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Characterization of RNA-Like Oligomers from Lipid-Assisted Nonenzymatic Synthesis: Implications for Origin of Informational Molecules on Early Earth.

Mungi CV, Rajamani S - Life (Basel) (2015)

Bottom Line: The resultant products were characterized to understand their chemical makeup.Formation of such oligomers would have permitted sampling of a large variety of bases on a preformed polymer backbone, resulting in "prebiotic phosphodiester polymers" prior to the emergence of modern RNA-like molecules.This suggests that primitive genetic polymers could have utilized bases that conferred greater N-glycosyl bond stability, a feature crucial for information propagation in low pH and high temperature regimes of early Earth.

View Article: PubMed Central - PubMed

Affiliation: Indian Institute of Science Education and Research (IISER), Pune, Maharashtra 411008, India. cvmungi@students.iiserpune.ac.in.

ABSTRACT
Prebiotic polymerization had to be a nonenzymatic, chemically driven process. These processes would have been particularly favored in scenarios which push reaction regimes far from equilibrium. Dehydration-rehydration (DH-RH) cycles are one such regime thought to have been prevalent on prebiotic Earth in niches like volcanic geothermal pools. The present study defines the optimum DH-RH reaction conditions for lipid-assisted polymerization of nucleotides. The resultant products were characterized to understand their chemical makeup. Primarily, our study demonstrates that the resultant RNA-like oligomers have abasic sites, which means these oligomers lack information-carrying capability because of losing most of their bases during the reaction process. This results from low pH and high temperature conditions, which, importantly, also allows the formation of sugar-phosphate oligomers when ribose 5'-monophosphates are used as the starting monomers instead. Formation of such oligomers would have permitted sampling of a large variety of bases on a preformed polymer backbone, resulting in "prebiotic phosphodiester polymers" prior to the emergence of modern RNA-like molecules. This suggests that primitive genetic polymers could have utilized bases that conferred greater N-glycosyl bond stability, a feature crucial for information propagation in low pH and high temperature regimes of early Earth.

No MeSH data available.


HPLC chromatograms obtained from Cyc7 samples of DH-RH reactions of 5'-AMP (5 mM) and POPC (1 mM) performed with various acids including HCl, H2SO4, HNO3, and H3PO4, at pH 2. Polymerization using H2SO4 and H3PO4 resulted in oligomers, while not much was observed with HCl and HNO3.
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life-05-00065-f003: HPLC chromatograms obtained from Cyc7 samples of DH-RH reactions of 5'-AMP (5 mM) and POPC (1 mM) performed with various acids including HCl, H2SO4, HNO3, and H3PO4, at pH 2. Polymerization using H2SO4 and H3PO4 resulted in oligomers, while not much was observed with HCl and HNO3.

Mentions: Since pH 2 was observed to be the optimum pH for polymerization, we next investigated if the acid used played any mechanistic role in the polymerization process. In other words, is polymerization favored by any acid that could bring the pH down to 2, or is it specific to only certain type of acids? To address this question, we carried out cycling with various mineral acids including hydrochloric acid (HCl), sulfuric acid (H2SO4), nitric acid (HNO3), orthophosphoric acid (H3PO4), and organic acids like formic acid and acetic acid. Some of these acids, e.g., HNO3 and formic acid, are known to be thermolabile and hence were replenished after every dehydration cycle in order to maintain pH ~2. As indicated in Figure 3, lesser polymerization was observed with HCl and HNO3, whereas H2SO4 and H3PO4 both resulted in reasonable oligomer yields. However, the two organic acids failed to promote any polymerization despite repeated addition of these acids over the cycling period.


Characterization of RNA-Like Oligomers from Lipid-Assisted Nonenzymatic Synthesis: Implications for Origin of Informational Molecules on Early Earth.

Mungi CV, Rajamani S - Life (Basel) (2015)

HPLC chromatograms obtained from Cyc7 samples of DH-RH reactions of 5'-AMP (5 mM) and POPC (1 mM) performed with various acids including HCl, H2SO4, HNO3, and H3PO4, at pH 2. Polymerization using H2SO4 and H3PO4 resulted in oligomers, while not much was observed with HCl and HNO3.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4390841&req=5

life-05-00065-f003: HPLC chromatograms obtained from Cyc7 samples of DH-RH reactions of 5'-AMP (5 mM) and POPC (1 mM) performed with various acids including HCl, H2SO4, HNO3, and H3PO4, at pH 2. Polymerization using H2SO4 and H3PO4 resulted in oligomers, while not much was observed with HCl and HNO3.
Mentions: Since pH 2 was observed to be the optimum pH for polymerization, we next investigated if the acid used played any mechanistic role in the polymerization process. In other words, is polymerization favored by any acid that could bring the pH down to 2, or is it specific to only certain type of acids? To address this question, we carried out cycling with various mineral acids including hydrochloric acid (HCl), sulfuric acid (H2SO4), nitric acid (HNO3), orthophosphoric acid (H3PO4), and organic acids like formic acid and acetic acid. Some of these acids, e.g., HNO3 and formic acid, are known to be thermolabile and hence were replenished after every dehydration cycle in order to maintain pH ~2. As indicated in Figure 3, lesser polymerization was observed with HCl and HNO3, whereas H2SO4 and H3PO4 both resulted in reasonable oligomer yields. However, the two organic acids failed to promote any polymerization despite repeated addition of these acids over the cycling period.

Bottom Line: The resultant products were characterized to understand their chemical makeup.Formation of such oligomers would have permitted sampling of a large variety of bases on a preformed polymer backbone, resulting in "prebiotic phosphodiester polymers" prior to the emergence of modern RNA-like molecules.This suggests that primitive genetic polymers could have utilized bases that conferred greater N-glycosyl bond stability, a feature crucial for information propagation in low pH and high temperature regimes of early Earth.

View Article: PubMed Central - PubMed

Affiliation: Indian Institute of Science Education and Research (IISER), Pune, Maharashtra 411008, India. cvmungi@students.iiserpune.ac.in.

ABSTRACT
Prebiotic polymerization had to be a nonenzymatic, chemically driven process. These processes would have been particularly favored in scenarios which push reaction regimes far from equilibrium. Dehydration-rehydration (DH-RH) cycles are one such regime thought to have been prevalent on prebiotic Earth in niches like volcanic geothermal pools. The present study defines the optimum DH-RH reaction conditions for lipid-assisted polymerization of nucleotides. The resultant products were characterized to understand their chemical makeup. Primarily, our study demonstrates that the resultant RNA-like oligomers have abasic sites, which means these oligomers lack information-carrying capability because of losing most of their bases during the reaction process. This results from low pH and high temperature conditions, which, importantly, also allows the formation of sugar-phosphate oligomers when ribose 5'-monophosphates are used as the starting monomers instead. Formation of such oligomers would have permitted sampling of a large variety of bases on a preformed polymer backbone, resulting in "prebiotic phosphodiester polymers" prior to the emergence of modern RNA-like molecules. This suggests that primitive genetic polymers could have utilized bases that conferred greater N-glycosyl bond stability, a feature crucial for information propagation in low pH and high temperature regimes of early Earth.

No MeSH data available.