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The dawn of the RNA World: Toward functional complexity through ligation of random RNA oligomers
Open accessAbstract
A main unsolved problem in the RNA World scenario for the origin of life is how a template-dependent RNA polymerase ribozyme emerged from short RNA oligomers obtained by random polymerization on mineral surfaces. A number of computational studies have shown that the structural repertoire yielded by that process is dominated by topologically simple structures, notably hairpin-like ones. A fraction of these could display RNA ligase activity and catalyze the assembly of larger, eventually functional RNA molecules retaining their previous modular structure: molecular complexity increases but template replication is absent. This allows us to build up a stepwise model of ligation-based, modular evolution that could pave the way to the emergence of a ribozyme with RNA replicase activity, step at which information-driven Darwinian evolution would be triggered.
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“These first inefficient ribozymes could then ‘jump-start’ the evolution of sequences with greater function and complexity through natural selection, especially within a spatially restricted context (44,63,68).”
From Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences (2012) · cites this paper as [44]
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2 retracted
RNA-Mediated Metal-Metal Bond Formation in the Synthesis of Hexagonal Palladium Nanoparticles
Gugliotti, L. A., Feldheim, D. L., & Eaton, B. E. (2004) · Science · doi:10.1126/science.1095678 · Cited by 197
RetractedRETRACTED: RNA-Mediated Synthesis of Palladium Nanoparticles on Au Surfaces
Liu, D., Gugliotti, L. A., Wu, T. S., Dolska, M., Ткаченко, А. Г., Shipton, M. K., Eaton, B. E., & Feldheim, D. L. (2006) · Langmuir · doi:10.1021/la060426c · Cited by 37
RetractedSelforganization of matter and the evolution of biological macromolecules
Eigen, M. (1971) · Die Naturwissenschaften · doi:10.1007/bf00623322 · Cited by 3,788
Gilbert, W. (1986) · Nature · doi:10.1038/319618a0 · Cited by 2,721
Fast folding and comparison of RNA secondary structures
Hofacker, I. L., Fontana, W., Stadler, P. F., Bonhoeffer, S., Tacker, M., & Schuster, P. M. (1994) · Monatshefte für Chemie - Chemical Monthly · doi:10.1007/bf00818163 · Cited by 2,314
SELEX—A (r)evolutionary method to generate high-affinity nucleic acid ligands
Stoltenburg, R., Reinemann, C., & Strehlitz, B. (2007) · Biomolecular Engineering · doi:10.1016/j.bioeng.2007.06.001 · Cited by 1,485
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
The antiquity of RNA-based evolution.
Joyce, G. F. (2002) · Nature · doi:10.1038/418214a · Cited by 1,070
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
Experimental 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
From sequences to shapes and back: a case study in RNA secondary structures
Schuster, P., Fontana, W., Stadler, P. F., & Hofacker, I. L. (1994) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.1994.0040 · Cited by 802
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
Template-directed synthesis of a genetic polymer in a model protocell
Mansy, S. S., Schrum, J. P., Krishnamurthy, M., Tobé, S., Treco, D. A., & Szostak, J. W. (2008) · Nature · doi:10.1038/nature07018 · Cited by 684
Self-Sustained Replication of an RNA Enzyme
Lincoln, T. A., & Joyce, G. F. (2009) · Science · doi:10.1126/science.1167856 · Cited by 670
Directed Evolution of Nucleic Acid Enzymes
Joyce, G. F. (2004) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.73.011303.073717 · Cited by 515
Plasticity, evolvability, and modularity in RNA
Ancel, L. W., & Fontana, W. (2000) · Journal of Experimental Zoology · doi:10.1002/1097-010x(20001015)288:3 · Cited by 471
Structurally Complex and Highly Active RNA Ligases Derived from Random RNA Sequences
Ekland, E. H., Szostak, J. W., & Bartel, D. P. (1995) · Science · doi:10.1126/science.7618102 · Cited by 422
RNA catalytic properties of the minimum (-)sTRSV sequence
HAMPEL, A. E., & Tritz, R. (1989) · Biochemistry · doi:10.1021/bi00438a002 · Cited by 366
Non-enzymatic cleavage and ligation of RNAs complementary to a plant virus satellite RNA
Buzayan, J. M., Gerlach, W. L., & Bruening, G. E. (1986) · Nature · doi:10.1038/323349a0 · Cited by 330
Statistics of RNA secondary structures
Fontana, W., Konings, D. A. M., Stadler, P. F., & Schuster, P. M. (1993) · Biopolymers · doi:10.1002/bip.360330909 · Cited by 293
A self-replicating ligase ribozyme
Paul, N., & Joyce, G. F. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202471099 · Cited by 264 · cited 1×
“synthesize an exact copy of itself (Paul and Joyce 2002).”
Ferris, J. P. (2006) · Philosophical Transactions of the Royal Society B: Biological Sciences · doi:10.1098/rstb.2006.1903 · Cited by 253
Hairpin RNA: a secondary structure of primary importance
Svoboda, P., & Cara, A. D. (2006) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-005-5558-5 · Cited by 241
RNA structural motifs: building blocks of a modular biomolecule
Hendrix, D. K., Brenner, S. E., & Holbrook, S. R. (2005) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583506004215 · Cited by 217
Ferris, J. P., & Ertem, G. (1993) · Journal of the American Chemical Society · doi:10.1021/ja00079a006 · Cited by 212
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
Ferris, J. P. (2002) · Origins of life and evolution of the biosphere · doi:10.1023/a:1020543312109 · Cited by 183
One-Step, Regioselective Synthesis of up to 50-mers of RNA Oligomers by Montmorillonite Catalysis
Huang, W., & Ferris, J. P. (2006) · Journal of the American Chemical Society · doi:10.1021/ja061782k · Cited by 182
Functional information and the emergence of biocomplexity
Hazen, R. M., Griffin, P. L., Carothers, J. M., & Szostak, J. W. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0701744104 · Cited by 167
Viroids: the minimal non-coding RNAs with autonomous replication
Flores, R., Delgado, S., Gas, M.-E., Carbonell, A., Molina‐Serrano, D., Gago‐Zachert, S., & de la Peña, M. (2004) · FEBS Letters · doi:10.1016/j.febslet.2004.03.118 · Cited by 113
The Structural Basis of Ribozyme-Catalyzed RNA Assembly
Robertson, M. P., & Scott, W. G. (2007) · Science · doi:10.1126/science.1136231 · Cited by 111
Synthesis of 35–40 mers of RNA oligomers from unblocked monomers. A simple approach to the RNA world
Huang, W., & Ferris, J. P. (2003) · Chem. Commun. · doi:10.1039/b303134a · Cited by 110
Ribozymes: recent advances in the development of RNA tools
Puerta‐Fernández, E., Romero‐López, C., Jesus, A. B.-D., & Berzal‐Herranz, A. (2003) · FEMS Microbiology Reviews · doi:10.1016/s0168-6445(03)00020-2 · Cited by 106
A complex ligase ribozyme evolved in vitro from a group I ribozyme domain
Jaeger, L., Wright, M. C., & Joyce, G. F. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.26.14712 · Cited by 102
In vitro RNA random pools are not structurally diverse: A computational analysis
Gevertz, J. L., Gan, H. H., & Tamar Schlick, A. (2005) · RNA · doi:10.1261/rna.7271405 · Cited by 94
Tertiary Structure Stabilization Promotes Hairpin Ribozyme Ligation
Fedor, M. J. (1999) · Biochemistry · doi:10.1021/bi991069q · Cited by 94
Ligation activity of fragmented ribozymes in frozen solution: implications for the RNA world
Vlassov, A. V. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh601 · Cited by 83
Compact and ordered collapse of randomly generated RNA sequences
Schultes, E., Spasic, A., Mohanty, U., & Bartel, D. P. (2005) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1014 · Cited by 79
Sequence- and regioselectivity in the montmorillonite-catalyzed synthesis of RNA
Miyakawa, S., & Ferris, J. P. (2003) · Journal of the American Chemical Society · doi:10.1021/ja034328e · Cited by 78
The internal equilibrium of the hairpin ribozyme: temperature, ion and pH effects
Nesbitt, S., Erlacher, H. A., & Fedor, M. J. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2543 · Cited by 75
Evolution of complexity in RNA-like replicator systems
Takeuchi, N., & Hogeweg, P. (2008) · Biology Direct · doi:10.1186/1745-6150-3-11 · Cited by 72
Recombination, RNA evolution, and bifunctional RNA molecules isolated through Chimeric SELEX
Burke, D. H., & Willis, J. H. (1998) · RNA · doi:10.1017/s1355838298980542 · Cited by 67
Horiya, S., Li, X., Kawai, G., Saito, R., Katoh, A., Kobayashi, K., & Harada, K. (2003) · Chemistry & Biology · doi:10.1016/s1074-5521(03)00146-7 · Cited by 64
Finding specific RNA motifs: function in a zeptomole world?
KNIGHT, R., & YARUS, M. (2003) · RNA · doi:10.1261/rna.2138803 · Cited by 58
Monnard, P., & Szostak, J. W. (2008) · Journal of Inorganic Biochemistry · doi:10.1016/j.jinorgbio.2008.01.026 · Cited by 55
Modular evolution and increase of functional complexity in replicating RNA molecules
Manrubia, S. C., & Briones, C. (2006) · RNA · doi:10.1261/rna.203006 · Cited by 55
Self-citationMembrane compartments in prebiotic evolution
Deamer, D. W. (1998) · Cambridge University Press eBooks · doi:10.1017/cbo9780511626180.010 · Cited by 50
Emergence of a fast-reacting ribozyme that is capable of undergoing continuous evolution
Voytek, S. B., & Joyce, G. F. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0707490104 · Cited by 50
On the structural repertoire of pools of short, random RNA sequences
Stich, M., Briones, C., & Manrubia, S. C. (2008) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2008.02.018 · Cited by 50
Self-citation2 Progress toward Understanding the Origin of the RNA WorldPreprint
Joyce, G. F., & Orgel, L. E. (2006) · Cold Spring Harbor Monograph Archive · doi:10.1101/087969739.43.23 · Cited by 48
The distribution of RNA motifs in natural sequences
Bourdeau, V., Ferbeyre, G., Pageau, M., Paquin, B., & Cedergren, R. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.22.4457 · Cited by 47
Improved polymerase ribozyme efficiency on hydrophobic assemblies
Müller, U. F., & Bartel, D. P. (2008) · RNA · doi:10.1261/rna.494508 · Cited by 46
Ligation of the hairpin ribozyme in cis induced by freezing and dehydration
Kazakov, S. A., Balatskaya, S. V., & Johnston, B. H. (2006) · RNA · doi:10.1261/rna.2123506 · Cited by 45
Selectivity of montmorillonite catalyzed prebiotic reactions of D, L-nucleotides
Joshi, P. C., Pitsch, S., & Ferris, J. P. (2007) · Origins of Life and Evolution of Biospheres · doi:10.1007/s11084-006-9013-x · Cited by 43
Cheng, C., Panavas, T., Luo, G. G., & Nagy, P. D. (2005) · Virology · doi:10.1016/j.virol.2005.06.042 · Cited by 36
Pasquali, S. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki267 · Cited by 33
Ivanov, S. A., Vauléon, S., & Müller, S. (2005) · FEBS Journal · doi:10.1111/j.1742-4658.2005.04865.x · Cited by 22
Catalysis in abiotic structured media: an approach to selective synthesis of biopolymers
Monnard, P.-A. (2005) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-004-4342-2 · Cited by 20
A modular, bifunctional RNA that integrates itself into a target RNA
Kumar, R., & Joyce, G. F. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1334190100 · Cited by 18
Ertem, G., Hazen, R. M., & Dworkin, J. P. (2007) · Astrobiology · doi:10.1089/ast.2007.0138 · Cited by 16
Gaur, S., Heckman, J. E., & Burke, J. M. (2007) · RNA · doi:10.1261/rna.716108 · Cited by 11
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Self-citationBernhardt, H. S. (2012) · Biology Direct · doi:10.1186/1745-6150-7-23 · Cited by 284
Viroids: Survivors from the RNA World?
Flores, R., Gago‐Zachert, S., Serra, P., Sanjuán, R., & Elena, S. F. (2014) · Annual Review of Microbiology · doi:10.1146/annurev-micro-091313-103416 · Cited by 168
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Metadata
- Authors
- Briones, C., Stich, M., & Manrubia, S. C.
- Affiliations
- Centro de Astrobiología (ES)
- Venue
- RNA
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2009-03-24
- Volume
- 15
- Issue
- 5
- Pages
- 743-749
- ISSN
- 1355-8382 (ISSN-L)
- 1469-9001
- PMC
- PMC2673073
- OpenAlex
- W2127447806
- Cited by
- 114
- References
- 61
- Citations by year
- 2026: 7 · 2025: 5 · 2024: 11 · 2023: 4 · 2022: 6 · 2021: 7 · 2020: 4 · 2019: 12 · 2018: 8 · 2017: 8 · 2016: 5 · 2015: 7 · 2014: 8 · 2013: 4 · 2012: 9
- FWCI
- 2.85
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- RNA (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Aston Publications Explorer (Aston University) (submittedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- Indian National Science Academy
- 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, origin of life, RNA oligomers, mineral surfaces, ribozyme evolution, RNA replicase, hairpin structure, Darwinian evolution
- MeSH terms
- Origin of Life, Nucleic Acid Conformation, RNA, Catalytic, Evolution, Molecular, Inverted Repeat Sequences
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