Questions and Answers Related to the Prebiotic Production of Oligonucleotide Sequences from 3',5' Cyclic Nucleotide Precursors

. 2021 Aug 08 ; 11 (8) : . [epub] 20210808

Status PubMed-not-MEDLINE Jazyk angličtina Země Švýcarsko Médium electronic

Typ dokumentu časopisecké články, přehledy

Perzistentní odkaz   https://www.medvik.cz/link/pmid34440544

Grantová podpora
CZ.02.1.01/0.0/0.0/ 15_003/0000477 European Regional Development Fund

Template-free nonenzymatic polymerization of 3',5' cyclic nucleotides is an emerging topic of the origin of life research. In the last ten years, a number of papers have been published addressing various aspects of this process. These works evoked a vivid discussion among scientists working in the field of prebiotic chemistry. The aim of the current review is to answer the most frequently raised questions related to the detection and characterization of oligomeric products as well as to the geological context of this chemistry.

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Verlander M.S., Lohrmann R., Orgel L.E. Catalysts for self-polymerization of adenosine cyclic 2', 3'-phosphate. J. Mol. Evol. 1973;2:303–316. doi: 10.1007/BF01654098. PubMed DOI

Usher D.A., Yee D. Geometry of the dry-state oligomerization of 2',3'-cyclic phosphates. J. Mol. Evol. 1979;13:287–293. doi: 10.1007/BF01731369. PubMed DOI

Tapiero C.M., Nagyvary J. Prebiotic formation of cytidine nucleotides. Nature. 1971;231:42–43. doi: 10.1038/231042a0. PubMed DOI

Morávek J., Kopecký J., Škoda J. Thermic phosphorylations. 6. Formation of oligonucleotides from uridine 2'(3')-phosphate. Collect. Czech. Chem. Commun. 1968;33:4120–4124. doi: 10.1135/cccc19684120. DOI

Powner M.W., Gerland B., Sutherland J.D. Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature. 2009;459:239–242. doi: 10.1038/nature08013. PubMed DOI

Powner M.W., Sutherland J.D., Szostak J.W. Chemoselective multicomponent one-pot assembly of purine precursors in water. J. Am. Chem. Soc. 2010;132:16677–16688. doi: 10.1021/ja108197s. PubMed DOI PMC

Costanzo G., Saladino R., Crestini C., Ciciriello F., Di Mauro E. Nucleoside phosphorylation by phosphate minerals. J. Biol. Chem. 2007;282:16729–16735. doi: 10.1074/jbc.M611346200. PubMed DOI

Crowe M.A., Sutherland J.D. Reaction of cytidine nucleotides with cyanoacetylene: Support for the intermediacy of nucleoside-2 ',3 '-cyclic phosphates in the prebiotic synthesis of RNA. Chembiochem. 2006;7:951–956. doi: 10.1002/cbic.200600024. PubMed DOI

Shabarova Z., Bogdanov A. Advanced Organic Chemistry of Nucleic Acids. VCH Verlagsgesellshaft mbH; Weinheim, Germany: 1994.

Mulkidjanian A.Y., Bychkov A.Y., Dibrova D.V., Galperin M.Y., Koonin E.V. Origin of first cells at terrestrial, anoxic geothermal fields. Proc. Natl. Acad. Sci. USA. 2012;109:E821–E830. doi: 10.1073/pnas.1117774109. PubMed DOI PMC

Kompanichenko V.N. Exploring the Kamchatka geothermal region in the context of life's beginning. Life. 2019;9:41. doi: 10.3390/life9020041. PubMed DOI PMC

Newton A.C., Bootman M.D., Scott J.D. Second messengers. Cold Spring Harb. Perspect. Biol. 2016;8:a005926. doi: 10.1101/cshperspect.a005926. PubMed DOI PMC

Costanzo G., Pino S., Ciciriello F., Di Mauro E. Generation of long RNA chains in water. J. Biol. Chem. 2009;284:33206–33216. doi: 10.1074/jbc.M109.041905. PubMed DOI PMC

Costanzo G., Saladino R., Botta G., Giorgi A., Scipioni A., Pino S., Di Mauro E. Generation of RNA molecules by a base-catalysed click-like reaction. ChemBioChem. 2012;13:999–1008. doi: 10.1002/cbic.201200068. PubMed DOI

Morasch M., Mast C.B., Langer J.K., Schilcher P., Braun D. Dry polymerization of 3′,5′-cyclic GMP to long strands of RNA. ChemBioChem. 2014;15:879–883. doi: 10.1002/cbic.201300773. PubMed DOI

Šponer J.E., Šponer J., Giorgi A., Di Mauro E., Pino S., Costanzo G. Untemplated nonenzymatic polymerization of 3′,5′ cGMP: A plausible route to 3′,5′-linked oligonucleotides in primordia. J. Phys. Chem. B. 2015;119:2979–2989. doi: 10.1021/acs.jpcb.5b00601. PubMed DOI

Costanzo G., Šponer J.E., Šponer J., Cirigliano A., Benedetti P., Giliberti V., Polito R., Di Mauro E. Sustainability and chaos in the abiotic polymerization of 3′,5′ cyclic guanosine monophosphate: The role of aggregation. ChemSystemsChem. 2021;3:e2000056. doi: 10.1002/syst.202000011. DOI

Šponer J.E., Šponer J., Výravský J., Šedo O., Zdráhal Z., Costanzo G., Di Mauro E., Wunnava S., Braun D., Matyášek R., et al. Non-enzymatic, template-free polymerization of 3′,5′ cyclic guanosine monophosphate on mineral surfaces. [(accessed on 4 August 2021)];ChemSystemsChem. 2021 doi: 10.1002/syst.202100017. Available online: https://chemistry-europe.onlinelibrary.wiley.com/doi/full/10.1002/syst.202100017. DOI

Dorr M., Loffler P.M.G.L., Monnard P.A. Non-enzymatic polymerization of nucleic acids from monomers: Monomer self- condensation and template-directed reactions. Curr. Org. Synth. 2012;9:735–763. doi: 10.2174/157017912803901691. DOI

Eschenmoser A. Question 1: Commentary referring to the statement “The origin of life can be traced back to the origin of kinetic control” and the question “Do you agree with this statement; and how would you envisage the prebiotic evolutionary bridge between thermodynamic and kinetic control?” stated in section 1.1. Orig. Life Evol. Biosph. 2007;37:309–314. PubMed

Smith M., Drummond G.I., Khorana H.G. Cyclic phosphates. IV.1 Ribonucleoside-3′,5′ cyclic phosphates. A general method of synthesis and some properties. J. Am. Chem. Soc. 1961;83:698–706. doi: 10.1021/ja01464a039. DOI

Saladino R., Botta G., Delfino M., Di Mauro E. Meteorites as catalysts for prebiotic chemistry. Chem.-Eur. J. 2013;19:16916–16922. doi: 10.1002/chem.201303690. PubMed DOI

Iwasaki Y., Yamaguchi E. Synthesis of well-defined thermoresponsive polyphosphoester macroinitiators using organocatalysts. Macromolecules. 2010;43:2664–2666. doi: 10.1021/ma100242s. DOI

Steinbach T., Ritz S., Wurm F.R. Water-soluble poly(phosphonate)s via living ring-opening polymerization. ACS Macro Lett. 2014;3:244–248. doi: 10.1021/mz500016h. PubMed DOI

Wunnava S., Dirscherl C.F., Výravský J., Kovařík A., Matyášek R., Šponer J., Braun D., Šponer J.E. Acid-catalyzed RNA-oligomerization from 3,5-cGMP at an air-water interface. Chem. Eur. J. 2021 in press. PubMed PMC

Reineke K., Mathys A., Knorr D. Shift of pH-value during thermal treatments in buffer solutions and selected foods. Int. J. Food Prop. 2011;14:870–881. doi: 10.1080/10942910903456978. DOI

Carey F.A., Sundberg R.J. Advanced Organic Chemistry. Part A: Structure and Mechanism. Springer Science+Business Media, LLC; New York, NY, USA: 2007. p. 325.

Chwang A.K., Sundaralingam M. The crystal and molecular structure of guanosine 3′,5′-cyclic monophosphate (cyclic GMP) sodium tetrahydrate. Acta Crystallogr. B. 1974;30:1233–1240. doi: 10.1107/S0567740874004602. DOI

Varughese K.I., Lu C.T., Kartha G. Crystal and molecular structure of cyclic adenosine 3′,5′-monophosphate sodium salt, monoclinic form. J. Am. Chem. Soc. 1982;104:3398–3401. doi: 10.1021/ja00376a026. DOI

Scognamiglio P.L., Platella C., Napolitano E., Musumeci D., Roviello G.N. From prebiotic chemistry to supramolecular biomedical materials: Exploring the properties of self-assembling nucleobase-containing peptides. Molecules. 2021;26:3558. doi: 10.3390/molecules26123558. PubMed DOI PMC

Slepokura K. Purine 3′:5′-cyclic nucleotides with the nucleobase in a syn orientation: cAMP, cGMP and cIMP. Acta Crystallogr. C. 2016;72:465–479. doi: 10.1107/S2053229616006999. PubMed DOI

Costanzo G., Pino S., Timperio A.M., Šponer J.E., Šponer J., Nováková O., Šedo O., Zdráhal Z., Di Mauro E. Non-enzymatic oligomerization of 3′,5′ cyclic AMP. PLoS ONE. 2016;11:e0165723. doi: 10.1371/journal.pone.0165723. PubMed DOI PMC

Burcar B.T., Cassidy L.M., Moriarty E.M., Joshi P.C., Coari K.M., McGown L.B. Potential pitfalls in MALDI-TOF MS analysis of abiotically synthesized RNA oligonucleotides. Orig. Life Evol. Biosph. 2013;43:247–261. doi: 10.1007/s11084-013-9334-5. PubMed DOI

Costanzo G., Giorgi A., Scipioni A., Timperio A.M., Mancone C., Tripodi M., Kapralov M., Krasavin E., Kruse H., Šponer J., et al. Nonenzymatic oligomerization of 3′,5′-cyclic CMP induced by proton and UV irradiation hints at a nonfastidious origin of RNA. ChemBioChem. 2017;18:1535–1543. doi: 10.1002/cbic.201700122. PubMed DOI

Šponer J.E., Šponer J., Nováková O., Brabec V., Šedo O., Zdráhal Z., Costanzo G., Pino S., Saladino R., Di Mauro E. Emergence of the first catalytic oligonucleotides in a formamide-based origin scenario. Chem.-Eur. J. 2016;22:3572–3586. doi: 10.1002/chem.201503906. PubMed DOI

Hazen R.M. Paleomineralogy of the Hadean eon: A preliminary species list. Am. J. Sci. 2013;313:807–843. doi: 10.2475/09.2013.01. DOI

Kunkel T.A. Mutational specificity of depurination. Proc. Natl. Acad. Sci. USA. 1984;81:1494–1498. doi: 10.1073/pnas.81.5.1494. PubMed DOI PMC

Mungi C.V., Bapat N.V., Hongo Y., Rajamani S. Formation of abasic oligomers in nonenzymatic polymerization of canonical nucleotides. Life. 2019;9:57. doi: 10.3390/life9030057. PubMed DOI PMC

Whicher A., Camprubi E., Pinna S., Herschy B., Lane N. Acetyl phosphate as a primordial energy currency at the origin of life. Orig. Life Evol. Biosph. 2018;48:159–179. doi: 10.1007/s11084-018-9555-8. PubMed DOI PMC

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