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.
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?
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.
“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]
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
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 · see citing works
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 · see citing works
RetractedSelforganization of matter and the evolution of biological macromolecules
Eigen, M. (1971) · Die Naturwissenschaften · doi:10.1007/bf00623322 · Cited by 3,788 · see citing works
Gilbert, W. (1986) · Nature · doi:10.1038/319618a0 · Cited by 2,721 · see citing works
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 · see citing works
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 1,432 · 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
The antiquity of RNA-based evolution.
Joyce, G. F. (2002) · Nature · doi:10.1038/418214a · Cited by 1,070 · 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
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 · see citing works
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 · 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
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 · see citing works
Self-Sustained Replication of an RNA Enzyme
Lincoln, T. A., & Joyce, G. F. (2009) · Science · doi:10.1126/science.1167856 · Cited by 670 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
RNA catalytic properties of the minimum (-)sTRSV sequence
HAMPEL, A. E., & Tritz, R. (1989) · Biochemistry · doi:10.1021/bi00438a002 · Cited by 366 · see citing works
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 336 · see citing works
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 · see citing works
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× · see citing works
“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 · see citing works
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 · see citing works
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 · see citing works
Ferris, J. P., & Ertem, G. (1993) · Journal of the American Chemical Society · doi:10.1021/ja00079a006 · Cited by 208 · 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
Ferris, J. P. (2002) · Origins of life and evolution of the biosphere · doi:10.1023/a:1020543312109 · Cited by 183 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
The Structural Basis of Ribozyme-Catalyzed RNA Assembly
Robertson, M. P., & Scott, W. G. (2007) · Science · doi:10.1126/science.1136231 · Cited by 111 · see citing works
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 · see citing works
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 105 · see citing works
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 · see citing works
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 · see citing works
Tertiary Structure Stabilization Promotes Hairpin Ribozyme Ligation
Fedor, M. J. (1999) · Biochemistry · doi:10.1021/bi991069q · Cited by 94 · see citing works
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 82 · see citing works
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 · see citing works
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 77 · see citing works
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 · see citing works
Evolution of complexity in RNA-like replicator systems
Takeuchi, N., & Hogeweg, P. (2008) · Biology Direct · doi:10.1186/1745-6150-3-11 · Cited by 68 · see citing works
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 · see citing works
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 · see citing works
Finding specific RNA motifs: function in a zeptomole world?
KNIGHT, R., & YARUS, M. (2003) · RNA · doi:10.1261/rna.2138803 · Cited by 58 · see citing works
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 54 · see citing works
Self-citationMonnard, P., & Szostak, J. W. (2008) · Journal of Inorganic Biochemistry · doi:10.1016/j.jinorgbio.2008.01.026 · Cited by 52 · see citing works
Membrane compartments in prebiotic evolution
Deamer, D. W. (1998) · Cambridge University Press eBooks · doi:10.1017/cbo9780511626180.010 · Cited by 50 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
Improved polymerase ribozyme efficiency on hydrophobic assemblies
Müller, U. F., & Bartel, D. P. (2008) · RNA · doi:10.1261/rna.494508 · Cited by 46 · see citing works
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 · see citing works
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 · see citing works
Cheng, C., Panavas, T., Luo, G. G., & Nagy, P. D. (2005) · Virology · doi:10.1016/j.virol.2005.06.042 · Cited by 36 · see citing works
Pasquali, S. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki267 · Cited by 32 · see citing works
Ivanov, S. A., Vauléon, S., & Müller, S. (2005) · FEBS Journal · doi:10.1111/j.1742-4658.2005.04865.x · Cited by 22 · see citing works
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 · see citing works
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 · see citing works
Ertem, G., Hazen, R. M., & Dworkin, J. P. (2007) · Astrobiology · doi:10.1089/ast.2007.0138 · Cited by 16 · see citing works
Gaur, S., Heckman, J. E., & Burke, J. M. (2007) · RNA · doi:10.1261/rna.716108 · Cited by 11 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Prebiotic Systems Chemistry: New Perspectives for the Origins of Life
Ruiz-Mirazo, K., Briones, C., & de la Escosura, A. (2014) · Chemical Reviews · doi:10.1021/cr2004844 · Cited by 930 · see citing works
Self-citationBernhardt, H. S. (2012) · Biology Direct · doi:10.1186/1745-6150-7-23 · Cited by 273 · see citing works
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 164 · see citing works
When Did Life Likely Emerge on Earth in an RNA‐First Process?
Benner, S. A., Bell, E. A., Biondi, E., Brasser, R., Carell, T., Kim, H., Mojzsis, S. J., Omran, A., Pasek, M. A., & Trail, D. (2020) · ChemSystemsChem · doi:10.1002/syst.201900035 · Cited by 162 · see citing works
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 · see citing works
Comprehensive experimental fitness landscape and evolutionary network for small RNA
Jiménez, J. I., Xulvi-Brunet, R., Campbell, G. W., Turk-MacLeod, R., & Chen, I. A. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1307604110 · Cited by 140 · see citing works
Ruiz‐Mirazo, K., Briones, C., & de la Escosura, A. (2017) · Open Biology · doi:10.1098/rsob.170050 · Cited by 104 · see citing works
Self-citationManrubia, S., Cuesta, J. A., Aguirre, J., Ahnert, S. E., Altenberg, L., Cano, A. V., Catalán, P., Diaz-Uriarte, R., Elena, S. F., García-Martín, J. A., et al. (2021) · Physics of Life Reviews · doi:10.1016/j.plrev.2021.03.004 · Cited by 88 · see citing works
Self-citationCamprubí, E., de Leeuw, J. W., House, C. H., Raulin, F., Russell, M. J., Spang, A., Tirumalai, M. R., & Westall, F. (2019) · Space Science Reviews · doi:10.1007/s11214-019-0624-8 · Cited by 84 · see citing works
Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences
Derr, J., Manapat, M. L., Rajamani, S., Leu, K., Xulvi-Brunet, R., Joseph, I., Nowak, M. A., & Chen, I. A. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks065 · Cited by 74 · see citing works
The dynamics of the RNA world: insights and challenges
Kun, Á., Szilágyi, A., Könnyű, B., Boza, G., Zachar, I., & Szathmáry, E. (2015) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.12700 · Cited by 65 · see citing works
Nucleic acids: function and potential for abiogenesis
Wachowius, F., Attwater, J., & Holliger, P. (2017) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583517000038 · Cited by 62 · see citing works
Enhanced Ribozyme‐Catalyzed Recombination and Oligonucleotide Assembly in Peptide‐RNA Condensates
Vay, K. K. L., Song, E. Y., Ghosh, B., Tang, T. ‐. D., & Mutschler, H. (2021) · Angewandte Chemie International Edition · doi:10.1002/anie.202109267 · Cited by 58 · see citing works
Origin of self-replicating biopolymers: autocatalytic feedback can jump-start the RNA world
Wu, M., & Higgs, P. G. (2009) · Journal of Molecular Evolution · doi:10.1007/s00239-009-9276-8 · Cited by 52 · see citing works
From Prelife to Life: How Chemical Kinetics Become Evolutionary Dynamics
Chen, I. A., & Nowak, M. A. (2012) · Accounts of Chemical Research · doi:10.1021/ar2002683 · Cited by 50 · see citing works
Random-sequence genetic oligomer pools display an innate potential for ligation and recombination
Mutschler, H., Taylor, A. I., Porebski, B. T., Lightowlers, A., Houlihan, G., Abramov, M., Herdewijn, P. A., & Holliger, P. (2018) · eLife · doi:10.7554/elife.43022 · Cited by 50 · see citing works
Rethinking quasispecies theory: from fittest type to cooperative consortia
Villarreal, L. P., & Witzany, G. (2013) · World Journal of Biological Chemistry · doi:10.4331/wjbc.v4.i4.79 · Cited by 49 · see citing works
Pragmatic turn in biology: From biological molecules to genetic content operators
Witzany, G. (2014) · World Journal of Biological Chemistry · doi:10.4331/wjbc.v5.i3.279 · Cited by 47 · see citing works
That is life: communicating RNA networks from viruses and cells in continuous interaction
Villarreal, L. P., & Witzany, G. (2019) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.14040 · Cited by 47 · see citing works
Non‐Enzymatic Assembly of a Minimized RNA Polymerase Ribozyme
Wachowius, F., & Holliger, P. (2019) · ChemSystemsChem · doi:10.1002/syst.201900004 · Cited by 46 · see citing works
The systems perspective at the crossroads between chemistry and biology
de la Escosura, A., Briones, C., & Ruiz‐Mirazo, K. (2015) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2015.04.036 · Cited by 45 · see citing works
Self-citationEmergence of information transmission in a prebiotic RNA reactor.
Obermayer, B., Krammer, H., Braun, D., & Gerland, U. (2011) · Physical Review Letters · doi:10.1103/physrevlett.107.018101 · Cited by 44 · see citing works
Viroids and the Origin of Life
Moelling, K., & Broecker, F. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22073476 · Cited by 39 · see citing works
Aguirre, J., Buldú, J. M., & Manrubia, S. C. (2009) · Physical Review E · doi:10.1103/physreve.80.066112 · Cited by 39 · see citing works
Self-citationApplications of high dimensionality experiments to biomolecular NMR
Nowakowski, M. E., Saxena, S., Stanek, J., Żerko, S., & Koźmiński, W. (2015) · Progress in Nuclear Magnetic Resonance Spectroscopy · doi:10.1016/j.pnmrs.2015.07.001 · Cited by 38 · see citing works
Thresholds in Origin of Life Scenarios
Jeancolas, C., Malaterre, C., & Nghe, P. (2020) · iScience · doi:10.1016/j.isci.2020.101756 · Cited by 36 · see citing works
When Competing Viruses Unify: Evolution, Conservation, and Plasticity of Genetic Identities
Villarreal, L. P., & Witzany, G. (2015) · Journal of Molecular Evolution · doi:10.1007/s00239-015-9683-y · Cited by 36 · see citing works
Mineral surfaces select for longer RNA molecules
Mizuuchi, R., Blokhuis, A. W. P., Vincent, L., Nghe, P., Lehman, N., & Baum, D. (2019) · Chemical Communications · doi:10.1039/c8cc10319d · Cited by 35 · see citing works
Force for ancient and recent life: viral and stem‐loop RNA consortia promote life
Villarreal, L. P. (2014) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.12565 · Cited by 35 · see citing works
Witzany, G. (2020) · Frontiers in Astronomy and Space Sciences · doi:10.3389/fspas.2020.00007 · Cited by 31 · see citing works
Mutschler, H., & Holliger, P. (2014) · Journal of the American Chemical Society · doi:10.1021/ja4127714 · Cited by 30 · see citing works
Emergence of life in an inflationary universe
Totani, T. (2020) · Scientific Reports · doi:10.1038/s41598-020-58060-0 · Cited by 29 · see citing works
“It is theoretically speculated that terminal ligation of oligomers may hierarchically produce further longer polymers [22], but there is no experimental or quantitative demonstration of this starting from realistic prebiotic conditions.”
BackgroundFlores, R., Navarro, B., Serra, P., & Serio, F. D. (2022) · Virus Evolution · doi:10.1093/ve/veab107 · Cited by 29 · see citing works
In vitro evolution of distinct self-cleaving ribozymes in diverse environments
Popović, M., Fliss, P. S., & Ditzler, M. A. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv648 · Cited by 28 · see citing works
Abiogenesis through gradual evolution of autocatalysis into template‐based replication
Pavlinova, P., Lambert, C. N., Malaterre, C., & Nghe, P. (2022) · FEBS Letters · doi:10.1002/1873-3468.14507 · Cited by 26 · see citing works
Spontaneous advent of genetic diversity in RNA populations through multiple recombination mechanisms
Smail, B. A., Clifton, B. E., Mizuuchi, R., & Lehman, N. (2019) · RNA · doi:10.1261/rna.068908.118 · Cited by 26 · see citing works
Simulating a Model of Metabolic Closure
Cornish-Bowden, A. J., Piedrafita, G., Morán, F., Cárdenas, M. L., & Montero, F. (2013) · Biological Theory · doi:10.1007/s13752-013-0132-0 · Cited by 24 · see citing works
Social Networking of Quasi-Species Consortia drive Virolution via Persistence
Villarreal, L. P., Witzany, G., & Telos-Philosophische Praxis, B. (2021) · AIMS Microbiology · doi:10.3934/microbiol.2021010 · Cited by 22 · see citing works
Göppel, T., Rosenberger, J. H., Altaner, B., & Gerland, U. (2022) · Life · doi:10.3390/life12040567 · Cited by 21 · see citing works
Life and living beings under the perspective of organic macrocodes
Prosdocimi, F., & de Farías, S. T. (2021) · Biosystems · doi:10.1016/j.biosystems.2021.104445 · Cited by 21 · see citing works
Witzany, G. (2017) · Communicative & Integrative Biology · doi:10.1080/19420889.2017.1297352 · Cited by 20 · see citing works
Mechanically Induced Homochirality in Nucleated Enantioselective Polymerization
Blanco, C., Stich, M., & Hochberg, D. (2017) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.6b10705 · Cited by 20 · see citing works
Self-citationMotif frequency and evolutionary search times in RNA populations
Stich, M., & Manrubia, S. C. (2011) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2011.03.010 · Cited by 17 · see citing works
Self-citationEarly evolution of efficient enzymes and genome organization
Szilágyi, A., Kun, Á., & Szathmáry, E. (2012) · Biology Direct · doi:10.1186/1745-6150-7-38 · Cited by 17 · see citing works
Molina, A. G., Barvı́k, I., Müller, S., Vasseur, J., & Smietana, M. (2018) · Organic & Biomolecular Chemistry · doi:10.1039/c8ob02182a · Cited by 17 · see citing works
Evolution of ribozymes in the presence of a mineral surface
Stephenson, J. D., Popović, M., Bristow, T. F., & Ditzler, M. A. (2016) · RNA · doi:10.1261/rna.057703.116 · Cited by 17 · see citing works
Parsimonious Scenario for the Emergence of Viroid-Like Replicons De Novo
Catalán, P., Elena, S. F., Cuesta, J. A., & Manrubia, S. C. (2019) · Viruses · doi:10.3390/v11050425 · Cited by 17 · see citing works
Self-citationSex in a test tube: testing the benefits of in vitro recombination
Pesce, D., Lehman, N., & de Visser, J. A. G. M. (2016) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2015.0529 · Cited by 15 · see citing works
Ariza‐Mateos, A., Briones, C., Perales, C., Domingo, E., & Gómez, J. (2019) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.14173 · Cited by 15 · see citing works
Self-citationMacDermott, A. J. (2012) · Elsevier eBooks · doi:10.1016/b978-0-08-095167-6.00804-1 · Cited by 15 · see citing works
RNA Sociology: Group Behavioral Motifs of RNA Consortia
Witzany, G. (2014) · Life · doi:10.3390/life4040800 · Cited by 14 · see citing works
Isoxazole Nucleosides as Building Blocks for a Plausible Proto‐RNA
Xu, F., Crisp, A. L., Schinkel, T., Dubini, R. C. A., Hübner, S., Becker, S. M., Schelter, F., Rovó, P., & Carell, T. (2022) · Angewandte Chemie International Edition · doi:10.1002/anie.202211945 · Cited by 13 · see citing works
Complexity through Recombination: From Chemistry to Biology
Lehman, N., Arenas, C. D., White, W. A., & Schmidt, F. J. (2010) · Entropy · doi:10.3390/e13010017 · Cited by 13 · see citing works
The elusive quest for RNA knots
Burton, A. S., Stefano, M. D., Lehman, N., Orland, H., & Micheletti, C. (2016) · RNA Biology · doi:10.1080/15476286.2015.1132069 · Cited by 13 · see citing works
Enumerating secondary structures and structural moieties for circular RNAs
Cuesta, J. A., & Manrubia, S. C. (2017) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2017.02.024 · Cited by 13 · see citing works
Self-citationThe simple emergence of complex molecular function
Manrubia, S. (2022) · Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences · doi:10.1098/rsta.2020.0422 · Cited by 13 · see citing works
Self-citationExploring the space of self-reproducing ribozymes using generative models
Lambert, C. N., Opuu, V., Calvanese, F., Pavlinova, P., Zamponi, F., Hayden, E. J., Weigt, M., Smerlak, M., & Nghe, P. (2025) · Nature Communications · doi:10.1038/s41467-025-63151-5 · Cited by 12 · see citing works
Ball, R. V., & Brindley, J. (2017) · Royal Society Open Science · doi:10.1098/rsos.170141 · Cited by 12 · see citing works
Self-empowerment of life through RNA networks, cells and viruses
Villarreal, L. P., & Witzany, G. (2023) · F1000Research · doi:10.12688/f1000research.130300.1 · Cited by 11 · see citing works
Non-enzymatic recombination of RNA: Ligation in loops
Staroseletz, Y., Nechaev, S., Bichenkova, E. V., Bryce, R. A., Watson, C., Vlassov, V. V., & Аркадьевна, З. М. (2017) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2017.10.019 · Cited by 11 · see citing works
Communication as the Main Characteristic of Life
Witzany, G. (2018) · CRC Press eBooks · doi:10.1201/b22230-9 · Cited by 11 · see citing works
Key Levels of Biocommunication
Witzany, G. (2016) · WORLD SCIENTIFIC (EUROPE) eBooks · doi:10.1142/9781786340450_0002 · Cited by 10 · see citing works
Editorial: Genome Invading RNA Networks
Villarreal, L. P., & Witzany, G. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00581 · Cited by 10 · see citing works
Three Biopolymers and Origin of Life Scenarios
Agmon, I. (2024) · Life · doi:10.3390/life14020277 · Cited by 9 · see citing works
A stepwise emergence of evolution in the RNA world
Nghe, P. (2025) · FEBS Letters · doi:10.1002/1873-3468.70065 · Cited by 7 · see citing works
Saxena, S., Stanek, J., Cevec, M., Plavec, J., & Koźmiński, W. (2014) · Journal of Biomolecular NMR · doi:10.1007/s10858-014-9861-z · Cited by 7 · see citing works
Evolution of Genetic Information without Error Replication
Witzany, G. (2020) · WORLD SCIENTIFIC eBooks · doi:10.1142/9789813277496_0014 · Cited by 7 · see citing works
Enhanced Ribozyme‐Catalyzed Recombination and Oligonucleotide Assembly in Peptide‐RNA Condensates
Vay, K. K. L., Song, E. Y., Ghosh, B., Tang, T. ‐. D., & Mutschler, H. (2021) · Angewandte Chemie · doi:10.1002/ange.202109267 · Cited by 7 · see citing works
Escalation of error catastrophe for enzymatic self-replicators
Obermayer, B., & Frey, E. (2009) · Europhysics Letters (EPL) · doi:10.1209/0295-5075/88/48006 · Cited by 7 · see citing works
Physical Basis for the Emergence of Autopoiesis, Cognition and Knowledge
Hall, W. P. (2011) · PhilPapers (PhilPapers Foundation) · Cited by 7 · see citing works
On the nature and origin of biological information: The curious case of RNA
Grabow, W. W., & Andrews, G. E. (2019) · Biosystems · doi:10.1016/j.biosystems.2019.104031 · Cited by 7 · see citing works
Genome Evolution from Random Ligation of RNAs of Autocatalytic Sets
Broecker, F. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222413526 · Cited by 6 · see citing works
Archaeological approaches to RNA virus evolution
Ariza‐Mateos, A., Briones, C., Perales, C., Sobrino, F., Domingo, E., & Gómez, J. (2023) · The Journal of Physiology · doi:10.1113/jp284416 · Cited by 6 · see citing works
Self-citationAgmon, I. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19124021 · Cited by 6 · see citing works
Computer Simulations of Prebiotic Systems
Fornaro, T., & Carnimeo, I. (2014) · Elsevier eBooks · doi:10.1016/b978-0-12-409547-2.11025-x · Cited by 5 · see citing works
On the emergence of structural complexity in RNA replicators
Oliver, C., Reinharz, V., & Waldispühl, J. (2019) · RNA · doi:10.1261/rna.070391.119 · Cited by 5 · see citing works
Domingo, E., & Witzany, G. (2024) · Die Naturwissenschaften · doi:10.1007/s00114-024-01897-6 · Cited by 4 · see citing works
Compositional memory matters for early molecular systems
Ledoux, B., Kuwabara, R., Ichihashi, N., Mizuuchi, R., & Lacoste, D. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2537522123 · Cited by 4 · see citing works
Selective Nonenzymatic Formation of Biologically Common RNA Hairpins
Wu, L.-F., Zhang, J., Cornwell-Arquitt, R., Hendrix, D. A., Radakovic, A., & Szostak, J. W. (2024) · Angewandte Chemie International Edition · doi:10.1002/anie.202417370 · Cited by 4 · see citing works
Evolution from Composome to RNA Replicase
Deng, S., Lancet, D., & Yaniv, R. (2026) · Life · doi:10.3390/life16020219 · Cited by 3 · see citing works
Paczkó, M., Szathmáry, E., & Szilágyi, A. (2024) · eLife · doi:10.7554/elife.93208 · Cited by 3 · see citing works
Did organs precede organisms in the origin of life?
Baquero, F., Bever, G. S., de Lorenzo, V., Lanza, V. F., & Briones, C. (2024) · microLife · doi:10.1093/femsml/uqae025 · Cited by 3 · see citing works
Self-citationPolymerization and replication of primordial RNA induced by clay-water interface dynamics
Alejandre, C., Aguirre‐Tamaral, A., Briones, C., & Aguirre, J. (2025) · Communications Chemistry · doi:10.1038/s42004-025-01632-w · Cited by 3 · see citing works
Self-citationAre We the First: Was There Life Before Our Solar System?
Laine, P., & Jheeta, S. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-811940-2.00014-9 · Cited by 3 · see citing works
Exploration of RNA Sequence Space in the Absence of a Replicase
Tirumalai, M. R., Tran, Q., Paci, M., Chavan, D., Marathe, A., & Fox, G. E. (2018) · Journal of Molecular Evolution · doi:10.1007/s00239-018-9846-8 · Cited by 3 · see citing works
On the origin of biological teleonomy
Deng, S. (2025) · Biosystems · doi:10.1016/j.biosystems.2025.105662 · Cited by 2 · see citing works
Selective Nonenzymatic Formation of Biologically Common RNA Hairpins
Wu, L.-F., Zhang, J., Cornwell-Arquitt, R., Hendrix, D. A., Radakovic, A., & Szostak, J. W. (2024) · Angewandte Chemie · doi:10.1002/ange.202417370 · Cited by 2 · see citing works
Dhar, N., Weinberg, M. S., Michod, R. E., & Durand, P. M. (2017) · Royal Society Open Science · doi:10.1098/rsos.170376 · Cited by 2 · see citing works
Neutral networks and chemical function in RNA
Manrubia, S. C. (2012) · Physics of Life Reviews · doi:10.1016/j.plrev.2012.06.003 · Cited by 2 · see citing works
Self-citationTakeuchi, N., & Hogeweg, P. (2012) · Physics of Life Reviews · doi:10.1016/j.plrev.2012.07.009 · Cited by 2 · see citing works
MacDermott, A. J. (2012) · Elsevier eBooks · doi:10.1016/b978-0-32-390644-9.00307-3 · Cited by 1 · see citing works
Saxena, S., Stanek, J., Cevec, M., Plavec, J., & Koźmiński, W. (2015) · Journal of Biomolecular NMR · doi:10.1007/s10858-015-9989-5 · Cited by 1 · see citing works
When transfer‐messenger RNA scars reveal its ancient origins
Guyomar, C., & Gillet, R. (2019) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.14035 · Cited by 1 · see citing works
von Meijenfeldt, F. A. B. (2014) · Cited by 1 · see citing works
Coding triplets in the tRNA acceptor-TΨC arm and their role in present and past tRNA recognitionPreprint
Agmon, I., Fayerverker, I., & Mor, T. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/559948 · Cited by 1 · see citing works
On the possible origin and evolution of genetic codingPreprint
Daniel, J. (2019) · arXiv (Cornell University) · doi:10.48550/arxiv.1910.13622 · Cited by 1 · see citing works
Populations of RNA Molecules as Computational Model for Evolution
Stich, M., Briones, C., Lázaro, E., & Manrubia, S. C. (2010) · Springer eBooks · doi:10.1007/978-3-642-12340-5_4
Self-citationDynamics of pore synthesis and degradation in protocells
Kubitschke, H., & Fütterer, C. (2012) · New Journal of Physics · doi:10.1088/1367-2630/14/10/103008
Modeling of Evolving RNA Replicators
Aguirre, J., & Stich, M. (2016) · SEMA SIMAI Springer series · doi:10.1007/978-3-319-33054-9_1
Self-citation
- 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
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