A viscous solvent enables information transfer from gene-length nucleic acids in a model prebiotic replication cycle (original) (raw)

• Oro, J. Mechanism of synthesis of adenine from hydrogen cyanide under possible primitive Earth conditions. Nature 191, 1193–1194 (1961).
  Article CAS Google Scholar
• Joyce, G. F. The antiquity of RNA-based evolution. Nature 418, 214–221 (2002).
  Article CAS Google Scholar
• Cafferty, B. J. & Hud, N. V. Abiotic synthesis of RNA in water: a common goal of prebiotic chemistry and bottom-up synthetic biology. Curr. Opin. Chem. Biol. 22, 146–157 (2014).
  Article CAS Google Scholar
• Robertson, M. P. & Joyce, G. F. The origins of the RNA world. Cold Spring Harb. Perspect. Biol. 4, a003608 (2012).
  Article Google Scholar
• Ekland, E. H. & Bartel, D. P. RNA-catalysed RNA polymerization using nucleoside triphosphates. Nature 382, 373–376 (1996).
  Article CAS Google Scholar
• Sczepanski, J. T. & Joyce, G. F. A cross-chiral RNA polymerase ribozyme. Nature 515, 440–442 (2014).
  Article CAS Google Scholar
• Wochner, A., Attwater, J., Coulson, A. & Holliger, P. Ribozyme-catalyzed transcription of an active ribozyme. Science 332, 209–212 (2011).
  Article CAS Google Scholar
• Szostak, J. W. The eightfold path to non-enzymatic RNA replication. J. Syst. Chem. 3, 2 (2012).
  Article CAS Google Scholar
• Grossmann, T. N., Strohbach, A. & Seitz, O. Achieving turnover in DNA-templated reactions. ChemBioChem 9, 2185–2192 (2008).
  Article CAS Google Scholar
• Fernando, C., Von Kiedrowski, G. & Szathmary, E. A stochastic model of nonenzymatic nucleic acid replication: ‘Elongators’ sequester replicators. J. Mol. Evol. 64, 572–585 (2007).
  Article CAS Google Scholar
• Luther, A., Brandsch, R. & von Kiedrowski, G. Surface-promoted replication and exponential amplification of DNA analogues. Nature 396, 245–248 (1998).
  Article CAS Google Scholar
• Deck, C., Jauker, M. & Richert, C. Efficient enzyme-free copying of all four nucleobases templated by immobilized RNA. Nat. Chem. 3, 603–608 (2011).
  Article CAS Google Scholar
• Dose, C., Ficht, S. & Seitz, O. Reducing product inhibition in DNA-template-controlled ligation reactions. Angew. Chem. Int. Ed. 45, 5369–5373 (2006).
  Article CAS Google Scholar
• Zhan, Z. Y. J. & Lynn, D. G. Chemical amplification through template-directed synthesis. J. Am. Chem. Soc. 119, 12420–12421 (1997).
  Article CAS Google Scholar
• Kausar, A. et al. Tuning DNA stability to achieve turnover in template for an enzymatic ligation reaction. Angew. Chem. Int. Ed. 50, 8922–8926 (2011).
  Article CAS Google Scholar
• Mutschler, H., Wochner, A. & Holliger, P. Freeze–thaw cycles as drivers of complex ribozyme assembly. Nat. Chem. 7, 502–508 (2015).
  Article CAS Google Scholar
• Kreysing, M., Keil, L., Lanzmich, S. & Braun, D. Heat flux across an open pore enables the continuous replication and selection of oligonucleotides towards increasing length. Nat. Chem. 7, 203–208 (2015).
  Article CAS Google Scholar
• Walker, S. I., Grover, M. A. & Hud, N. V. Universal sequence replication, reversible polymerization and early functional biopolymers: a model for the initiation of prebiotic sequence evolution. PLoS ONE 7, e34166 (2012).
  Article CAS Google Scholar
• Kramers, H. A. Brownian motion in a field of force and the diffusion model of chemical reactions. Physica 7, 284–304 (1940).
  Article CAS Google Scholar
• Gállego, I., Grover, M. A. & Hud, N. V. Folding and imaging of DNA nanostructures in anhydrous and hydrated deep-eutectic solvents. Angew. Chem. Int. Ed. 54, 6765–6769 (2015).
  Article Google Scholar
• Mamajanov, I., Engelhart, A. E., Bean, H. D. & Hud, N. V. DNA and RNA in anhydrous media: duplex, triplex, and G-quadruplex secondary structures in a deep eutectic solvent. Angew. Chem. Int. Ed. 49, 6310–6314 (2010).
  Article CAS Google Scholar
• Lannan, F. M., Mamajanov, I. & Hud, N. V. Human telomere sequence DNA in water-free and high-viscosity solvents: G-quadruplex folding governed by kramers rate theory. J. Am. Chem. Soc. 134, 15324–15330 (2012).
  Article CAS Google Scholar
• Sorin, E. J., Rhee, Y. M., Nakatani, B. J. & Pande, V. S. Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations. Biophys. J. 85, 790–803 (2003).
  Article CAS Google Scholar
• Doty, P., Marmur, J., Eigner, J. & Schildkraut, C. Strand separation and specific recombination in deoxyribonucleic acids—physical chemical studies. Proc. Natl Acad. Sci. USA 46, 461–476 (1960).
  Article CAS Google Scholar
• Viasnoff, V., Meller, A. & Isambert, H. DNA nanomechanical switches under folding kinetics control. Nano Lett. 6, 101–104 (2006).
  Article CAS Google Scholar
• Zhang, X. et al. Interconversion between three overstretched DNA structures. J. Am. Chem. Soc. 136, 16073–16080 (2014).
  Article CAS Google Scholar
• Panyutin, I. G. & Hsieh, P. The kinetics of spontaneous DNA branch migration. Proc. Natl Acad. Sci. USA 91, 2021–2025 (1994).
  Article CAS Google Scholar
• Green, C. & Tibbetts, C. Reassociation rate limited displacement of DNA-strands by branch migration. Nucleic Acids Res. 9, 1905–1918 (1981).
  Article CAS Google Scholar
• Radding, C. M., Beattie, K. L., Holloman, W. K. & Wiegand, R. C. Uptake of homologous single-stranded fragments by superhelical DNA: IV. Branch migration. J. Mol. Biol. 116, 825–839 (1977).
  Article CAS Google Scholar
• Hud, N. V., Cafferty, B. J., Krishnamurthy, R. & Williams, L. D. The origin of RNA and ‘My Grandfather's axe’. Chem. Biol. 20, 466–474 (2013).
  Article CAS Google Scholar
• Joyce, G. F. & Orgel, L. E. Non-enzymatic template-directed synthesis on RNA random copolymers: poly(C,A) templates. J. Mol. Biol. 202, 677–681 (1988).
  Article CAS Google Scholar
• Orgel, L. E. Unnatural selection in chemical systems. Acc. Chem. Res. 28, 109–118 (1995).
  Article CAS Google Scholar
• Weimann, B. J., Lohrmann, R., Orgel, L. E., Schneider-Bernloehr, H. & Sulston, J. E. Template-directed synthesis with adenosine-5′-phosphorimidazolide. Science 161, 387 (1968).
  Article CAS Google Scholar
• von Kiedrowski, G. A self-replicating hexadeoxynucleotide. Angew. Chem. Int. Ed. 25, 932–935 (1986).
  Article Google Scholar
• Zielinski, W. S. & Orgel, L. E. Autocatalytic synthesis of a tetranucleotide analog. Nature 327, 346–347 (1987).
  Article CAS Google Scholar
• Sievers, D. & von Kiedrowski, G. Self replication of complementary nucleotide-based oligomers. Nature 369, 221–224 (1994).
  Article CAS Google Scholar
• Li, T. & Nicolaou, K. C. Chemical self-replication of palindromic duplex DNA. Nature 369, 218–221 (1994).
  Article CAS Google Scholar
• Ferris, J. P., Hill, A. R. Jr, Liu, R. & Orgel, L. E. Synthesis of long prebiotic oligomers on mineral surfaces. Nature 381, 59–61 (1996).
  Article CAS Google Scholar
• Engelhart, A. E. et al. Nonenzymatic ligation of DNA with a reversible step and a final linkage that can be used in PCR. ChemBioChem 13, 1121–1124 (2012).
  Article CAS Google Scholar
• Gull, M., Zhou, M. S., Fernandez, F. M. & Pasek, M. A. Prebiotic phosphate ester syntheses in a deep eutectic solvent. J. Mol. Evol. 78, 109–117 (2014).
  Article CAS Google Scholar
• Schoffstall, A. M., Barto, R. J. & Ramos, D. L. Nucleoside and deoxynucleoside phosphorylation in formamide solutions. Orig. Life 12, 143–151 (1982).
  Article CAS Google Scholar
• Powner, M. W., Gerland, B. & Sutherland, J. D. Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature 459, 239–242 (2009).
  Article CAS Google Scholar
• Mamajanov, I. et al. Ester formation and hydrolysis during wet–dry cycles: generation of far-from-equilibrium polymers in a model prebiotic reaction. Macromolecules 47, 1334–1343 (2014).
  Article CAS Google Scholar
• Mast, C. B., Schink, S., Gerland, U. & Braun, D. Escalation of polymerization in a thermal gradient. Proc. Natl Acad. Sci. USA 110, 8030–8035 (2013).
  Article CAS Google Scholar
• Apel, C. L. & Deamer, D. W. The formation of glycerol monodecanoate by a dehydration/condensation reaction: increasing the chemical complexity of amphiphiles on the early earth. Orig. Life Evol. Biosph. 35, 323–332 (2005).
  Article CAS Google Scholar
• Monnard, P. A. & Szostak, J. W. Metal-ion catalyzed polymerization in the eutectic phase in water-ice: a possible approach to template-directed RNA polymerization. J. Inorg. Biochem. 102, 1104–1111 (2008).
  Article CAS Google Scholar
• Deamer, D. W. & Barchfeld, G. L. Encapsulation of macromolecules by lipid vesicles under simulated prebiotic conditions. J. Mol. Evol. 18, 203–206 (1982).
  Article CAS Google Scholar
• Usher, D. A. Early chemical evolution of nucleic-acids—theoretical-model. Science 196, 311–313 (1977).
  Article CAS Google Scholar