Skip to main content
SpringerLink
Log in

Searching for Possible Ancestors of RNA: The Self-Assembly Hypothesis for the Origin of Proto-RNA

  • Chapter
  • First Online:
Book cover Prebiotic Chemistry and Chemical Evolution of Nucleic Acids

Part of the book series: Nucleic Acids and Molecular Biology ((NUCLEIC,volume 35))

Abstract

There are currently two main schools of thought regarding the origins of RNA. In one school, RNA is considered to be a product of nonenzymatic, prebiotic reactions. In the other, RNA is considered to be a product of chemical and/or biological evolution. The numerous challenges to demonstrating a plausible prebiotic synthesis of RNA support the hypothesis that life started with an ancestral RNA-like polymer, or proto-RNA. If RNA is an “invention” of early life, then it is logical to assume that identifying the chemical structure of proto-RNA, and intermediate pre-RNAs, would require exploration of a seemingly insurmountable number of possible proto-RNA building blocks and prebiotic reactions. Here we report progress toward finding a proto-RNA that is the product of molecular self-assembly. Results obtained thus far demonstrate that seemingly minor changes to the structure of the extant building blocks of RNA (e.g., the substitution of uracil by barbituric acid) alleviate several long-standing problems associated with finding a prebiotic synthesis for RNA.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Abo-Riziq A, Grace L, Nir E, Kabelac M, Hobza P, de Vries MS (2005) Photochemical selectivity in guanine-cytosine base-pair structures. Proc Natl Acad Sci U S A 102:20–23

    Article  PubMed  CAS  Google Scholar 

  • Arnott S, Bond PJ (1973) Triple-stranded polynucleotide helix containing only purine bases. Science 181:68

    Article  PubMed  CAS  Google Scholar 

  • Ban N, Nissen P, Hansen J, Moore PB, Steitz TA (2000) The complete atomic structure of the large ribosomal subunit at 2.4 Ångstrom resolution. Science 289:905–920

    Article  PubMed  CAS  Google Scholar 

  • Barks HL, Buckley R, Grieves GA, Di Mauro E, Hud NV, Orlando TM (2010) Guanine, adenine, and hypoxanthine production in UV-irradiated formamide solutions: relaxation of the requirements for prebiotic purine nucleobase formation. Chembiochem 11:1240–1243

    Article  PubMed  CAS  Google Scholar 

  • Battersby TR, Albalos M, Friesenhahn MJ (2007) An unusual mode of DNA duplex association: Watson-Crick interaction of all-purine deoxyribonucleic acids. Chem Biol 14:525–531

    Article  PubMed  CAS  Google Scholar 

  • Benner SA (2004) Understanding nucleic acids using synthetic chemistry. Acc Chem Res 37:784–797

    Article  PubMed  CAS  Google Scholar 

  • Benner SA, Ricardo A, Carrigan MA (2004) Is there a common chemical model for life in the universe? Curr Opin Chem Biol 8:672–689

    Article  PubMed  CAS  Google Scholar 

  • Benner SA, Kim H-J, Carrigan MA (2012) Asphalt, water, and the prebiotic synthesis of ribose, ribonucleosides, and RNA. Acc Chem Res 45:2025–2034

    Article  PubMed  CAS  Google Scholar 

  • Bernhardt HS (2012) The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others)(a). Biol Direct 7:23–23

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bogert MT (1910) The instability of alloxan. J Am Chem Soc 32:809–810

    Article  CAS  Google Scholar 

  • Bohanon TM, Denzinger S, Fink R, Paulus W, Ringsdorf H, Weck M (1995) Barbituric-acid 2,4,6-triaminopyrimidine aggregates in water and their competitive interaction with a monolayer of barbituric-acid lipids at the gas-water interface. Angew Chem Int Ed Engl 34:58–60

    Article  CAS  Google Scholar 

  • Bolli M, Micura R, Eschenmoser A (1997) Pyranosyl-RNA: chiroselective self-assembly of base sequences by ligative oligomerization of tetra nucleotide-2′,3′-cyclophosphates (with a commentary concerning the origin of biomolecular homochirality). Chem Biol 4:309–320

    Article  PubMed  CAS  Google Scholar 

  • Borquez E, Cleaves HJ, Lazcano A, Miller SL (2005) An investigation of prebiotic purine synthesis from the hydrolysis of HCN polymers. Orig Life Evol Biosph 35:79–90

    Article  PubMed  CAS  Google Scholar 

  • Botta O, Bada JL (2002) Extraterrestrial organic compounds in meteorites. Surv Geophys 23:411–467

    Article  Google Scholar 

  • Bowman J, Hud N, Williams L (2015) The ribosome challenge to the RNA world. J Mol Evol 80:143–161

    Article  PubMed  CAS  Google Scholar 

  • Brister MM, Pollum M, Crespo-Hernandez CE (2016) Photochemical etiology of promising ancestors of the RNA nucleobases. Phys Chem Chem Phys 18:20097–20103

    Article  PubMed  CAS  Google Scholar 

  • Buckley R, Enekwa CD, Williams LD, Hud NV (2011) Molecular recognition of Watson-Crick-like purine-purine base pairs. Chembiochem 12:2155–2158

    Article  PubMed  CAS  Google Scholar 

  • Cafferty BJ, Hud NV (2014) Abiotic synthesis of RNA in water: a common goal of prebiotic chemistry and bottom-up synthetic biology. Curr Opin Chem Biol 22:146–157

    Article  PubMed  CAS  Google Scholar 

  • Cafferty BJ, Hud NV (2015) Was a pyrimidine-pyrimidine base pair the ancestor of Watson-Crick base pairs? Insights from a systematic approach to the origin of RNA. Isr J Chem 55:891–905

    Article  CAS  Google Scholar 

  • Cafferty BJ, Gallego I, Chen MC, Farley KI, Eritja R, Hud NV (2013) Efficient self-assembly in water of long noncovalent polymers by nucleobase analogues. J Am Chem Soc 135:2447–2450

    Article  PubMed  CAS  Google Scholar 

  • Cafferty BJ, Avirah RR, Schuster GB, Hud NV (2014) Ultra-sensitive pH control of supramolecular polymers and hydrogels: pK(a) matching of biomimetic monomers. Chem Sci 5:4681–4686

    Article  CAS  Google Scholar 

  • Cafferty BJ, Fialho DM, Khanam J, Krishnamurthy R, Hud NV (2016) Spontaneous formation and base pairing of plausible prebiotic nucleotides in water. Nat Commun 7:11328

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Callahan MP, Smith KE, Cleaves HJ, Ruzicka J, Stern JC, Glavin DP, House CH, Dworkin JP (2011) Carbonaceous meteorites contain a wide range of extraterrestrial nucleobases. Proc Natl Acad Sci U S A 108:13995–13998

    Article  PubMed  PubMed Central  Google Scholar 

  • Cassidy LM, Burcar BT, Stevens W, Moriarty EM, McGown LB (2014) Guanine-centric self-assembly of nucleotides in water: an important consideration in prebiotic chemistry. Astrobiology 14:876–886

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chen MC, Cafferty BJ, Mamajanov I, Gállego I, Khanam J, Krishnamurthy R, Hud NV (2014) Spontaneous prebiotic formation of a β-ribofuranoside that self-assembles with a complementary heterocycle. J Am Chem Soc 136:5640–5646

    Article  PubMed  CAS  Google Scholar 

  • Cleaves HJ, Nelson KE, Miller SL (2006) The prebiotic synthesis of pyrimidines in frozen solution. Naturwissenschaften 93:228–231

    Article  PubMed  CAS  Google Scholar 

  • Cnossen I, Sanz-Forcada J, Favata F, Witasse O, Zegers T, Arnold NF (2007) Habitat of early life: solar X-ray and UV radiation at Earth’s surface 4-3.5 billion years ago. J Geophys Res Planets 112:10

    Article  CAS  Google Scholar 

  • Crespo-Hernandez CE, Cohen B, Hare PM, Kohler B (2004) Ultrafast excited-state dynamics in nucleic acids. Chem Rev 104:1977–2019

    Article  PubMed  CAS  Google Scholar 

  • Crick FHC (1968) The origin of the genetic code. J Mol Biol 38:367–379

    Article  PubMed  CAS  Google Scholar 

  • Davis JT (2004) G-quartets 40 years later: from 5'-GMP to molecular biology and supramolecular chemistry. Angew Chem Int Ed Engl 43:668–698

    Article  PubMed  CAS  Google Scholar 

  • Davis JT, Spada GP (2007) Supramolecular architectures generated by self-assembly of guanosine derivatives. Chem Soc Rev 36:296–313

    Article  PubMed  CAS  Google Scholar 

  • Decker P, Schweer P, Pohlmann R (1982) Identification of formose sugars, presumable prebiotic metabolites, using capillary gas chromatography/gas chromatography-mass spectroscopy of n-butoxime trifluoroacetates on OV-225. J Chromatogr 244:281–291

    Article  CAS  Google Scholar 

  • Dorr M, Loffler PMG, Monnard PA (2012) Non-enzymatic polymerization of nucleic acids from monomers: monomer self-condensation and template-directed reactions. Curr Org Synth 9:735–763

    Article  CAS  Google Scholar 

  • Egli M, Pallan PS, Pattanayek R, Wilds CJ, Lubini P, Minasov G, Dobler M, Leumann CJ, Eschenmoser A (2006) Crystal structure of homo-DNA and Nature’s choice of pentose over hexose in the genetic system. J Am Chem Soc 128:10847–10856

    Article  PubMed  CAS  Google Scholar 

  • Engelhart AE, Hud NV (2010) Primitive genetic polymers. Cold Spring Harb Perspect Biol 2:a002196. https://doi.org/10.1101/cshperspect.a002196

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Eschenmoser A (1999) Chemical etiology of nucleic acid structure. Science 284:2118–2124

    Article  PubMed  CAS  Google Scholar 

  • Eschenmoser A (2004) The TNA-family of nucleic acid systems: properties and prospects. Orig Life Evol Biosph 34:277–306

    Article  PubMed  CAS  Google Scholar 

  • Eschenmoser A (2007) The search for the chemistry of life’s origin. Tetrahedron 63:12821–12844

    Article  CAS  Google Scholar 

  • Eschenmoser A (2011) Etiology of potentially primordial biomolecular structures: from vitamin B12 to the nucleic acids and an inquiry into the chemistry of life’s origin: A retrospective. Angew Chem Int Ed Engl 50:12412–12472

    Article  PubMed  CAS  Google Scholar 

  • Fernando C, Von Kiedrowski G, Szathmary E (2007) A stochastic model of nonenzymatic nucleic acid replication: “Elongators” sequester replicators. J Mol Evol 64:572–585

    Article  PubMed  CAS  Google Scholar 

  • Ferris JP, Hagan WJ (1984) HCN and chemical evolution - the possible role of cyano compounds in prebiotic synthesis. Tetrahedron 40:1093–1120

    Article  PubMed  CAS  Google Scholar 

  • Ferris JP, Sanchez RA, Orgel LE (1968) Synthesis of pyrimidines from cyanoacetylene and cyanate. J Mol Biol 33:693–704

    Article  PubMed  CAS  Google Scholar 

  • Ferris JP, Hill AR, Liu RH, Orgel LE (1996) Synthesis of long prebiotic oligomers on mineral surfaces. Nature 381:59–61

    Article  PubMed  CAS  Google Scholar 

  • Fialho DM, Clarke KC, Moore MK, Schuster GB, Krishnamurthy R, Hud NV (2018) Glycosylation of a model proto-RNA nucleobase with non-ribose sugars: implications for the prebiotic synthesis of nucleosides. Org Biomol Chem 16:1263–1271

    Article  PubMed  CAS  Google Scholar 

  • Forsythe JG, Yu SS, Mamajanov I, Grover MA, Krishnamurthy R, Fernandez FM, Hud NV (2015) Ester-mediated amide bond formation driven by wet-dry cycles: a possible path to polypeptides on the prebiotic Earth. Angew Chem Int Ed Engl 54:9871–9875

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Fripiat JJ, Cruzcump M (1974) Clays as catalysts for natural processes. Annu Rev Earth Planet Sci 2:239–256

    Article  Google Scholar 

  • Fuller WD, Sanchez RA, Orgel LE (1972a) Studies in prebiotic synthesis. VI. Synthesis of purine nucleosides. J Mol Biol 67:25–33

    Article  PubMed  CAS  Google Scholar 

  • Fuller WD, Sanchez RA, Orgel LE (1972b) Studies in prebiotic synthesis: VII. Solid-state synthesis of purine nucleosides. J Mol Evol 1:249–257

    Article  PubMed  CAS  Google Scholar 

  • Gavette JV, Stoop M, Hud NV, Krishnamurthy R (2016) RNA-DNA chimeras in the context of an RNA world transition to an RNA/DNA world. Angew Chem Int Ed Engl 55:13204–13209

    Article  PubMed  CAS  Google Scholar 

  • Gellert M, Lipsett MN, Davies DR (1962) Helix formation by guanylic acid. Proc Natl Acad Sci U S A 48:2013–2018

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gesteland RF, Cech TR, Atkins JF (2006) The RNA world, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY

    Google Scholar 

  • Grew ES, Bada JL, Hazen RM (2011) Borate minerals and origin of the RNA world. Origins Life Evol Biosph 41:307–316

    Article  CAS  Google Scholar 

  • Groebke K, Hunziker J, Fraser W, Peng L, Diederichsen U, Zimmermann K, Holzner A, Leumann C, Eschenmoser A (1998) Why pentose- and not hexose-nucleic acids? Purine-purine pairing in homo-DNA: guanine, isoguanine, 2,6-diaminopurine, and xanthine. Helv Chim Acta 81:375–474

    Article  CAS  Google Scholar 

  • Grossmann TN, Strohbach A, Seitz O (2008) Achieving turnover in DNA-templated reactions. Chembiochem 9:2185–2192

    Article  PubMed  CAS  Google Scholar 

  • Guerrier-Takada C, Gardiner K, Marsh T, Pace N, Altman S (1983) The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35:849–857

    Article  PubMed  CAS  Google Scholar 

  • Harvey GR, Degens ET, Mopper K (1971) Synthesis of nitrogen heterocycles on kaolinite from CO2 and NH3. Naturwissenschaften 58:624–625

    Article  CAS  Google Scholar 

  • Hayatsu R, Studier MH, Oda A, Fuse K, Anders E (1968) Origin of organic matter in early solar system 2. Nitrogen compounds. Geochim Cosmochim Acta 32:175–190

    Article  CAS  Google Scholar 

  • Hayatsu R, Studier MH, Moore LP, Anders E (1975) Purines and triazines in murchison meteorite. Geochim Cosmochim Acta 39:471–488

    Article  CAS  Google Scholar 

  • He C, Gallego I, Laughlin B, Grover MA, Hud NV (2017) A viscous solvent enables information transfer from gene-length nucleic acids in a model prebiotic replication cycle. Nat Chem 9:318–324

    Article  PubMed  CAS  Google Scholar 

  • Herdewijn P (2001) TNA as a potential alternative to natural nucleic acids. Angew Chem Int Ed Eng 40:2249–2251

    Article  CAS  Google Scholar 

  • Heuberger BD, Switzer C (2008) An alternative nucleobase code: characterization of purine-purine DNA double helices bearing guanine-isoguanine and diaminopurine-7-deaza-xanthine base pairs. Chembiochem 9:2779–2783

    Article  PubMed  CAS  Google Scholar 

  • Hoogsteen K (1959) The structure of crystals containing a hydrogen-bonded complex of 1-methylthymine and 9-methyladenine. Acta Crystallogr 12:822–823

    Article  CAS  Google Scholar 

  • Horowitz ED, Lilavivat S, Holladay BW, Germann MW, Hud NV (2009) Solution structure and thermodynamics of 2′,5′ RNA intercalation. J Am Chem Soc 131:5831–5838

    Article  PubMed  CAS  Google Scholar 

  • Howard FB, Miles HT (1977) Interaction of poly(A) and poly(I), a reinvestigation. Biochemistry 16:4647–4650

    Article  PubMed  CAS  Google Scholar 

  • Hud NV (2017) Our odyssey to find a plausible prebiotic path to RNA: the first twenty years. Synlett 28:36–55

    Article  CAS  Google Scholar 

  • Hud NV, Anet FAL (2000) Intercalation-mediated synthesis and replication: a new approach to the origin of life. J Theor Biol 205:543–562

    Article  PubMed  CAS  Google Scholar 

  • Hud NV, Jain SS, Li X, Lynn DG (2007) Addressing the problems of base pairing and strand cyclization in template-directed synthesis. Chem Biodivers 4:768–783

    Article  PubMed  CAS  Google Scholar 

  • Hud NV, Cafferty BJ, Krishnamurthy R, Williams LD (2013) The origin of RNA and ‘My grandfather’s axe’. Chem Biol 20:466–474

    Article  PubMed  CAS  Google Scholar 

  • Johnson AP, Cleaves HJ, Dworkin JP, Glavin DP, Lazcano A, Bada JL (2008) The Miller volcanic spark discharge experiment. Science 322:404–404

    Article  PubMed  CAS  Google Scholar 

  • Joyce GF, Schwartz AW, Miller SL, Orgel LE (1987) The case for an ancestral genetic system involving simple analogs of the nucleotides. Proc Natl Acad Sci U S A 84:4398–4402

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kim HJ, Benner SA (2015) Prebiotic glycosylation of uracil with electron-donating substituents. Astrobiology 15:301–306

    Article  PubMed  CAS  Google Scholar 

  • Kim HJ, Ricardo A, Illangkoon HI, Kim MJ, Carrigan MA, Frye F, Benner SA (2011) Synthesis of carbohydrates in mineral-guided prebiotic cycles. J Am Chem Soc 133:9457–9468

    Article  PubMed  CAS  Google Scholar 

  • Kolb VM, Dworkin JP, Miller SL (1994) Alternative bases in the RNA world: the prebiotic synthesis of urazole and its ribosides. J Mol Evol 38:549–557

    Article  PubMed  CAS  Google Scholar 

  • Krishnamurthy R (2015) On the emergence of RNA. Isr J Chem 55:837–850

    Article  CAS  Google Scholar 

  • Krishnamurthy R, Pitsch S, Minton M, Miculka C, Windhab N, Eschenmoser A (1996) Pyranosyl-RNA: base pairing between homochiral oligonucleotide strands of opposite sense of chirality. Angew Chem Int Ed Engl 35:1537–1541

    Article  CAS  Google Scholar 

  • Kruger K, Grabowski PJ, Zaug AJ, Sands J, Gottschling DE, Cech TR (1982) Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell 31:147–157

    Article  PubMed  CAS  Google Scholar 

  • Kurland CG (2010) The RNA dreamtime. BioEssays 32:866–871

    Article  PubMed  CAS  Google Scholar 

  • Kuruvilla E, Schuster GB, Hud NV (2013) Enhanced non-enzymatic ligation of homo-purine miniduplexes: Support for greater base stacking in a pre-RNA world. Chembiochem 14(1):45–48. https://doi.org/10.1002/cbic.201200601

    Article  PubMed  CAS  Google Scholar 

  • Larralde R, Robertson MP, Miller SL (1995) Rates of decomposition of ribose and other sugars: implications for chemical evolution. Proc Natl Acad Sci U S A 92:8158–8160

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lehn J-M, Mascal M, Decian A, Fischer J (1990) Molecular recognition directed self-assembly of ordered supramolecular strands by cocrystallization of complementary molecular components. J Chem Soc Chem Commun:479–481

    Google Scholar 

  • Levy M, Miller SL (1998) The stability of the RNA bases: implications for the origin of life. Proc Natl Acad Sci U S A 95:7933–7938

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Li C, Cafferty BJ, Karunakaran SC, Schuster GB, Hud NV (2016) Formation of supramolecular assemblies and liquid crystals by purine nucleobases and cyanuric acid in water: Implications for the possible origins of RNA. Phys Chem Chem Phys 18:20091–20096

    Google Scholar 

  • Ma M, Bong D (2011) Determinants of cyanuric acid and melamine assembly in water. Langmuir 27:8841–8853

    Article  PubMed  CAS  Google Scholar 

  • Martins Z, Botta O, Fogel ML, Sephton MA, Glavin DP, Watson JS, Dworkin JP, Schwartz AW, Ehrenfreund P (2008) Extraterrestrial nucleobases in the Murchison meteorite. Earth Planet Sci Lett 270:130–136

    Article  CAS  Google Scholar 

  • Menor-Salván C, Marin-Yaseli MR (2013) A new route for the prebiotic synthesis of nucleobases and hydantoins in water/ice solutions involving the photochemistry of acetylene. Chem Eur J 19:6488–6497

    Article  PubMed  CAS  Google Scholar 

  • Menor-Salván C, Ruiz-Bermejo DM, Guzman MI, Osuna-Esteban S, Veintemillas-Verdaguer S (2009) Synthesis of pyrimidines and triazines in ice: implications for the prebiotic chemistry of nucleobases. Chem Eur J 15:4411–4418

    Article  PubMed  CAS  Google Scholar 

  • Miller SL (1953) A production of amino acids under possible primitive Earth conditions. Science 117:528–529

    Article  PubMed  CAS  Google Scholar 

  • Miller SL (1957) The mechanism of synthesis of amino acids by electric discharges. Biochim Biophys Acta 23:480–489

    Article  PubMed  CAS  Google Scholar 

  • Miller SL, Urey HC (1959) Organic compound synthesis on the primitive Earth. Science 130:245–251

    Article  PubMed  CAS  Google Scholar 

  • Mittapalli GK, Osornio YM, Guerrero MA, Reddy KR, Krishnamurthy R, Eschenmoser A (2007) Mapping the landscape of potentially primordial informational oligomers: oligodipeptides tagged with 2,4-disubstituted 5-aminopyrimidines as recognition elements. Angew Chem Int Ed Engl 46:2478–2484

    Article  PubMed  CAS  Google Scholar 

  • Monnard P-A (2016) Taming prebiotic chemistry: the role of heterogeneous and interfacial catalysis in the emergence of a prebiotic catalytic/information polymer system. Life 6:E40

    Article  PubMed  CAS  Google Scholar 

  • Nielsen PE (2007) Peptide nucleic acids and the origin of life. Chem Biodivers 4:1996–2002

    Article  PubMed  CAS  Google Scholar 

  • Nuevo M, Milam SN, Sandford SA (2012) Nucleobases and prebiotic molecules in organic residues produced from the ultraviolet photo-irradiation of pyrimidine in NH3 and H2O+NH3 ices. Astrobiology 12:295–314

    Article  PubMed  CAS  Google Scholar 

  • Olby R (2003) Quiet debut for the double helix. Nature 421:402–405

    Article  PubMed  CAS  Google Scholar 

  • Onimaru K, Kuraku S, Takagi W, Hyodo S, Sharpe J, Tanaka M (2015) A shift in anterior–posterior positional information underlies the fin-to-limb evolution. elife 4:e07048

    Article  PubMed Central  Google Scholar 

  • Orgel LE (1968) Evolution of the genetic apparatus. J Mol Biol 38:381–393

    Article  PubMed  CAS  Google Scholar 

  • Orgel LE (1998) The origin of life – a review of facts and speculations. TIBS 23:491–495

    PubMed  CAS  Google Scholar 

  • Orgel LE (2004) Prebiotic chemistry and the origin of the RNA world. Crit Rev Biochem Mol Biol 39:99–123

    Article  PubMed  CAS  Google Scholar 

  • Oró J (1960) Synthesis of adenine from ammonium cyanide. Biochem Biophys Res Commun 2:407–412

    Article  Google Scholar 

  • Oró J (2002) In: Schopf W (ed) Life’s origin: the beginnings of biological evolution. University of California, Berkeley, pp 7–45

    Google Scholar 

  • Petrov AS, Bernier CR, Hsiao CL, Norris AM, Kovacs NA, Waterbury CC, Stepanov VG, Harvey SC, Fox GE, Wartell RM et al (2014) Evolution of the ribosome at atomic resolution. Proc Natl Acad Sci U S A 111:10251–10256

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Pitsch S, Wendeborn S, Jaun B, Eschenmoser A (1993) Why pentose- and not hexose-nucleic acids? Part VII. Pyranosyl-RNA(‘p-RNA’). Helv Chim Acta 76:2161–2183

    Article  CAS  Google Scholar 

  • Pongs O, Ts’o POP (1971) Polymerization of unprotected 2′-deoxyribonucleoside 5′-phosphates at elevated temperature. J Am Chem Soc 93:5241–5250

    Article  PubMed  CAS  Google Scholar 

  • Powner MW, Gerland B, Sutherland JD (2009) Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature 459:239–242

    Article  PubMed  CAS  Google Scholar 

  • Powner MW, Sutherland JD, Szostak JW (2011) The origins of nucleotides. Synlett 14:1956–1964

    Article  CAS  Google Scholar 

  • Prins LJ, Reinhoudt DN, Timmerman P (2001) Noncovalent synthesis using hydrogen bonding. Angew Chem Int Ed 40:2382–2426

    Article  CAS  Google Scholar 

  • Rajamani S, Vlassov A, Benner S, Coombs A, Olasagasti F, Deamer D (2008) Lipid-assisted synthesis of RNA-like polymers from mononucleotides. Orig Life Evol Biosph 38:57–74

    Article  PubMed  CAS  Google Scholar 

  • Rakotondradany F, Palmer A, Toader V, Chen BZ, Whitehead MA, Sleiman HF (2005) Hydrogen-bond self-assembly of DNA-analogues into hexameric rosettes. Chem Comm:5441–5443

    Google Scholar 

  • Rhodes D, Lipps HJ (2015) G-quadruplexes and their regulatory roles in biology. Nucleic Acids Res 43:8627–8637

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ricardo A, Carrigan MA, Olcott AN, Benner SA (2004) Borate minerals stabilize ribose. Science 303:196–196

    Article  PubMed  CAS  Google Scholar 

  • Rich A (1962) In: Kasha M, Pullmann B (eds) Horizons in biochemistry. Academic Press, New York, pp 103–126

    Google Scholar 

  • Roberts C, Chaput JC, Switzer C (1997) Beyond guanine quartets: cation-induced formation of homogenous and chimeric DNA tetraplexes incorporating iso-guanine and guanine. Chem Biol 4:899–908

    Article  PubMed  CAS  Google Scholar 

  • Robertson MP, Miller SL (1995) An efficient prebiotic synthesis of cytosine and uracil (vol 375, pg 772, 1995). Nature 377:257–257

    Article  CAS  Google Scholar 

  • Rode BM (1999) Peptide and the origin of life. Peptides 20:773–786

    Article  PubMed  CAS  Google Scholar 

  • Sagi VN, Punna V, Hu F, Meher G, Krishnamurthy R (2012) Exploratory experiments on the chemistry of the “glyoxylate scenario”: Formation of ketosugars from dihydroxyfumarate. J Am Chem Soc 134:3577–3589

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Saladino R, Crestini C, Costanzo G, Negri R, DiMauro E (2001) A possible prebiotic synthesis of purine, adenine, cytosine, and 4(3H)-pyrimidinone from formamide: implications for the origin of life. Bioorgan Med Chem 9:1249–1253

    Article  CAS  Google Scholar 

  • Saladino R, Crestini C, Costanzo G, DiMauro E (2004) Advances in the prebiotic synthesis of nucleic acids bases: implications for the origin of life. Curr Org Chem 8:1425–1443

    Article  CAS  Google Scholar 

  • Saladino R, Šponer JE, Šponer J, Di Mauro E (2018) Rewarming the primordial soup: revisitations and rediscoveries in prebiotic chemistry. Chembiochem 19(1):22–25

    Article  PubMed  CAS  Google Scholar 

  • Sanchez RA, Orgel LE (1970) Studies in prebiotic synthesis. V. Synthesis and photoanomerization of pyrimidine nucleosides. J Mol Biol 47:531–543

    Article  PubMed  CAS  Google Scholar 

  • Sanchez RA, Ferris JP, Orgel LE (1968) Studies in prebiotic synthesis. 4. Conversion of 4-aminoimidazole-5-carbonitrile derivatives to purines. J Mol Biol 38:121–128

    Article  PubMed  CAS  Google Scholar 

  • Schöning KU, Scholz P, Guntha S, Wu X, Krishnamurthy R, Eschenmoser A (2000) Chemical etiology of nucleic acid structure: the alpha-threofuranosyl-(3′->2′) oligonucleotide system. Science 290:1347–1351

    Article  PubMed  Google Scholar 

  • Schwartz AW (1997) Speculation on the RNA precursor problem. J Theor Biol 187:523–527

    Article  PubMed  CAS  Google Scholar 

  • Schwartz AW (2006) Phosphorus in prebiotic chemistry. Philos Trans R Soc Lond B:1743–1749

    Google Scholar 

  • Seto CT, Whitesides GM (1990) Self-assembly based on the cyanuric acid melamine lattice. J Am Chem Soc 112:6409–6411

    Article  CAS  Google Scholar 

  • Shapiro R (1988) Prebiotic ribose synthesis: a critical analysis. Orig Life Evol Biosph 18:71–85

    Article  PubMed  CAS  Google Scholar 

  • Shapiro R (1999) Prebiotic cytosine synthesis: a critical analysis and implications for the origin of life. Proc Natl Acad Sci U S A 96:4396–4401

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sheng Y, Bean HD, Mamajanova I, Hud NV, Leszczynski J (2009) A comprehensive investigation of the energetics of pyrimidine nucleoside formation in a model prebiotic reaction. J Am Chem Soc 131:16088–16095

    Article  PubMed  CAS  Google Scholar 

  • Sheng J, Li L, Engelhart AE, Gan JH, Wang JW, Szostak JW (2014) Structural insights into the effects of 2′-5′ linkages on the RNA duplex. Proc Natl Acad Sci U S A 111:3050–3055

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Shubin N (2008) Your inner fish: a journey into the 3.5-billion-year history of the human body. Pantheon, New York

    Google Scholar 

  • Stoks PG, Schwartz AW (1979) Uracil in carbonaceous meteorites. Nature 282:709–710

    Article  CAS  Google Scholar 

  • Strecker A (1850) Ueber die künstliche Bildung der Milchsäure und einen neuen, dem Glycocoll homologen Körper. Justus Liebigs Ann Chem 75:27–45

    Article  Google Scholar 

  • Sun ZH, Chen DL, Lan T, McLaughlin LW (2002) Importance of minor groove functional groups for the stability of DNA duplexes. Biopolymers 65:211–217

    Article  PubMed  CAS  Google Scholar 

  • Watson JD, Crick FHC (1953) Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature 171:737–738

    Article  PubMed  CAS  Google Scholar 

  • Weber AL (1992) Prebiotic sugar synthesis: hexose and hydroxy acid synthesis from glyceraldehyde catalyzed by iron(III) hydroxide oxide. J Mol Evol 35:1–6

    Article  PubMed  CAS  Google Scholar 

  • Westheimer FH (1987) Why nature chose phosphates. Science 235:1173–1178

    Article  PubMed  CAS  Google Scholar 

  • Wimberly BT, Brodersen DE, Clemons WM, Morgan-Warren RJ, Carter AP, Vonrhein C, Hartsch T, Ramakrishnan V (2000) Structure of the 30S ribosomal subunit. Nature 407:327–339

    Article  PubMed  CAS  Google Scholar 

  • Woese C (1967) The genetic code. Harper & Row, New York, pp 179–195

    Google Scholar 

  • Wulff G, Clarkson G (1994) On the synthesis of C-glycosyl compounds containing double-bonds without the use of protecting groups. Carbohydr Res 257:81–95

    Article  CAS  Google Scholar 

  • Yang Y-W, Zhang S, McCullum EO, Chaput JC (2007) Experimental evidence that GNA and TNA were not sequential polymers in the prebiotic evolution of RNA. J Mol Evol 65:289–295

    Article  PubMed  CAS  Google Scholar 

  • Yu Y, Nakamura D, DeBoyace K, Neisius AW, McGown LB (2008) Tunable thermoassociation of binary guanosine gels. J Phys Chem B 112:1130–1134

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

We thank Profs. Frank A. L. Anet, Ram Krishnamurthy, Gary B. Schuster, and Loren Dean Williams, who have been valuable collaborators and consultants on much of the work described in this chapter from our laboratory. This work was supported by the NSF and the NASA Astrobiology Program, under the NSF Center for Chemical Evolution (CHE-1504217) and the NASA Exobiology Program NNX13AI02G.

Author information

Authors and Affiliations

  1. School of Chemistry and Biochemistry, NSF-NASA Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, GA, USA

    Brian J. Cafferty, David M. Fialho & Nicholas V. Hud

Authors
  1. Brian J. Cafferty
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. David M. Fialho
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Nicholas V. Hud
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Nicholas V. Hud .

Editor information

Editors and Affiliations

  1. NSF-NASA Center for Chemical Evolution, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA; Unidad de Bioquímica y Biología Molecular, Dept. Biologia de Sistemas, Universidad de Alcala, Madrid, Spain

    César Menor-Salván

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer International Publishing AG, part of Springer Nature

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Cafferty, B.J., Fialho, D.M., Hud, N.V. (2018). Searching for Possible Ancestors of RNA: The Self-Assembly Hypothesis for the Origin of Proto-RNA. In: Menor-Salván , C. (eds) Prebiotic Chemistry and Chemical Evolution of Nucleic Acids. Nucleic Acids and Molecular Biology, vol 35. Springer, Cham. https://doi.org/10.1007/978-3-319-93584-3_5

Download citation

Publish with us

Policies and ethics

Search

Navigation