A step into the RNA world: Conditional analysis of hydrogel formation of adenosine 5′-monophosphate induced by cyanuric acid
Nucleotide polymerization occurs by the nucleophilic attack of 3′-oxygen of the 3′-terminal nucleotide on the α-phosphorus of the incoming nucleotide 5′-triphosphate. The π-stacking of mononucleotides is an important factor for prebiotic RNA polymerization in terms of attaining the proximity of two...
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Veröffentlicht in: | BioSystems 2017-12, Vol.162, p.53-58 |
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creator | Yokosawa, Takumi Enomoto, Ryota Uchino, Sho Hirasawa, Ito Umehara, Takuya Tamura, Koji |
description | Nucleotide polymerization occurs by the nucleophilic attack of 3′-oxygen of the 3′-terminal nucleotide on the α-phosphorus of the incoming nucleotide 5′-triphosphate. The π-stacking of mononucleotides is an important factor for prebiotic RNA polymerization in terms of attaining the proximity of two reacting moieties. Adenosine and adenosine 5′-monophosphate (AMP) are known to form hydrogel in the presence of cyanuric acid at neutral pH. However, we observed that other canonical ribonucleotides did not gel under the same condition. The π-stacking-induced hydrogel formation of AMP was destroyed at pH 2.0, suggesting that the protonation of N at position 1 of adenine abolished hydrogen bonding with the NH of cyanuric acid and resulted in the deformation of the hexad of adenine and cyanuric acid. A liquid-like gel was formed in the case of adenosine with cyanuric acid and boric acid, whereas AMP caused the formation of a solid gel, implying that the negative charge inherent to AMP prevented the formation of esters of boric acid with the cis-diols of ribose. Cyanuric acid-driven oligomerizations of AMP might have been the first crucial event in the foundation of the RNA world. |
doi_str_mv | 10.1016/j.biosystems.2017.09.004 |
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The π-stacking of mononucleotides is an important factor for prebiotic RNA polymerization in terms of attaining the proximity of two reacting moieties. Adenosine and adenosine 5′-monophosphate (AMP) are known to form hydrogel in the presence of cyanuric acid at neutral pH. However, we observed that other canonical ribonucleotides did not gel under the same condition. The π-stacking-induced hydrogel formation of AMP was destroyed at pH 2.0, suggesting that the protonation of N at position 1 of adenine abolished hydrogen bonding with the NH of cyanuric acid and resulted in the deformation of the hexad of adenine and cyanuric acid. A liquid-like gel was formed in the case of adenosine with cyanuric acid and boric acid, whereas AMP caused the formation of a solid gel, implying that the negative charge inherent to AMP prevented the formation of esters of boric acid with the cis-diols of ribose. Cyanuric acid-driven oligomerizations of AMP might have been the first crucial event in the foundation of the RNA world.</description><identifier>ISSN: 0303-2647</identifier><identifier>EISSN: 1872-8324</identifier><identifier>DOI: 10.1016/j.biosystems.2017.09.004</identifier><identifier>PMID: 28887177</identifier><language>eng</language><publisher>Ireland: Elsevier B.V</publisher><subject>Adenine ; Cyanuric acid ; Hydrogel formation ; Hydrogen bond ; RNA world ; π-Stacking</subject><ispartof>BioSystems, 2017-12, Vol.162, p.53-58</ispartof><rights>2017 Elsevier B.V.</rights><rights>Copyright © 2017 Elsevier B.V. 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The π-stacking of mononucleotides is an important factor for prebiotic RNA polymerization in terms of attaining the proximity of two reacting moieties. Adenosine and adenosine 5′-monophosphate (AMP) are known to form hydrogel in the presence of cyanuric acid at neutral pH. However, we observed that other canonical ribonucleotides did not gel under the same condition. The π-stacking-induced hydrogel formation of AMP was destroyed at pH 2.0, suggesting that the protonation of N at position 1 of adenine abolished hydrogen bonding with the NH of cyanuric acid and resulted in the deformation of the hexad of adenine and cyanuric acid. A liquid-like gel was formed in the case of adenosine with cyanuric acid and boric acid, whereas AMP caused the formation of a solid gel, implying that the negative charge inherent to AMP prevented the formation of esters of boric acid with the cis-diols of ribose. Cyanuric acid-driven oligomerizations of AMP might have been the first crucial event in the foundation of the RNA world.</description><subject>Adenine</subject><subject>Cyanuric acid</subject><subject>Hydrogel formation</subject><subject>Hydrogen bond</subject><subject>RNA world</subject><subject>π-Stacking</subject><issn>0303-2647</issn><issn>1872-8324</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><recordid>eNqFkM-u1CAUh4nReMerr2BYummFQgu4Gyf-S240MbomFE4dJi1UaK_pxvhMPpJPIpO56lIWh-TkO7-T8yGEKakpod3zU937mLe8wJTrhlBRE1UTwu-hHZWiqSRr-H20I4ywqum4uEKPcj6R8lpJH6KrRkopqBA79H2PS8qMfVgiXo6AP77f428xje4FPsTg_OJjMCM2pWzZZxwHfNxcil9gxENMkzkD565xEGL2AXD768fPaoohzseY56NZoMS71YLD_YbtZsKavMXGevcYPRjMmOHJ3X-NPr9-9enwtrr58ObdYX9TWSb4UkHPGgCq2qF3lg2Sya4beN8OIGXTUQm0ta6njKuOcAbcNLYzIIXkQpm-69k1enbJnVP8ukJe9OSzhXE0AeKaNVVMtI1SRBVUXlCbYs4JBj0nP5m0aUr02b4-6X_29dm-JkoX-2X06d2WtZ_A_R38o7sALy8AlFtvPSSdrYdQzPgEdtEu-v9v-Q23Ep7A</recordid><startdate>201712</startdate><enddate>201712</enddate><creator>Yokosawa, Takumi</creator><creator>Enomoto, Ryota</creator><creator>Uchino, Sho</creator><creator>Hirasawa, Ito</creator><creator>Umehara, Takuya</creator><creator>Tamura, Koji</creator><general>Elsevier B.V</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>201712</creationdate><title>A step into the RNA world: Conditional analysis of hydrogel formation of adenosine 5′-monophosphate induced by cyanuric acid</title><author>Yokosawa, Takumi ; Enomoto, Ryota ; Uchino, Sho ; Hirasawa, Ito ; Umehara, Takuya ; Tamura, Koji</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c374t-eb32ee195fbdc3f83866f4b5fe882618e15cdb13496043e4a2c6ae878479ab6b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Adenine</topic><topic>Cyanuric acid</topic><topic>Hydrogel formation</topic><topic>Hydrogen bond</topic><topic>RNA world</topic><topic>π-Stacking</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yokosawa, Takumi</creatorcontrib><creatorcontrib>Enomoto, Ryota</creatorcontrib><creatorcontrib>Uchino, Sho</creatorcontrib><creatorcontrib>Hirasawa, Ito</creatorcontrib><creatorcontrib>Umehara, Takuya</creatorcontrib><creatorcontrib>Tamura, Koji</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>BioSystems</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Yokosawa, Takumi</au><au>Enomoto, Ryota</au><au>Uchino, Sho</au><au>Hirasawa, Ito</au><au>Umehara, Takuya</au><au>Tamura, Koji</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A step into the RNA world: Conditional analysis of hydrogel formation of adenosine 5′-monophosphate induced by cyanuric acid</atitle><jtitle>BioSystems</jtitle><addtitle>Biosystems</addtitle><date>2017-12</date><risdate>2017</risdate><volume>162</volume><spage>53</spage><epage>58</epage><pages>53-58</pages><issn>0303-2647</issn><eissn>1872-8324</eissn><abstract>Nucleotide polymerization occurs by the nucleophilic attack of 3′-oxygen of the 3′-terminal nucleotide on the α-phosphorus of the incoming nucleotide 5′-triphosphate. The π-stacking of mononucleotides is an important factor for prebiotic RNA polymerization in terms of attaining the proximity of two reacting moieties. Adenosine and adenosine 5′-monophosphate (AMP) are known to form hydrogel in the presence of cyanuric acid at neutral pH. However, we observed that other canonical ribonucleotides did not gel under the same condition. The π-stacking-induced hydrogel formation of AMP was destroyed at pH 2.0, suggesting that the protonation of N at position 1 of adenine abolished hydrogen bonding with the NH of cyanuric acid and resulted in the deformation of the hexad of adenine and cyanuric acid. A liquid-like gel was formed in the case of adenosine with cyanuric acid and boric acid, whereas AMP caused the formation of a solid gel, implying that the negative charge inherent to AMP prevented the formation of esters of boric acid with the cis-diols of ribose. Cyanuric acid-driven oligomerizations of AMP might have been the first crucial event in the foundation of the RNA world.</abstract><cop>Ireland</cop><pub>Elsevier B.V</pub><pmid>28887177</pmid><doi>10.1016/j.biosystems.2017.09.004</doi><tpages>6</tpages></addata></record> |
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subjects | Adenine Cyanuric acid Hydrogel formation Hydrogen bond RNA world π-Stacking |
title | A step into the RNA world: Conditional analysis of hydrogel formation of adenosine 5′-monophosphate induced by cyanuric acid |
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