Four Ways to Oligonucleotides Without Phosphoimidazolides

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• 作者：Judit E. Šponer ; Jiří Šponer ; Ernesto Di Mauro
• 关键词：RNA ; Polymerization ; Origin of life ; Oligonucleotides
• 刊名：Journal of Molecular Evolution
• 出版年：2016
• 出版时间：January 2016
• 年：2016
• 卷：82
• 期：1
• 页码：5-10
• 全文大小：411 KB
• 参考文献：Allen F (2002) The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Crystallogr Sect B Struct Sci Cryst Eng Mat 58:380–388CrossRef
  Barone V, Cossi M (1998) Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model. J Phys Chem A 102:1995–2001CrossRef
  Beaucage SL, Caruthers MH (1981) Deoxynucleoside phosphoramidites—a new class of key intermediates for deoxypolynucleotide synthesis. Tetrahedron Lett 22:1859–1862CrossRef
  Chwang AK, Sundaralingam M (1974) The crystal and molecular structure of guanosine 3′,5′-cyclic monophosphate (cyclic GMP) sodium tetrahydrate. Acta Crystallogr B 30:1233–1240CrossRef
  Cossi M, Rega N, Scalmani G, Barone V (2003) Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model. J Comput Chem 24:669–681PubMed CrossRef
  Costanzo G, Pino S, Ciciriello F, Di Mauro E (2009) Generation of long RNA chains in water. J Biol Chem 284:33206–33216PubMed PubMedCentral CrossRef
  Costanzo G, Saladino R, Botta G, Giorgi A, Scipioni A, Pino S, Di Mauro E (2012) Generation of RNA molecules by a base-catalysed click-like reaction. ChemBioChem 13:999–1008PubMed CrossRef
  Da Silva L, Maurel MC, Deamer D (2015) Salt-promoted synthesis of RNA-like molecules in simulated hydrothermal conditions. J Mol Evol 80:86–97PubMed CrossRef
  DeGuzman V, Vercoutere W, Shenasa H, Deamer D (2014) Generation of oligonucleotides under hydrothermal conditions by non-enzymatic polymerization. J Mol Evol 78:251–262PubMed CrossRef
  Hill A Jr, Orgel L, Wu T (1993) The limits of template-directed synthesis with nucleoside-5′-phosphoro(2-methyl)imidazolides. Orig Life Evol Biosph 23:285–290PubMed CrossRef
  Jauker M, Griesser H, Richert C (2015) Spontaneous formation of RNA strands, peptidyl RNA, and cofactors. Angew Chem Int Ed. doi:10.​1002/​anie.​201506593
  Kraut J, Jensen LH (1963) Refinement of the crystal structure of adenosine-5′-phosphate. Acta Crystallogr 16:79–88CrossRef
  Liu Y, Gregersen BA, Lopez X, York DM (2005) Density functional study of the in-line mechanism of methanolysis of cyclic phosphate and thiophosphate esters in solution: insight into thio effects in RNA transesterification. J Phys Chem B 109:19987–20003PubMed CrossRef
  Morasch M, Mast CB, Langer JK, Schilcher P, Braun D (2014) Dry polymerization of 3′,5′-cyclic GMP to long strands of RNA. ChemBioChem 15:879–883PubMed CrossRef
  Parker ET et al (2011) Primordial synthesis of amines and amino acids in a 1958 Miller H2S-rich spark discharge experiment. Proc Natl Acad Sci USA 108:5526–5531PubMed PubMedCentral CrossRef
  Pearlman DA, Kim S-H (1985) Determinations of atomic partial charges for nucleic acid constituents from x-ray diffraction data. I. 2′-Deoxycytidine-5′-monophosphate. Biopolymers 24:327–357PubMed CrossRef
  Perras FA, Korobkov I, Bryce DL (2012) 23Na double-rotation NMR of sodium nucleotides leads to the discovery of a new dCMP hendecahydrate. Phys Chem Chem Phys 14:4677–4681PubMed CrossRef
  Powner MW, Gerland B, Sutherland JD (2009) Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature 459:239–242PubMed CrossRef
  Powner MW, Sutherland JD, Szostak JW (2011) The origins of nucleotides. Synlett 22:1956–1964CrossRef
  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 38:57–74PubMed CrossRef
  Saladino R, Botta G, Pino S, Costanzo G, Di Mauro E (2012a) From the one-carbon amide formamide to RNA all the steps are prebiotically possible. Biochimie 94:1451–1456PubMed CrossRef
  Saladino R, Botta G, Pino S, Costanzo G, Di Mauro E (2012b) Genetics first or metabolism first? The formamide clue. Chem Soc Rev 41:5526–5565PubMed CrossRef
  Schrum JP, Ricardo A, Krishnamurthy M, Blain JC, Szostak JW (2009) Efficient and rapid template-directed nucleic acid copying using 2′-amino-2′,3′-dideoxyribonucleoside−5′-phosphorimidazolide monomers. J Am Chem Soc 131:14560–14570PubMed PubMedCentral CrossRef
  Silverton JV, Limn W, Miles HT (1982) 2-Amino-8-methyladenosine 5′-monophosphate dihydrate. A nucleotide with syn C4′-exo conformation and “triple-stranded” packing. J Am Chem Soc 104:1081–1087CrossRef
  Sponer JE, Sponer J, Giorgi A, Di Mauro E, Pino S, Costanzo G (2015) Untemplated nonenzymatic polymerization of 3′,5′cGMP: a plausible route to 3′,5′-linked oligonucleotides in primordia. J Phys Chem B 119:2979–2989PubMed CrossRef
  Sundaralingam M (1966) Stereochemistry of nucleic acid constituents. III. Crystal and molecular structure of adenosine 3′-phosphate dihydrate (adenylic acid b). Acta Crystallogr 21:495–506PubMed CrossRef
  Sundaralingam M, Prusiner P (1978) Zwitterionic character of nucleotides: possible significance in the evolution of nucleic acids. Nucleic Acids Res 5:4375–4383PubMed PubMedCentral CrossRef
  Szostak J (2012) The eightfold path to non-enzymatic RNA replication. J Syst Chem 3:2CrossRef
  Usher DA, Yee D (1979) Geometry of the dry-state oligomerization of 2′,3′-cyclic phosphates. J Mol Evol 13:287–293PubMed CrossRef
  Verlander MS, Lohrmann R, Orgel LE (1973) Catalysts for self-polymerization of adenosine cyclic 2′,3′-phosphate. J Mol Evol 2:303–316PubMed CrossRef
  von Kiedrowski G, Wlotzka B, Helbing J, Matzen M, Jordan S (1991) Parabolic growth of a self-replicating hexadeoxynucleotide bearing a 3′,5′-phosphoamidate linkage. Angew Chem Int Ed 30:423–426CrossRef
  Zielinski WS, Orgel LE (1987) Autocatalytic synthesis of a tetranucleotide analog. Nature 327:346–347PubMed CrossRef
  
• 作者单位：Judit E. Šponer (1) (2)
  Jiří Šponer (1) (2)
  Ernesto Di Mauro (3)
  
  1. Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265, Brno, Czech Republic
  2. CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 62500, Brno, Czech Republic
  3. Dipartimento di Biologia e Biotecnologie “Charles Darwin”, “Sapienza” Università di Roma, Piazzale Aldo Moro, 5, 00185, Rome, Italy
  
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Life Sciences
  Cell Biology
  Microbiology
  Plant Sciences
  
• 出版者：Springer New York
• ISSN：1432-1432

文摘

Emergence of the very first RNA or RNA-like oligomers from simple nucleotide precursors is one of the most intriguing questions of the origin of life research. In the current paper, we analyse the mechanism of four non-enzymatic template-free scenarios suggested for the oligomerization of chemically non-modified cyclic and acyclic nucleotides in the literature. We show that amines may have a twofold role in these syntheses: due to their high affinity to bind protons they may activate the phosphorus of the phosphate group via proton transfer reactions, or indirectly they may serve as charge compensating species and influence the self-assembling of nucleotides to supramolecular architectures compatible with the oligomerization reactions. Effect of cations and pH on the reactions is also discussed. Keywords RNA Polymerization Origin of life Oligonucleotides