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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 after seven DH-RH cycles using 5'-AMP (5 mM) and DLPC (1 mM) at specified pH values that were initially adjusted with H2SO4. Subsequent rehydrations were carried out with H2O. Polymerization is more efficient in reactions performed at a pH of 2 or below.
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life-05-00065-f002: HPLC chromatograms obtained after seven DH-RH cycles using 5'-AMP (5 mM) and DLPC (1 mM) at specified pH values that were initially adjusted with H2SO4. Subsequent rehydrations were carried out with H2O. Polymerization is more efficient in reactions performed at a pH of 2 or below.

Mentions: In order to optimize the reaction for obtaining better oligomer yields, several parameters were varied and their effects on the typical reaction mixture were studied. Since the mechanism proposed for this type of polymerization is similar to that of acid-catalyzed ester formation, we investigated the optimum pH conditions for polymerization of non-activated nucleotides. Mixtures of 5'-AMP, with and without lipids, were subjected to cycling at various pH values in the range of 1–4 (at intervals of 1 pH unit). The pH was adjusted to a particular value using H2SO4 and subsequent rehydrations were carried out using water. Polymerization of 5'-AMP was assessed using HPLC analysis. Figure 2 shows chromatograms that were obtained for cycling of 5'-AMP with DLPC at specified pH values. As seen in the figure, pH values above 2 did not produce good oligomer yields. Polymerization was more efficient at a pH of 2 or below, resulting in oligomers which elute from the column along the salt gradient. A pH of 1, however, resulted in higher breakdown than pH 2, as was evident from comparative analysis of these HPLC chromatograms at 280 nm (data not shown). Suboptimal absorbance at this wavelength allowed for better comparison of the breakdown peaks, which did not saturate, unlike what was seen at 260 nm (Figure 2, last two chromatograms). These results indicated pH 2 to be the optimum pH for polymerization of 5'-AMP under these conditions. At this pH, the phosphate group in 5'-AMP is thought to be protonated, enabling nucleophilic attack by a neighboring nucleotide’s 2'-OH or 3'-OH, resulting in a phosphodiester bond [15,16].


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 after seven DH-RH cycles using 5'-AMP (5 mM) and DLPC (1 mM) at specified pH values that were initially adjusted with H2SO4. Subsequent rehydrations were carried out with H2O. Polymerization is more efficient in reactions performed at a pH of 2 or below.
© Copyright Policy
Related In: Results  -  Collection

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

life-05-00065-f002: HPLC chromatograms obtained after seven DH-RH cycles using 5'-AMP (5 mM) and DLPC (1 mM) at specified pH values that were initially adjusted with H2SO4. Subsequent rehydrations were carried out with H2O. Polymerization is more efficient in reactions performed at a pH of 2 or below.
Mentions: In order to optimize the reaction for obtaining better oligomer yields, several parameters were varied and their effects on the typical reaction mixture were studied. Since the mechanism proposed for this type of polymerization is similar to that of acid-catalyzed ester formation, we investigated the optimum pH conditions for polymerization of non-activated nucleotides. Mixtures of 5'-AMP, with and without lipids, were subjected to cycling at various pH values in the range of 1–4 (at intervals of 1 pH unit). The pH was adjusted to a particular value using H2SO4 and subsequent rehydrations were carried out using water. Polymerization of 5'-AMP was assessed using HPLC analysis. Figure 2 shows chromatograms that were obtained for cycling of 5'-AMP with DLPC at specified pH values. As seen in the figure, pH values above 2 did not produce good oligomer yields. Polymerization was more efficient at a pH of 2 or below, resulting in oligomers which elute from the column along the salt gradient. A pH of 1, however, resulted in higher breakdown than pH 2, as was evident from comparative analysis of these HPLC chromatograms at 280 nm (data not shown). Suboptimal absorbance at this wavelength allowed for better comparison of the breakdown peaks, which did not saturate, unlike what was seen at 260 nm (Figure 2, last two chromatograms). These results indicated pH 2 to be the optimum pH for polymerization of 5'-AMP under these conditions. At this pH, the phosphate group in 5'-AMP is thought to be protonated, enabling nucleophilic attack by a neighboring nucleotide’s 2'-OH or 3'-OH, resulting in a phosphodiester bond [15,16].

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.