Shin Miyakawa

Rensselaer Polytechnic Institute, Troy, New York, United States

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Publications (20)40.07 Total impact

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    ABSTRACT: Activated mononucleotides oligomerize in the presence of montmorillonite clay to form RNA oligomers. In the present study, effects of salts, temperature and pH on the clay-catalyzed synthesis of RNA oligomers were investigated. This reaction is favored by relatively high concentration of salts, such as 1 M NaCl. It was shown that the presence of divalent cations was not required for this reaction. High concentrations of NH4+ and HCO3- and 0.01 M HPO4(2-) inhibit the reaction. The yields of RNA oligomers decreased as the temperature was raised from 4 degrees C to 50 degrees C. A5' ppA was the major product at pH's below 6. The catalytic activity of a variety of minerals and three meteorites were investigated but none of them except galena catalyzed the oligomerization. ATP was generated from ADP but it was due to the presence of HEPES buffer and not due to the minerals. Meteorites catalyzed the hydrolysis of the pyrophosphate bonds of ATP. The results suggest that oligomers of RNA could have formed in pH 7-9 solutions of alkali metal salts in the presence of montmorillonite clay.
    Origins of Life and Evolution of Biospheres 09/2006; 36(4):343-61. · 1.83 Impact Factor
  • J. P. Ferris, S. Miyakawa, W. Huang, P. Joshi
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    ABSTRACT: It is proposed that catalysis had a central role in the origins of life. This will be illustrated using the montmorillonite clay-catalyzed synthesis of oligomers of RNA from activated monomers, (Ferris and Ertem, 1993) a possible step in the origin of the RNA world (Ferris, 2005). Structural analysis of oligomers formed in the reaction of the activated monomer of 5'-AMP with that of 5'-CMP demonstrated that the oligomers formed were not produced by random synthesis but rather the sequences observed were directed by the montmorillonite catalyst (Miyakawa and Ferris, 2003). RNA oligomers containing up to 40 mers have been synthesized in reactions performed in water at 25 oC in the presence of montmorillonite (Huang and Ferris, 2003). Analysis of the structure elements in these oligomers from the 7 to 39 mers showed that they did not vary. Reaction of D, L-mixtures of the activated monomers of A and U resulted in the formation of greater amounts of the homochiral amounts of dimers and trimers of A than would be expected if there was no selectivity in the reaction. A limited number of the dimers and trimers of U were also formed but here the selectivity was for the formation of an excess of heterochiral products (Joshi et al., 2000). A postulate that explains why homochiral trimers of U are not formed and the significance of catalysis in prebiotic synthesis will be discussed. Ferris, J.P. (2005) Origins of life, molecular basis of. In R.A. Meyers, Ed. Encyclopedia of Molecular Cell Biology and Molecular Medicine, 10. Wiley-VCH Verlag, Weinheim, Germany. Ferris, J.P., and Ertem, G. (1993) Montmorillonite catalysis of RNA oligomer formation in aqueous solution. A model for the prebiotic formation of RNA. J. Am. Chem. Soc., 115, 12270-12275. Huang, W., and Ferris, J.P. (2003) Synthesis of 35-40 mers of RNA oligomers from unblocked monomers. A simple approach to the RNA world. Chem. Commun., 1458-1459. Joshi, P.C., Pitsch, S., and Ferris, J.P. (2000) Homochiral selection in the montmorillonite-catalyzed and uncatalyzed prebiotic synthesis of RNA. Chem. Commun., 2497-2498. Miyakawa, S., and Ferris, J.P. (2003) Sequence- and Regioselectivity in the montmorillonite-catalyzed synthesis of RNA. J. Am. Chem. Soc., 125, 8202-8208.
    AGU Fall Meeting Abstracts. 12/2005;
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    ABSTRACT: The role of catalysis in prebiotic synthesis is illustrated using the montmorillonite clay catalyzed synthesis of RNA oligomers. Reaction of activated monomers of nucleotides in pH 8 aqueous solution containing Mg2+ in the presence of montmorillonite yields 6–14 mers. The reaction takes place at the clay interlayer. The catalyst controls the synthesis of RNA oligomers in that a limited number of sequences are formed, there is control on the selectivity of phosphodiester bond formation and there is homochiral selectivity. Oligomers of length greater than 40 mers can be formed in reactions where the activated monomer is added daily to a primer. The need for catalysis in prebiotic synthesis is discussed.
    Advances in Space Research 01/2004; · 1.18 Impact Factor
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    ABSTRACT: Gas mixtures of methane and nitrogen were subjected to proton irradiation (PI), gamma irradiation (GI), UV irradiation (UV) or spark discharges (SD), and the products were analyzed to compare possible energy sources for synthesis of organics in Titan. SD mainly gave unsaturated hydrocarbons, while PI gave saturated hydrocarbons. N-containing organics were detected in PI, GI and SD, but not in UV. The formers yielded amino acids after acid-hydrolysis of solid phase products (tholin). Comparison of the present results with those by Cassini-Huygens [correction of Heygens] mission will make it possible to prove major energy sources for organic synthesis in Titan atmosphere.
    Biological Sciences in Space 11/2003; 17(3):188-9.
  • Geochmica et Cosmochimica Acta 09/2003; 67(18).
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    Shin Miyakawa, James P Ferris
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    ABSTRACT: The possible role of catalysis in forming a limited number of RNAs from activated monomers is investigated by examining the sequence- and regioselectivity in the montmorillonite-catalyzed formation of RNA dimers and trimers. The reactivity of A was similar to that of G, and C was comparable in reactivity to U. Yet the reactivity of the purine nucleotides differed from that of the pyrimidines. In the reaction of nucleotides (pN) with activated monomers (ImpN), the sequence- and regioselectivity was Pu(3')Py > Pu(3')Pu = Pu(2')Py > Pu(2')Pu. The 5'-pyrimidine initiated dimers formed less efficiently than the 5'-purine initiated dimers. Trimer formation was investigated by the synthesis of 8 dimers (pNpN) and measuring the yields of trimers formed in the reaction of each dimer with a mixture of equal molar amounts of four activated monomers. The reactivity of the dimers depended on the nucleotide attached to the 3'-end of the RNA and the regiochemistry of the phosphodiester bond. Rules based on these studies are proposed to predict the sequence- and regioselectivity of the RNAs formed in montmorillonite-catalyzed reactions. These rules are consistent with the structures of the 2-5-mers formed in the reaction of equimolar amounts of ImpA and ImpC. This research establishes that the montmorillonite catalyst limits the number of RNA oligomer isomers formed. The potential significance of these findings to the origins of life is discussed.
    Journal of the American Chemical Society 07/2003; 125(27):8202-8. · 10.68 Impact Factor
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    ABSTRACT: Most models of the primitive atmosphere around the time life originated suggest that the atmosphere was dominated by carbon dioxide, largely based on the notion that the atmosphere was derived via volcanic outgassing, and that those gases were similar to those found in modern volcanic effluent. These models tend to downplay the possibility of a strongly reducing atmosphere, which had been thought to be important for prebiotic synthesis and thus the origin of life. However, there is no definitive geologic evidence for the oxidation state of the early atmosphere and bioorganic compounds are not efficiently synthesized from CO(2) atmospheres. In the present study, it was shown that a CO-CO(2)-N(2)-H(2)O atmosphere can give a variety of bioorganic compounds with yields comparable to those obtained from a strongly reducing atmosphere. Atmospheres containing carbon monoxide might therefore have been conducive to prebiotic synthesis and perhaps the origin of life. CO-dominant atmospheres could have existed if the production rate of CO from impacts of extraterrestrial materials were high or if the upper mantle had been more reduced than today.
    Proceedings of the National Academy of Sciences 12/2002; 99(23):14628-31. · 9.74 Impact Factor
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    ABSTRACT: It has been suggested that hydrogen cyanide (HCN) would not have been present in sufficient concentration to polymerize in the primitive ocean to produce nucleic acid bases and amino acids. We have measured the hydrolysis rates of HCN and formamide over the range of 30-150 degrees C and pH 0-14, and estimated the steady state concentrations in the primitive ocean. At 100 degrees C and pH 8, the steady state concentration of HCN and formamide were calculated to be 7 x 10(-13) M and 1 x 10(-15) M, respectively. Thus, it seems unlikely that HCN could have polymerized in a warm primitive ocean. It is suggested that eutectic freezing might have been required to have concentrated HCN sufficiantly for it to polymerize. If the HCN polymerization was important for the origin of life, some regions of the primitive earth might have been frozen.
    Origins of Life and Evolution of Biospheres 07/2002; 32(3):195-208. · 1.83 Impact Factor
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    ABSTRACT: A wide variety of pyrimidines and purines were identified as products of a dilute frozen ammonium cyanide solution that had been held at -78 degrees C for 27 years. This demonstrates that both pyrimidines and purines could have been produced on the primitive earth in a short time by eutectic concentration of HCN, even though the concentration of HCN in the primitive ocean may have been low. We suggest that eutectic freezing is the most plausible demonstrated mechanism by which HCN polymerizations could have produced biologically important prebiotic compounds.
    Origins of Life and Evolution of Biospheres 07/2002; 32(3):209-18. · 1.83 Impact Factor
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    ABSTRACT: The origin of guanine has been unknown, though there are some reports concerning its abiotic synthesis. We show here that guanine, as well as uracil and cytosine, are synthesized from a 90%N2-10%CO-H2O gas mixture via a complex organic product produced with the high-temperature and rapid quenching technique. This result implies that a large amount of complex organic matter including precursors of bioorganic compounds might have been produced on the primitive earth after cometary impacts.
    Origins of Life and Evolution of Biospheres 01/2001; 30(6):557-66. · 1.83 Impact Factor
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    ABSTRACT: Cytosine and uracil, which are components of RNA molecules, were obtained from complex organic matter produced by quenching a CO−N2−H2O high-temperature plasma. The carbon yields of cytosine and uracil were 0.01% and 0.08%, respectively, which were almost as much as those of amino acids. It was understood that processes of high activation and rapid quenching, which may be found in meteoritic impact or lightning, are important for the formation of bioorganic compounds from the CO−N2−H2O gas mixture.
    Journal of The American Chemical Society - J AM CHEM SOC. 08/1999; 121(36).
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    ABSTRACT: Magnetoplasma dynamic arc jet was characterized by optical emission spectroscopy (OES) in order to study the mechanisms of amino acid formation induced by electric discharge. Nitrogen, oxygen, and hydrogen atoms and CN radicals were produced by instantaneously heating a CO–N2–H2O gas mixture to 10 000 K. These plasma species were rapidly cooled to form an amorphous film containing amino acid precursors by directly colliding against a wall of a glass tube. This is a new method of producing amino acid precursors without involving the reaction among hydrogen cyanide (HCN), formaldehyde (H2CO), and ammonia (NH3); HCN, H2CO, and NH3 are generally considered important intermediates in amino acid formation. Spark discharge (SD), which is a typical electric discharge in amino acid synthesis, was also characterized by OES. Only CN radicals were observed in a CO–N2–H2O mixture plasma. These radicals became more stable molecules by colliding against other molecules, and sufficiently cooled molecules were dissolved in water. Although HCN appeared to have been formed by SD, amino acids were not effectively synthesized. Therefore, the high activation and rapid cooling processes should be important for the amino acid formation from a CO–N2–H2O gas mixture. © 1999 American Institute of Physics.
    Journal of Applied Physics 04/1999; 85(9):6853-6857. · 2.21 Impact Factor
  • S Miyakawa, K Kobayashi, A B Sawaoka
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    ABSTRACT: Reaction among hydrogen cyanide (HCN), formaldehyde (H2CO) and ammonia (NH3) are generally considered an important reaction in amino acid synthesis by electric discharge. Precursors of glycine and aspartic acid were, however, synthesized by adding water to metastable complex compounds produced by quenching a CO-N2 high-temperature plasma. In order to investigate effects of water remaining in an experimental vacuum chamber, optical emission spectroscopic and mass spectrometric measurements were conducted with CO-N2 and CO-N2-H2 gas mixtures. Although residual hydrogen atoms were detected in the CO-N2 experiment, the amount of them was much less than that in the CO-N2-H2 experiment.
    Advances in Space Research 02/1999; 24(4):465-8. · 1.18 Impact Factor
  • S. Miyakawa, K. Kobayashi, A. B. Sawaoka
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    ABSTRACT: Reaction among hydrogen cyanide (HCN), formaldehyde (H2CO) and ammonia (NH3) are generally considered an important reaction in amino acid synthesis by electric discharge. Precursors of glycine and aspartic acid were, however, synthesized by adding water to metastable complex compounds produced by quenching a CO-N2 high-temperature plasma. In order to investigate effects of water remaining in an experimental vacuum chamber, optical emission spectroscopic and mass spectrometric measurements were conducted with CO-N2 and CO-N2-H2 gas mixtures. Although residual hydrogen atoms were detected in the CO-N2 experiment, the amount of them was much less than that in the CO-N2-H2 experiment.
    Advances in Space Research - ADV SPACE RES. 01/1999; 24(4):465-468.
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    ABSTRACT: Hydrogen cyanide, formaldehyde, and ammonia are considered important intermediates in amino acid synthesis by electric discharge. In this study, however, amino acid precursors were synthesized from a CO–N <sub> 2 </sub> mixture free of hydrogen atoms. An amorphous film composed of carbon, nitrogen, and oxygen was given from a highly activated plasma. When exposed to atmospheric moisture, this film incorporated hydrogen atoms to yield amino acid. This is a mechanism for amino acid synthesis without involving hydrogen cyanide, formaldehyde, and ammonia. © 1998 American Institute of Physics.
    Applied Physics Letters 03/1998; · 3.79 Impact Factor
  • Japanese Journal of Applied Physics 01/1997; 36:4481-4485. · 1.07 Impact Factor
  • Origins of Life and Evolution of Biospheres 01/1996; 26(3):342-343. · 1.83 Impact Factor
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    ABSTRACT: An electrical column explosion of a copper and graphite powder mixture was investigated and one possible model was established, in which such a powder mixture is anisotropically heated by an electric current due to the difference in resistivities of the constituents. One of the constituents of the powder mixture reaches its boiling point at a shorter time, thus leading to the column explosion.
    Japanese Journal of Applied Physics 01/1995; 34:2004-2005. · 1.07 Impact Factor
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    Shin Miyakawa
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    ABSTRACT: It remains uncertain whether life originated in a hot environment or a cold environment, although many studies have been done from several different perspectives. The theory of the hot origin of life is based on the presence of hyperthermophiles near the root of the phylogenetic tree, the discovery of unique environments for life surrounding hydrothermal vents, the greenhouse effect of a dense CO2 atmosphere, and the isotopic fluctuation of oxygen. However, bioorganic molecules are rather unstable at high temperatures. Here, I review previous studies concerning the hot and cold origins of life and re-assess which is more plausible. (Keyword) hot origins of life, cold origins of life, phylogenetic tree, dense CO2 atmosphere, meteoritic impacts, hydrothermal
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    ABSTRACT: It is proposed that catalysis by minerals and metal ions had a central role in the steps that led to the origins of life. In particular, the formation of biopolymers in the presence of water requires catalysis to compete with hydrolytic processes. Catalysis is required to limit the number of isomers generated so that the longer polymers necessary for the origins of life formed. Montmorillonite clay catalyzes the formation of 6 14 mers of RNA from activated monomers of A, G, U and C in- aqueous solution. Daily addition of activated monomers to a 10 mer primer results in the formation of 40-50 mers of adenylic acid and 30 mers of uridylic acid. The sequence selectivity and regioselectivity in phosphodiester bond formation results from the montmorillonite catalysis. Reaction of D, L-activated monomers of A and U leads to the preferential formation of homochiral dimers (eg. D, D and L, L-- pApA). These data and any more recent developments will be discussed.

Publication Stats

198 Citations
40 Downloads
619 Views
40.07 Total Impact Points

Institutions

  • 2003–2006
    • Rensselaer Polytechnic Institute
      Troy, New York, United States
  • 2001–2002
    • Yokohama National University
      Yokohama, Kanagawa, Japan
  • 1996–1999
    • Tokyo Institute of Technology
      • Materials and Structures Laboratory
      Tokyo, Tokyo-to, Japan