The RNA world as a model system to study the origin of life

Current Biology

Volumn 25, Issue 19, 2015, Pages R953-R963

  Pressman, Abe ^a   Blanco, Celia ^a   Chen, Irene A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

BIOGENESIS; BIOLOGICAL MODEL; CHEMISTRY; GENETICS; MOLECULAR EVOLUTION;

EVOLUTION, MOLECULAR; MODELS, BIOLOGICAL; MODELS, GENETIC; ORIGIN OF LIFE; RNA;

EID: 84943398217     PISSN: 09609822     EISSN: 18790445     Source Type: Journal    
DOI: 10.1016/j.cub.2015.06.016     Document Type: Review

References (204)

1. J.W. Szostak, D.P. Bartel, and P.L. Luisi Synthesizing life Nature 409 2001 387 390
2. W. Gilbert Origin of Life - the Rna World Nature 319 1986 618-618
3. F.H. Crick The origin of the genetic code J. Mol. Biol. 38 1968 367 379
4. L.E. Orgel Evolution of the genetic apparatus J. Mol. Biol. 38 1968 381 393
5. C.R. Woese, D.H. Dugre, S.A. Dugre, M. Kondo, and W.C. Saxinger On the fundamental nature and evolution of the genetic code Cold Spring Harb. Symp. Quant. Biol. 31 1966 723 736
6. T.R. Cech The ribosome is a ribozyme Science 289 2000 878 879
7. L.E. Orgel Prebiotic chemistry and the origin of the RNA world Crit. Rev. Biochem. Mol. Biol. 39 2004 99 123
8. A. Butlerow Bildung einer zuckerartigen Substanz durch Synthese Justus Liebigs Annalen der Chemie 120 1861 295 298
9. S.L. Miller A production of amino acids under possible primitive earth conditions Science 117 1953 528 529
10. J. Oro, and A.P. Kimball Synthesis of purines under possible primitive earth conditions. I. Adenine from hydrogen cyanide Arch. Biochem. Biophys. 94 1961 217 227
11. J. Oro, and A.P. Kimball Synthesis of purines under possible primitive earth conditions. II. Purine intermediates from hydrogen cyanide Arch. Biochem. Biophys. 96 1962 293 313
12. S. Yuasa, D. Flory, B. Basile, and J. Oro Abiotic synthesis of purines and other heterocyclic compounds by the action of electrical discharges J. Mol. Evol. 21 1984 76 80
13. A.L. Weber, and S.L. Miller Reasons for the occurrence of the 20 coded protein amino-acids J. Mol. Evol. 17 1981 273 284
14. E.T. Parker, H.J. Cleaves, J.P. Dworkin, D.P. Glavin, M. Callahan, A. Aubrey, A. Lazcano, and J.L. Bada Primordial synthesis of amines and amino acids in a 1958 Miller H2S-rich spark discharge experiment Proc. Natl. Acad. Sci. USA 108 2011 5526 5531
15. K.I. Oberg, V.V. Guzman, K. Furuya, C. Qi, Y. Aikawa, S.M. Andrews, R. Loomis, and D.J. Wilner The comet-like composition of a protoplanetary disk as revealed by complex cyanides Nature 520 2015 198 201
16. M.W. Powner, B. Gerland, and J.D. Sutherland Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions Nature 459 2009 239 242
17. B.H. Patel, C. Percivalle, D.J. Ritson, D. DuffyColm, and J.D. Sutherland Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism Nat Chem. 2015 10.1038/nchem.2202 advance online publication
18. C. Menor-Salvan, D.M. Ruiz-Bermejo, M.I. Guzman, S. Osuna-Esteban, and S. Veintemillas-Verdaguer Synthesis of pyrimidines and triazines in ice: implications for the prebiotic chemistry of nucleobases Chemistry 15 2009 4411 4418
19. C. Menor-Salvan, M. Ruiz-Bermejo, S. Osuna-Esteban, and S. Veintemillas-Verdaguer Efficient synthesis of pyrimidines and triazines from urea and methane in ice matrix Origins Life and Evol. Biospheres 39 2009 250 251
20. F.R. Bowler, C.K.W. Chan, C.D. Duffy, B. Gerland, S. Islam, M.W. Powner, J.D. Sutherland, and J.F. Xu Prebiotically plausible oligoribonucleotide ligation facilitated by chemoselective acetylation Nat. Chem. 5 2013 383 389
21. A.E. Engelhart, M.W. Powner, and J.W. Szostak Functional RNAs exhibit tolerance for non-heritable 2'-5' versus 3'-5' backbone heterogeneity Nat. Chem. 5 2013 390 394
22. N.V. Hud, B.J. Cafferty, R. Krishnamurthy, and L.D. Williams The origin of RNA and "My Grandfather's Axe" Chem. Biol. 20 2013 466 474
23. M. Levy, and S.L. Miller The stability of the RNA bases: implications for the origin of life Proc. Natl. Acad. Sci. USA 95 1998 7933 7938
24. R. Larralde, and S.L. Miller The kinetics of decomposition of ribose Abstracts Papers Am. Chem. Soc. 207 1994 42-Geoc
25. R. Larralde, M.P. Robertson, and S.L. Miller Rates of decomposition of ribose and other sugars - implications for chemical evolution Proc. Natl. Acad. Sci. USA 92 1995 8158 8160
26. R. Krishnamurthy RNA as an emergent entity: an understanding gained through studying its nonfunctional alternatives Synlett. 25 2014 1511 1517
27. G.F. Joyce The antiquity of RNA-based evolution Nature 418 2002 214 221
28. L.E. Orgel Did template-directed nucleation precede molecular replication Origins Life and Evol. Biosphere 17 1986 27 34
29. A. Eschenmoser Chemical etiology of nucleic acid structure Science 284 1999 2118 2124
30. K. Schoning, P. Scholz, S. Guntha, X. Wu, R. Krishnamurthy, and A. Eschenmoser Chemical etiology of nucleic acid structure: the alpha-threofuranosyl-(3' - >2') oligonucleotide system Science 290 2000 1347 1351
31. G.K. Mittapalli, K.R. Reddy, H. Xiong, O. Munoz, B. Han, F. De Riccardis, R. Krishnamurthy, and A. Eschenmoser Mapping the landscape of potentially primordial informational oligomers: Oligodipeptides and oligodipeptoids tagged with triazines as recognition elements Angewandte Chemie-International Edition 46 2007 2470 2477
32. R. Hayatsu, M.H. Studier, L.P. Moore, and E. Anders Purines and triazines in Murchison meteorite Geochimica Et Cosmochimica Acta 39 1975 471 488
33. A.M. Leconte, and F.E. Romesberg Amplify this! DNA and RNA get a third base pair Nat. Methods 3 2006 667 668
34. S. Matsuda, A.M. Leconte, and F.E. Romesberg Minor groove hydrogen bonds and the replication of unnatural base pairs J. Am. Chem. Soc. 129 2007 5551 5557
35. A.M. Leconte, G.T. Hwang, S. Matsuda, P. Capek, Y. Hari, and F.E. Romesberg Discovery, characterization, and optimization of an unnatural base pair for expansion of the genetic alphabet J. Am. Chem. Soc. 130 2008 2336 2343
36. D.A. Malyshev, D.A. Pfaff, S.I. Ippoliti, G.T. Hwang, T.J. Dwyer, and F.E. Romesberg Solution structure, mechanism of replication, and optimization of an unnatural base pair Chemistry 16 2010 12650 12659
37. M.C. Chen, B.J. Cafferty, I. Mamajanov, I. Gallego, J. Khanam, R. Krishnamurthy, and N.V. Hud Spontaneous prebiotic formation of a beta-ribofuranoside that self-assembles with a complementary heterocycle J. Am. Chem. Soc. 136 2014 5640 5646
38. B.J. Cafferty, I. Gallego, M.C. Chen, K.I. Farley, R. Eritja, and N.V. Hud Efficient self-assembly in water of long noncovalent polymers by nucleobase analogues J. Am. Chem. Soc. 135 2013 2447 2450
39. A.C. Rios, and Y. Tor On the origin of the canonical nucleobases: an assessment of selection pressures across chemical and early biological evolution Israel J. Chem. 53 2013 469 483
40. M.O. Ebert, C. Mang, R. Krishnamurthy, A. Eschenmoser, and B. Jaun The structure of a TNA-TNA complex in solution: NMR study of the octamer duplex derived from alpha-(L)-Threofuranosyl-(3'-2')-CGAATTCG J. Am. Chem. Soc. 130 2008 15105 15115
41. Y.W. Yang, S. Zhang, E.O. McCullum, and J.C. Chaput Experimental evidence that GNA and TNA were not sequential polymers in the prebiotic evolution of RNA J. Mol. Evol. 65 2007 289 295
42. M. Bohringer, H.J. Roth, J. Hunziker, M. Gobel, R. Krishnan, A. Giger, B. Schweizer, J. Schreiber, C. Leumann, and A. Eschenmoser Why pentose and not hexose nucleic-acids.2. Preparation of oligonucleotides containing 2',3'-dideoxy-beta-d-glucopyranosyl building-blocks Helvetica Chimica Acta 75 1992 1416 1477
43. A. Eschenmoser Hexose nucleic-acids Abstracts Papers Am. Chem. Soc. 203 1992 73-Carb
44. R. Krishnamurthy A search for structural alternatives of RNA J. Mexican Chem. Soc. 53 2009 23 33
45. V.B. Pinheiro, A.I. Taylor, C. Cozens, M. Abramov, M. Renders, S. Zhang, J.C. Chaput, J. Wengel, S.Y. Peak-Chew, S.H. McLaughlin, and et al. Synthetic genetic polymers capable of heredity and evolution Science 336 2012 341 344
46. G.F. Joyce, and L.E. Orgel Prospects for understanding the origin of the RNA World R.F. Gesteland, T.R. Cech, J.F. Atkins, The RNA World 2nd edn 1999 CSHL Press 49 77
47. J.W. Szostak The eightfold path to non-enzymatic RNA replication J. Syst. Chem. 3 2012 2
48. K. Mislow Absolute asymmetric synthesis: A commentary Collection Czechoslovak Chem. Commun. 68 2003 849 864
49. J.M. Ribo, C. Blanco, J. Crusats, Z. El-Hachemi, D. Hochberg, and A. Moyano Absolute asymmetric synthesis in enantioselective autocatalytic reaction networks: theoretical games, speculations on chemical evolution and perhaps a synthetic option Chemistry 20 2014 17250 17271
50. D.G. Blackmond Asymmetric autocatalysis and its implications for the origin of homochirality Proc. Natl. Acad. Sci. USA 101 2004 5732 5736
51. T. Kawasaki, Y. Matsumura, T. Tsutsumi, K. Suzuki, M. Ito, and K. Soai Asymmetric autocatalysis triggered by carbon isotope (C-13/C-12) chirality Science 324 2009 492 495
52. A. Matsumoto, S. Oji, S. Takano, K. Tada, T. Kawasaki, and K. Soai Asymmetric autocatalysis triggered by oxygen isotopically chiral glycerin Organic Biomol. Chem. 11 2013 2928 2931
53. K. Soai, and T. Kawasaki Asymmetric autocatalysis with amplification of chirality Amplification Chirality 284 2008 1 33
54. K. Soai, T. Shibata, H. Morioka, and K. Choji Asymmetric autocatalysis and amplification of enantiomeric excess of a chiral molecule Nature 378 1995 767 768
55. C. Viedma Chiral symmetry breaking during crystallization: complete chiral purity induced by nonlinear autocatalysis and recycling Phys. Rev. Lett. 94 2005 065504
56. C. Viedma Selective chiral symmetry breaking during crystallization: Parity violation or cryptochiral environment in control? Crystal Growth Design 7 2007 553 556
57. W.L. Noorduin, T. Izumi, A. Millemaggi, M. Leeman, H. Meekes, W.J. Van Enckevort, R.M. Kellogg, B. Kaptein, E. Vlieg, and D.G. Blackmond Emergence of a single solid chiral state from a nearly racemic amino acid derivative J. Am. Chem. Soc. 130 2008 1158 1159
58. B. Kaptein, W.L. Noorduin, H. Meekes, W.J. van Enckevort, R.M. Kellogg, and E. Vlieg Attrition-enhanced deracemization of an amino acid derivative that forms an epitaxial racemic conglomerate Angew. Chem. Int. Ed. Engl. 47 2008 7226 7229
59. W.L. Noorduin, B. Kaptein, H. Meekes, W.J. van Enckevort, R.M. Kellogg, and E. Vlieg Fast attrition-enhanced deracemization of naproxen by a gradual in situ feed Angew Chem. Int. Ed. Engl. 48 2009 4581 4583
60. W.L. Noorduin, P. van der Asdonk, H. Meekes, W.J.P. van Enckevort, B. Kaptein, M. Leeman, R.M. Kellogg, and E. Vlieg Complete chiral resolution using additive-induced crystal size bifurcation during grinding Angew. Chem. Int. Ed. 48 2009 3278 3280
61. Z. El-Hachemi, J. Crusats, J.M. Ribo, J.M. McBride, and S. Veintemillas-Verdaguer Metastability in supersaturated solution and transition towards chirality in the crystallization of NaClO3 Angew. Chem. Int. Ed. 50 2011 2359 2363
62. C. Viedma, and P. Cintas Homochirality beyond grinding: deracemizing chiral crystals by temperature gradient under boiling Chem. Commun. 47 2011 12786 12788
63. M. Uwaha A model for complete chiral crystallization J. Phys. Soc. Jap. 73 2004 2601 2603
64. J. Crusats, S. Veintemillas-Verdaguer, and J.M. Ribo Homochirality as a consequence of thermodynamic equilibrium? Chemistry 12 2006 7776 7781
65. C. Viedma Chiral symmetry breaking and complete chiral purity by thermodynamic-kinetic feedback near equilibrium: implications for the origin of biochirality Astrobiology 7 2007 312 319
66. D.G. Blackmond "Chiral amnesia" as a driving force for solid-phase homochirality Chemistry 13 2007 3290 3295
67. J.H.E. Cartwright, O. Piro, and I. Tuval Ostwald ripening, chiral crystallization, and the common-ancestor effect Phys. Rev. Lett. 98 2007 165501
68. W.L. Noorduin, H. Meekes, A.A.C. Bode, W.J.P. van Enckevort, B. Kaptein, R.M. Kellogg, and E. Vlieg Explanation for the emergence of a single chiral solid state during attrition-enhanced Ostwald ripening: survival of the fittest Crystal Growth Design 8 2008 1675 1681
69. J.M. McBride, and J.C. Tully Physical chemistry - did life grind to a start? Nature 452 2008 161 162
70. M. Uwaha Simple models for chirality conversion of crystals and molecules by grinding J. Phys. Soc. Jap. 77 2008
71. Y. Saito, and H. Hyuga Chiral crystal growth under grinding J. Phys. Soc. Jap. 77 2008
72. Z. El-Hachemi, J.Q. Crusats, J.M. Ribo, and S. Veintemillas-Verdaguer Spontaneous transition toward chirality in the NaClO3 crystallization in boiling solutions Crystal Growth Design 9 2009 4802 4806
73. C. Blanco, J. Crusats, Z. El-Hachemi, A. Moyano, S. Veintemillas-Verdaguer, D. Hochberg, and J.M. Ribo The viedma deracemization of racemic conglomerate mixtures as a paradigm of spontaneous mirror symmetry breaking in aggregation and polymerization Chemphyschem. 14 2013 3982 3993
74. I. Weissbuch, L. Addadi, Z. Berkovitchyellin, E. Gati, M. Lahav, and L. Leiserowitz Spontaneous generation and amplification of optical-activity in alpha-amino-acids by enantioselective occlusion into centrosymmetric crystals of glycine Nature 310 1984 161 164
75. I. Weissbuch, L. Addadi, L. Leiserowitz, and M. Lahav Total asymmetric transformations at interfaces with centrosymmetric crystals - role of hydrophobic and kinetic effects in the crystallization of the system glycine alpha-amino-acids J. Am. Chem. Soc. 110 1988 561 567
76. I. Weissbuch, L. Leiserowitz, and M. Lahav Stochastic "Mirror symmetry breaking" via self-assembly, reactivity and amplification of chirality: Relevance to abiotic conditions Prebiotic Chem. 259 2005 123 165
77. I. Weissbuch, and M. Lahav Crystalline architectures as templates of relevance to the origins of homochirality Chem. Rev. 111 2011 3236 3267
78. G.M. Munoz Caro, U.J. Meierhenrich, W.A. Schutte, B. Barbier, A. Arcones Segovia, H. Rosenbauer, W.H. Thiemann, A. Brack, and J.M. Greenberg Amino acids from ultraviolet irradiation of interstellar ice analogues Nature 416 2002 403 406
79. J.E. Elsila, D.P. Glavin, and J.P. Dworkin Cometary glycine detected in samples returned by Stardust Meteoritics Planetary Sci. 44 2009 1323 1330
80. T. Hitz, and P.L. Luisi Chiral amplification of oligopeptides in the polymerization of alpha-amino acid N-carboxyanhydrides in water Helvetica Chimica Acta 86 2003 1423 1434
81. T. Hitz, M. Blocher, P. Walde, and P.L. Luisi Stereoselectivity aspects in the condensation of racemic NCA-amino acids in the presence and absence of liposomes Macromolecules 34 2001 2443 2449
82. T. Hitz, and P.L. Luisi Enhancement of homochirality in oligopeptides by quartz Helvetica Chimica Acta 85 2002 3975 3983
83. M. Blocher, T. Hitz, and P.L. Luisi Stereoselectivity in the oligomerization of racemic tryptophan N-carboxyanhydride (NCA-Trp) as determined by isotope labeling and mass spectrometry Helvetica Chimica Acta 84 2001 842 848
84. H. Zepik, E. Shavit, M. Tang, T.R. Jensen, K. Kjaer, G. Bolbach, L. Leiserowitz, I. Weissbuch, and M. Lahav Chiral amplification of oligopeptides in two-dimensional crystalline self-assemblies on water Science 295 2002 1266 1269
85. I. Weissbuch, H. Zepik, G. Bolbach, E. Shavit, M. Tang, T.R. Jensen, K. Kjaer, L. Leiserowitz, and M. Lahav Homochiral oligopeptides by chiral amplification within two-dimensional crystalline self-assemblies at the air-water interface; Relevance to biomolecular handedness Chemistry 9 2003 1782 1794
86. K. Tamura Origin of amino acid homochirality: relationship with the RNA world and origin of tRNA aminoacylation Biosystems 92 2008 91 98
87. S.G. Trevino, N. Zhang, M.P. Elenko, A. Luptak, and J.W. Szostak Evolution of functional nucleic acids in the presence of nonheritable backbone heterogeneity Proc. Natl. Acad. Sci. USA 108 2011 13492 13497
88. G.F. Joyce, and L.E. Orgel 1 Prospects for understanding the origin of the RNA world Cold Spring Harbor Monograph Archive 24 1993 1 25
89. T.P. Prakash, C. Roberts, and C. Switzer Activity of 2',5'-linked RNA in the template-directed oligomerization of mononucleotides Angew. Chem. Int. Ed. Engl. 36 1997 1522 1523
90. I. Budin, N. Prwyes, N. Zhang, and J.W. Szostak Chain-length heterogeneity allows for the assembly of fatty acid vesicles in dilute solutions Biophys. J. 107 2014 1582 1590
91. C. Tuerk, and L. Gold Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase Science 249 1990 505 510
92. A.D. Ellington, and J.W. Szostak In vitro selection of RNA molecules that bind specific ligands Nature 346 1990 818 822
93. D.L. Robertson, and G.F. Joyce Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA Nature 344 1990 467 468
94. E.H. Ekland, and D.P. Bartel RNA-catalysed RNA polymerization using nucleoside triphosphates Nature 382 1996 373 376
95. W.K. Johnston, P.J. Unrau, M.S. Lawrence, M.E. Glasner, and D.P. Bartel RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension Science 292 2001 1319 1325
96. H.S. Zaher, and P.J. Unrau Selection of an improved RNA polymerase ribozyme with superior extension and fidelity RNA 13 2007 1017 1026
97. A. Wochner, J. Attwater, A. Coulson, and P. Holliger Ribozyme-catalyzed transcription of an active ribozyme Science 332 2011 209 212
98. A.C. Ferretti, and G.F. Joyce Kinetic properties of an RNA enzyme that undergoes self-sustained exponential amplification Biochemistry 52 2013 1227 1235
99. J. Attwater, S. Tagami, M. Kimoto, K. Butler, E.T. Kool, J. Wengel, P. Herdewijn, I. Hirao, and P. Holliger Chemical fidelity of an RNA polymerase ribozyme Chem. Sci. 4 2013 2804 2814
100. J. Attwater, A. Wochner, and P. Holliger In-ice evolution of RNA polymerase ribozyme activity Nat. Chem. 5 2013 1011 1018
101. M.S. Lawrence, and D.P. Bartel New ligase-derived RNA polymerase ribozymes RNA 11 2005 1173 1180
102. T.A. Lincoln, and G.F. Joyce Self-sustained replication of an RNA enzyme Science 323 2009 1229 1232
103. Q. Vicens, and T.R. Cech A natural ribozyme with 3',5' RNA ligase activity Nat. Chem. Biol. 5 2009 97 99
104. S. Gwiazda, K. Salomon, B. Appel, and S. Muller RNA self-ligation: from oligonucleotides to full length ribozymes Biochimie. 94 2012 1457 1463
105. S. Petkovic, and S. Muller RNA self-processing: formation of cyclic species and concatemers from a small engineered RNA FEBS Lett. 587 2013 2435 2440
106. G.F. Joyce Bit by bit: the Darwinian basis of life PLoS Biol. 10 2012 e1001323
107. E.N. Trifonov Definition of life: navigation through uncertainties J. Biomol. Struct. Dyn. 29 2012 647 650
108. J.T. Sczepanski, and G.F. Joyce A cross-chiral RNA polymerase ribozyme Nature 515 2014 440 442
109. M. Kreysing, L. Keil, S. Lanzmich, and D. Braun Heat flux across an open pore enables the continuous replication and selection of oligonucleotides towards increasing length Nat. Chem. 7 2015 203 208
110. D. Deamer, S. Singaram, S. Rajamani, V. Kompanichenko, and S. Guggenheim Self-assembly processes in the prebiotic environment Philos. Trans. R. Soc. Lond. B Biol. Sci. 361 2006 1809 1818
111. I. Mamajanov, P.J. MacDonald, J. Ying, D.M. Duncanson, G.R. Dowdy, C.A. Walker, A.E. Engelhart, F.M. Fernández, M.A. Grover, N.V. Hud, and et al. Ester formation and hydrolysis during wet-dry cycles: generation of far-from-equilibrium polymers in a model prebiotic reaction Macromolecules 47 2014 1334 1343
112. S.S. Mansy, and J.W. Szostak Thermostability of model protocell membranes Proc. Natl. Acad. Sci. USA 105 2008 13351 13355
113. K.E. Nelson, M.P. Robertson, M. Levy, and S.L. Miller Concentration by evaporation and the prebiotic synthesis of cytosine Orig. Life Evol. Biosph. 31 2001 221 229
114. H. Trinks, W. Schroder, and C.K. Biebricher Ice and the origin of life Orig. Life Evol. Biosph. 35 2005 429 445
115. J. Derr, M.L. Manapat, S. Rajamani, K. Leu, R. Xulvi-Brunet, I. Joseph, M.A. Nowak, and I.A. Chen Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences Nucleic Acids Res. 40 2012 4711 4722
116. M. Eigen Selforganization of matter and the evolution of biological macromolecules Naturwissenschaften 58 1971 465 523
117. K. Leu, E. Kervio, B. Obermayer, R.M. Turk-MacLeod, C. Yuan, J.M. Luevano Jr., E. Chen, U. Gerland, C. Richert, and I.A. Chen Cascade of reduced speed and accuracy after errors in enzyme-free copying of nucleic acid sequences J. Am. Chem. Soc. 135 2013 354 366
118. S. Rajamani, J.K. Ichida, T. Antal, D.A. Treco, K. Leu, M.A. Nowak, J.W. Szostak, and I.A. Chen Effect of stalling after mismatches on the error catastrophe in nonenzymatic nucleic acid replication J. Am. Chem. Soc. 132 2010 5880 5885
119. D.B. Saakian, C.K. Biebricher, and C.K. Hu Lethal mutants and truncated selection together solve a paradox of the origin of life PLoS One 6 2011 e21904
120. A.P. Gmyl, S.A. Korshenko, E.V. Belousov, E.V. Khitrina, and V.I. Agol Nonreplicative homologous RNA recombination: promiscuous joining of RNA pieces? RNA 9 2003 1221 1231
121. P.D. Nagy, and A.E. Simon New insights into the mechanisms of RNA recombination Virology 235 1997 1 9
122. C.A. Riley, and N. Lehman Generalized RNA-directed recombination of RNA Chem. Biol. 10 2003 1233 1243
123. N. Lehman, N. Vaidya, and J.A. Yeates RNA-directed recombination of RNA in vitro Methods Mol. Biol. 1240 2015 27 37
124. N. Lehman A recombination-based model for the origin and early evolution of genetic information Chem. Biodivers. 5 2008 1707 1717
125. N. Lehman Assessing the likelihood of recurrence during RNA evolution in vitro Artif. Life 10 2004 1 22
126. N. Vaidya, M.L. Manapat, I.A. Chen, R. Xulvi-Brunet, E.J. Hayden, and N. Lehman Spontaneous network formation among cooperative RNA replicators Nature 491 2012 72 77
127. L.P. Villarreal, and G. Witzany Rethinking quasispecies theory: from fittest type to cooperative consortia World J. Biol. Chem. 4 2013 79 90
128. E. Szathmary, and L. Demeter Group selection of early replicators and the origin of life J. Theor. Biol. 128 1987 463 486
129. E. Szathmary, and J.M. Smith The major evolutionary transitions Nature 374 1995 227 232
130. D. Grey, V. Hutson, and E. Szathmary A re-examination of the stochastic corrector model Proc. R. Soc. B Biol. Sci. 262 1995 29 35
131. E. Zintzaras, M. Santos, and E. Szathmary "Living" under the challenge of information decay: the stochastic corrector model vs. hypercycles J. Theor. Biol. 217 2002 167 181
132. G. Bianconi, K. Zhao, I.A. Chen, and M.A. Nowak Selection for replicases in protocells PLoS Comput. Biol. 9 2013 e1003051
133. K. Leu, B. Obermayer, S. Rajamani, U. Gerland, and I.A. Chen The prebiotic evolutionary advantage of transferring genetic information from RNA to DNA Nucleic Acids Res. 39 2011 8135 8147
134. S. Zhang, J.C. Blain, D. Zielinska, S.M. Gryaznov, and J.W. Szostak Fast and accurate nonenzymatic copying of an RNA-like synthetic genetic polymer Proc. Natl. Acad. Sci. USA 110 2013 17732 17737
135. J. Sheng, L. Li, A.E. Engelhart, J. Gan, J. Wang, and J.W. Szostak Structural insights into the effects of 2'-5' linkages on the RNA duplex Proc. Natl. Acad. Sci. USA 111 2014 3050 3055
136. S. Zhang, N. Zhang, J.C. Blain, and J.W. Szostak Synthesis of N3'-P5'-linked phosphoramidate DNA by nonenzymatic template-directed primer extension J. Am. Chem. Soc. 135 2013 924 932
137. N.A. Ivica, B. Obermayer, G.W. Campbell, S. Rajamani, U. Gerland, and I.A. Chen The paradox of dual roles in the RNA world: resolving the conflict between stable folding and templating ability J. Mol. Evol. 77 2013 55 63
138. S.S. Athavale, B. Spicer, and I.A. Chen Experimental fitness landscapes to understand the molecular evolution of RNA-based life Curr. Opin. Chem. Biol. 22 2014 35 39
139. J.A. de Visser, and J. Krug Empirical fitness landscapes and the predictability of evolution Nat. Rev. Genet. 15 2014 480 490
140. E.A. Curtis, and D.P. Bartel Synthetic shuffling and in vitro selection reveal the rugged adaptive fitness landscape of a kinase ribozyme RNA 19 2013 1116 1128
141. J.I. Jimenez, R. Xulvi-Brunet, G.W. Campbell, R. Turk-MacLeod, and I.A. Chen Comprehensive experimental fitness landscape and evolutionary network for small RNA Proc. Natl. Acad. Sci. USA 110 2013 14984 14989
142. K.L. Petrie, and G.F. Joyce Limits of neutral drift: lessons from the in vitro evolution of two ribozymes J. Mol. Evol. 79 2014 75 90
143. R. Saha, A. Pohorille, and I.A. Chen Molecular crowding and early evolution Orig. Life Evol. Biosph. 44 2014 319 324
144. R. Desai, D. Kilburn, H.T. Lee, and S.A. Woodson Increased ribozyme activity in crowded solutions J. Biol. Chem. 289 2014 2972 2977
145. R.J. Ellis Macromolecular crowding: obvious but underappreciated Trends Biochem. Sci. 26 2001 597 604
146. D. Kilburn, J.H. Roh, L. Guo, R.M. Briber, and S.A. Woodson Molecular crowding stabilizes folded RNA structure by the excluded volume effect J. Am. Chem. Soc. 132 2010 8690 8696
147. C.A. Strulson, N.H. Yennawar, R.P. Rambo, and P.C. Bevilacqua Molecular crowding favors reactivity of a human ribozyme under physiological ionic conditions Biochemistry 52 2013 8187 8197
148. P. Woolley, and P.R. Wills Excluded-volume effect of inert macromolecules on the melting of nucleic acids Biophys. Chem. 22 1985 89 94
149. H.T. Lee, D. Kilburn, R. Behrouzi, R.M. Briber, and S.A. Woodson Molecular crowding overcomes the destabilizing effects of mutations in a bacterial ribozyme Nucleic Acids Res. 43 2015 1170 1176
150. E.A. Schultes, and D.P. Bartel One sequence, two ribozymes: implications for the emergence of new ribozyme folds Science 289 2000 448 452
151. D.M. Held, S.T. Greathouse, A. Agrawal, and D.H. Burke Evolutionary landscapes for the acquisition of new ligand recognition by RNA aptamers J. Mol. Evol. 57 2003 299 308
152. M. Mandal, and R.R. Breaker Adenine riboswitches and gene activation by disruption of a transcription terminator Nat. Struct. Mol. Biol. 11 2004 29 35
153. M. Eigen, and P. Schuster The Hypercycle Naturwissenschaften 65 1978 7 41
154. K. Harris, and I.A. Chen Mathematical models of prebiotic replication of informational molecules Genesis - In the Beginning: Precursors of Life, Chemical Models and Early Biological Evolution Volume 22 2012 Springer Netherlands Dordrecht
155. I.A. Chen, K. Salehi-Ashtiani, and J.W. Szostak RNA catalysis in model protocell vesicles J. Am. Chem. Soc. 127 2005 13213 13219
156. S.S. Mansy, J.P. Schrum, M. Krishnamurthy, S. Tobe, D.A. Treco, and J.W. Szostak Template-directed synthesis of a genetic polymer in a model protocell Nature 454 2008 122 125
157. N. Ichihashi, K. Usui, Y. Kazuta, T. Sunami, T. Matsuura, and T. Yomo Darwinian evolution in a translation-coupled RNA replication system within a cell-like compartment Nat. Commun. 4 2013 2494
158. T. Matsuura, M. Yamaguchi, E.P. Ko-Mitamura, Y. Shima, I. Urabe, and T. Yomo Importance of compartment formation for a self-encoding system Proc. Natl. Acad. Sci. USA 99 2002 7514 7517
159. P. Szabo, I. Scheuring, T. Czaran, and E. Szathmary In silico simulations reveal that replicators with limited dispersal evolve towards higher efficiency and fidelity Nature 420 2002 340 343
160. J.P. Ferris, and G. Ertem Oligomerization of ribonucleotides on montmorillonite: reaction of the 5'-phosphorimidazolide of adenosine Science 257 1992 1387 1389
161. I.A. Chen, and J.W. Szostak Membrane growth can generate a transmembrane pH gradient in fatty acid vesicles Proc. Natl. Acad. Sci. USA 101 2004 7965 7970
162. S. Rajamani, A. Vlassov, S. Benner, A. Coombs, F. Olasagasti, and D. Deamer Lipid-assisted synthesis of RNA-like polymers from mononucleotides Orig. Life Evol. Biosph. 38 2008 57 74
163. W.V. Allen, and C. Ponnamperuma A possible prebiotic synthesis of monocarboxylic acids Curr. Mod. Biol. 1 1967 24 28
164. G.U. Yuen, and K.A. Kvenvold Monocarboxylic acids in Murray and Murchison carbonaceous meteorites Nature 246 1973 301 302
165. G.U. Yuen, J.G. Lawless, and E.H. Edelson Quantification of monocarboxylic acids from a spark discharge synthesis J. Mol. Evol. 17 1981 43 47
166. D.W. Deamer Boundary structures are formed by organic-components of the Murchison carbonaceous chondrite Nature 317 1985 792 794
167. T.M. McCollom, G. Ritter, and B.R. Simoneit Lipid synthesis under hydrothermal conditions by Fischer-Tropsch-type reactions Orig. Life Evol. Biosph. 29 1999 153 166
168. A. Loison, S. Dubant, P. Adam, and P. Albrecht Elucidation of an iterative process of carbon-carbon bond formation of prebiotic significance Astrobiology 10 2010 973 988
169. I. Budin, and J.W. Szostak Physical effects underlying the transition from primitive to modern cell membranes Proc. Natl. Acad. Sci. USA 108 2011 5249 5254
170. I.A. Chen, and J.W. Szostak A kinetic study of the growth of fatty acid vesicles Biophys. J. 87 2004 988 998
171. A.J. Markvoort, N. Pfleger, R. Staffhorst, P.A. Hilbers, R.A. van Santen, J.A. Killian, and B. de Kruijff Self-reproduction of fatty acid vesicles: a combined experimental and simulation study Biophys. J. 99 2010 1520 1528
172. P. Stano, E. Wehrli, and P.L. Luisi Insights into the self-reproduction of oleate vesicles J. Phys. Condensed Matter 18 2006 S2231 S2238
173. T.F. Zhu, and J.W. Szostak Coupled growth and division of model protocell membranes J. Am. Chem. Soc. 131 2009 5705 5713
174. K. Adamala, and J.W. Szostak Competition between model protocells driven by an encapsulated catalyst Nat. Chem. 5 2013 495 501
175. I.A. Chen, R.W. Roberts, and J.W. Szostak The emergence of competition between model protocells Science 305 2004 1474 1476
176. K. Kurihara, M. Tamura, K. Shohda, T. Toyota, K. Suzuki, and T. Sugawara Self-reproduction of supramolecular giant vesicles combined with the amplification of encapsulated DNA Nat. Chem. 3 2011 775 781
177. G.E. Fox Origin and evolution of the ribosome Cold Spring Harb. Perspect. Biol. 2 2010 a003483
178. T.W. Wiegand, R.C. Janssen, and B.E. Eaton Selection of RNA amide synthases Chem. Biol. 4 1997 675 683
179. B. Zhang, and T.R. Cech Peptide bond formation by in vitro selected ribozymes Nature 390 1997 96 100
180. N.V. Chumachenko, Y. Novikov, and M. Yarus Rapid and simple ribozymic aminoacylation using three conserved nucleotides J. Am. Chem. Soc. 131 2009 5257 5263
181. N. Lee, Y. Bessho, K. Wei, J.W. Szostak, and H. Suga Ribozyme-catalyzed tRNA aminoacylation Nat. Struct. Biol. 7 2000 28 33
182. H. Murakami, D. Kourouklis, and H. Suga Using a solid-phase ribozyme aminoacylation system to reprogram the genetic code Chem. Biol. 10 2003 1077 1084
183. H. Saito, D. Kourouklis, and H. Suga An in vitro evolved precursor tRNA with aminoacylation activity EMBO J. 20 2001 1797 1806
184. H. Saito, K. Watanabe, and H. Suga Concurrent molecular recognition of the amino acid and tRNA by a ribozyme RNA 7 2001 1867 1878
185. Y. Bessho, D.R. Hodgson, and H. Suga A tRNA aminoacylation system for non-natural amino acids based on a programmable ribozyme Nat. Biotechnol. 20 2002 723 728
186. H.F. Noller The driving force for molecular evolution of translation RNA 10 2004 1833 1837
187. E. Szathmary, and J. Maynard Smith From replicators to reproducers: the first major transitions leading to life J. Theor. Biol. 187 1997 555 571
188. J.T. Wong Origin of genetically encoded protein synthesis: a model based on selection for RNA peptidation Orig. Life Evol. Biosph. 21 1991 165 176
189. M. Illangasekare, and M. Yarus Small-molecule-substrate interactions with a self-aminoacylating ribozyme J. Mol. Biol. 268 1997 631 639
190. M. Illangasekare, and M. Yarus Specific, rapid synthesis of Phe-RNA by RNA Proc. Natl. Acad. Sci. USA 96 1999 5470 5475
191. M. Di Giulio The origin of the tRNA molecule: implications for the origin of protein synthesis J. Theor. Biol. 226 2004 89 93
192. M. Di Giulio A polyphyletic model for the origin of tRNAs has more support than a monophyletic model J. Theor. Biol. 318 2013 124 128
193. J. Widmann, M. Di Giulio, M. Yarus, and R. Knight tRNA creation by hairpin duplication J. Mol. Evol. 61 2005 524 530
194. M. Yarus, J.G. Caporaso, and R. Knight Origins of the genetic code: the escaped triplet theory Annu. Rev. Biochem. 74 2005 179 198
195. D. Penny An interpretive review of the origin of life research Biol. Phil. 20 2005 633 671
196. P. Schimmel, and B. Henderson Possible role of aminoacyl-RNA complexes in noncoded peptide synthesis and origin of coded synthesis Proc. Natl. Acad. Sci. USA 91 1994 11283 11286
197. K. Tamura, and P. Schimmel Peptide synthesis with a template-like RNA guide and aminoacyl phosphate adaptors Proc. Natl. Acad. Sci. USA 100 2003 8666 8669
198. H.S. Bernhardt, and W.P. Tate The transition from noncoded to coded protein synthesis: did coding mRNAs arise from stability-enhancing binding partners to tRNA? Biol. Direct 5 2010 16
199. A. Sievers, M. Beringer, M.V. Rodnina, and R. Wolfenden The ribosome as an entropy trap Proc. Natl. Acad. Sci. USA 101 2004 7897 7901
200. H.F. Noller Evolution of protein synthesis from an RNA world Cold Spring Harb. Perspect. Biol. 4 2012 a003681
201. L. Sun, Z. Cui, R.L. Gottlieb, and B. Zhang A selected ribozyme catalyzing diverse dipeptide synthesis Chem. Biol. 9 2002 619 628
202. K. Tamura, and P. Schimmel Oligonucleotide-directed peptide synthesis in a ribosome- and ribozyme-free system Proc. Natl. Acad. Sci. USA 98 2001 1393 1397
203. K. Adamala, and J.W. Szostak Nonenzymatic template-directed RNA synthesis inside model protocells Science 342 2013 1098 1100
204. S.A. Benner, A.D. Ellington, and A. Tauer Modern metabolism as a palimpsest of the RNA world Proc. Natl. Acad. Sci. USA 86 1989 7054 7058