074-5521(98)90116-8 · Cited by 374 · see citing works
A Method for the High Efficiency of Water-Soluble Carbodiimide-Mediated Amidation
Sehgal, D., & Vijay, I. K. (1994) · Analytical Biochemistry · doi:10.1006/abio.1994.1144 · Cited by 346 · see citing works
Direct organocatalytic aldol reactions in buffered aqueous media
Córdova, A., Notz, W., & Barbas, C. F. (2002) · Chemical Communications · doi:10.1039/b207664k · Cited by 308 · see citing works
Mazer, N. A., Carey, M. C., Kwasnick, R., et al. (1979) · Biochemistry · doi:10.1021/bi00581a024 · Cited by 298 · see citing works
Monnard, P.-A., Apel, C. L., Kanavarioti, A., & Deamer, D. W. (2002) · Astrobiology · doi:10.1089/15311070260192237 · Cited by 262 · see citing works
RNA Catalysis in Model Protocell Vesicles
Chen, I. A., Salehi-Ashtiani, K., & Szostak, J. W. (2005) · Journal of the American Chemical Society · doi:10.1021/ja051784p · Cited by 257 · see citing works
Selection of an improved RNA polymerase ribozyme with superior extension and fidelity
Zaher, H. S., & Unrau, P. J. (2007) · RNA · doi:10.1261/rna.548807 · Cited by 203 · see citing works
Pretsch, E., Bühlmann, P., & Badertscher, M. (2009) · Springer eBooks · doi:10.1007/978-3-540-93810-1_4 · Cited by 193 · see citing works
Sterol partitioning among intracellular membranes. Testing a model for cellular sterol distribution.
Wattenberg, B. W., & Silbert, D. F. (1983) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)32920-x · Cited by 162 · see citing works
METAL CHELATES OF ADENOSINE TRIPHOSPHATE1
Khán, M. M. T., & Martell, A. E. (1962) · The Journal of Physical Chemistry · doi:10.1021/j100807a003 · Cited by 138 · see citing works
Patist, A., Axelberd, T., & Shah, D. O. (1998) · Journal of Colloid and Interface Science · doi:10.1006/jcis.1998.5830 · Cited by 132 · see citing works
Proline catalyzed aldol reactions in aqueous micelles: an environmentally friendly reaction system
Peng, Y., Ding, Q., Li, Z., et al. (2003) · Tetrahedron Letters · doi:10.1016/s0040-4039(03)00692-0 · Cited by 130 · see citing works
The secondary structure and sequence optimization of an RNA ligase ribozyme
Ekland, E. H., & Bartel, D. P. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.16.3231 · Cited by 127 · see citing works
Self-citationNakano, S., Proctor, D. J., & Bevilacqua, P. C. (2001) · Biochemistry · doi:10.1021/bi011253n · Cited by 126 · see citing works
Factors contributing to the distribution of cholesterol among phospholipid vesicles.
Yèagle, P. L., & Young, J. E. (1986) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)83893-0 · Cited by 124 · see citing works
Emergence of a replicating species from an in vitro RNA evolution reaction.
Breaker, R. R., & Joyce, G. F. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.13.6093 · Cited by 102 · see citing works
Folding Mechanism of the Tetrahymena Ribozyme P4−P6 Domain
Deras, M. L., Brenowitz, M. D., Ralston, C. Y., et al. (2000) · Biochemistry · doi:10.1021/bi0010118 · Cited by 96 · see citing works
On the nature of dilute aqueous cholesterol suspensions
Renshaw, P. F., Janoff, A. S., & Miller, K. W. (1983) · Journal of Lipid Research · doi:10.1016/s0022-2275(20)38023-8 · Cited by 81 · see citing works
Müller, U. F. (2006) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-006-6047-1 · Cited by 79 · see citing works
Self-citationMatsuoka, K., Suzuki, M., Honda, C., et al. (2005) · Chemistry and Physics of Lipids · doi:10.1016/j.chemphyslip.2005.08.006 · Cited by 71 · see citing works
Structural Transitions in Short-Chain Lipid Assemblies Studied by 31P-NMR Spectroscopy
Kleinschmidt, J. H., & Tamm, L. K. (2002) · Biophysical Journal · doi:10.1016/s0006-3495(02)75225-9 · Cited by 69 · see citing works
New ligase-derived RNA polymerase ribozymes
LAWRENCE, M. S., & BARTEL, D. P. (2005) · RNA · doi:10.1261/rna.2110905 · Cited by 68 · see citing works
Self-citationProcessivity of Ribozyme-Catalyzed RNA Polymerization
Lawrence, M. S., & Bartel, D. P. (2003) · Biochemistry · doi:10.1021/bi034228l · Cited by 62 · see citing works
Self-citationBeugin, S., Edwards, K., Karlsson, G., et al. (1998) · Biophysical Journal · doi:10.1016/s0006-3495(98)78026-9 · Cited by 60 · see citing works
Tao, L., & Uhrich, K. E. (2006) · Journal of Colloid and Interface Science · doi:10.1016/j.jcis.2005.12.018 · Cited by 60 · see citing works
Quasielastic light scattering studies of aqueous biliary lipid systems and native bile.
Na, M. (1990) · PubMed · Cited by 57 · see citing works
Walter, A., Kuehl, G. E., Barnes, K., et al. (2000) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/s0304-4157(00)00005-8 · Cited by 56 · see citing works
Honda, C., Kamizono, H., Matsumoto, K., et al. (2004) · Journal of Colloid and Interface Science · doi:10.1016/j.jcis.2004.06.023 · Cited by 53 · see citing works
The Critical Micelle Concentration of Ether Alcohol Sulfates (ROC2H4)i-OSO3Na
Weil, J. K., Bistline, R. G., & Stirton, A. J. (1958) · The Journal of Physical Chemistry · doi:10.1021/j150567a014 · Cited by 46 · see citing works
James, K. D., & Ellington, A. D. (1999) · Origins of Life and Evolution of Biospheres · doi:10.1023/a:1006544611320 · Cited by 45 · see citing works
Cryoelectron Microscopy of a Nucleating Model Bile in Vitreous Ice: Formation of Primordial Vesicles
Gantz, D., Wang, D. Q. ‐., Carey, M. C., et al. (1999) · Biophysical Journal · doi:10.1016/s0006-3495(99)77304-2 · Cited by 40 · see citing works
Substrate 2′-Hydroxyl Groups Required for Ribozyme-Catalyzed Polymerization
Müller, U. F., & Bartel, D. P. (2003) · Chemistry & Biology · doi:10.1016/s1074-5521(03)00171-6 · Cited by 30 · see citing works
Self-citationEnhancement of RNA self‐cleavage by micellar catalysis
Riepe, A., Beier, H., & Gross, H. J. (1999) · FEBS Letters · doi:10.1016/s0014-5793(99)01038-8 · Cited by 26 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
In-ice evolution of RNA polymerase ribozyme activity
Attwater, J., Wochner, A., & Holliger, P. (2013) · Nature Chemistry · doi:10.1038/nchem.1781 · Cited by 279 · see citing works
“The G93A and C97A mutations that provide the main cold-specific activity boost are located in the single-stranded linker region of the ribozyme between the catalytic core (1-90) and the processivity domain (105-187).”
BackgroundSchrum, J. P., Zhu, T. F., & Szostak, J. W. (2010) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a002212 · Cited by 255 · see citing works
Ice as a protocellular medium for RNA replication
Attwater, J., Wochner, A., Pinheiro, V. B., Coulson, A., & Holliger, P. (2010) · Nature Communications · doi:10.1038/ncomms1076 · Cited by 165 · see citing works
The dawn of the RNA World: toward functional complexity through ligation of random RNA oligomers
Briones, C., Stich, M., & Manrubia, S. C. (2009) · RNA · doi:10.1261/rna.1488609 · Cited by 114 · see citing works
Schrum, J. P., Ricardo, A., Krishnamurthy, M., Blain, J. C., & Szostak, J. W. (2009) · Journal of the American Chemical Society · doi:10.1021/ja906557v · Cited by 103 · see citing works
Selection for replicases in protocells
Bianconi, G., Zhao, K., Chen, I. A., & Nowak, M. A. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003051 · Cited by 31 · see citing works
Characterization of the B6.61 polymerase ribozyme accessory domain
Wang, Q. S., Cheng, L. K. L., & Unrau, P. J. (2011) · RNA · doi:10.1261/rna.2495011 · Cited by 24 · see citing works
- Authors
- Müller, U. F., & Bartel, D. P.
- Affiliations
- Howard Hughes Medical Institute (US)
- Venue
- RNA
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2008-01-29
- Volume
- 14
- Issue
- 3
- Pages
- 552-562
- ISSN
- 1355-8382 (ISSN-L)
- 1469-9001
- PMC
- PMC2248263
- OpenAlex
- W2168126416
- Cited by
- 46
- References
- 50
- Citations by year
- 2025: 7 · 2024: 3 · 2022: 1 · 2021: 3 · 2019: 2 · 2018: 2 · 2017: 4 · 2015: 4 · 2013: 2 · 2012: 1
- FWCI
- 3.30
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- RNA (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- Deutsche Forschungsgemeinschaft
- National Institutes of Health
- National Institute of General Medical Sciences (GM071283, GM061835, R01GM061835, F32GM071283, R37GM061835)
- Topics
- Physical Sciences › Physics and Astronomy › Astronomy and Astrophysics › Origins and Evolution of Life
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- RNA world, RNA self-replication, hydrophobic anchor, micelles, RNA aggregation, origin of life, in vitro evolution
- MeSH terms
- Origin of Life, Base Sequence, Cholesterol, Genetic Engineering, Kinetics, Micelles, Models, Biological, Molecular Sequence Data, Nucleic Acid Conformation, Substrate Specificity, RNA, Catalytic, DNA Primers, Hydrophobic and Hydrophilic Interactions
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
