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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 chromatogram of Cyc7 sample from a typical DH-RH reaction containing only 5 mM of 5'-AMP (red trace) or 5 mM of 5'-AMP + 1 mM POPC (black trace). The identity of the peaks has been indicated. Inset shows tetramer cluster followed by a trail of unresolved higher oligomers. Trailing could result from low yields and high variability within each oligomer of a specific length.
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life-05-00065-f001: HPLC chromatogram of Cyc7 sample from a typical DH-RH reaction containing only 5 mM of 5'-AMP (red trace) or 5 mM of 5'-AMP + 1 mM POPC (black trace). The identity of the peaks has been indicated. Inset shows tetramer cluster followed by a trail of unresolved higher oligomers. Trailing could result from low yields and high variability within each oligomer of a specific length.

Mentions: Previous reports have suggested that HPLC analysis of these products is difficult due to variability in the chemical nature of the products formed, which, in turn, has a bearing on the resultant yields of the individual oligomers. We, however, carried out analysis of these reaction mixtures using DNAPac PA200 column. It is an anion exchange column that offers single nucleotide resolution and has been used extensively to analyze oligomers resulting from polymerization of activated nucleotides [17,18]. The gradient was standardized using 5'-AMP as a monomer control and hydrolyzed PolyA to ensure that the salt gradient was optimized for resolving smaller oligomers. A typical reaction mixture was used for the standardization of all reaction parameters, which consisted of 5 mM 5'-AMP and 1 mM POPC. This was subjected to seven DH-RH cycles under acidic conditions using H2SO4 and the samples were analyzed by HPLC. Figure 1 shows the chromatogram for the resultant mixture obtained from this reaction. Multiple peaks were observed in the reaction mixture, some of which were identified based on their retention times with respect to the controls.


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 chromatogram of Cyc7 sample from a typical DH-RH reaction containing only 5 mM of 5'-AMP (red trace) or 5 mM of 5'-AMP + 1 mM POPC (black trace). The identity of the peaks has been indicated. Inset shows tetramer cluster followed by a trail of unresolved higher oligomers. Trailing could result from low yields and high variability within each oligomer of a specific length.
© Copyright Policy
Related In: Results  -  Collection

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

life-05-00065-f001: HPLC chromatogram of Cyc7 sample from a typical DH-RH reaction containing only 5 mM of 5'-AMP (red trace) or 5 mM of 5'-AMP + 1 mM POPC (black trace). The identity of the peaks has been indicated. Inset shows tetramer cluster followed by a trail of unresolved higher oligomers. Trailing could result from low yields and high variability within each oligomer of a specific length.
Mentions: Previous reports have suggested that HPLC analysis of these products is difficult due to variability in the chemical nature of the products formed, which, in turn, has a bearing on the resultant yields of the individual oligomers. We, however, carried out analysis of these reaction mixtures using DNAPac PA200 column. It is an anion exchange column that offers single nucleotide resolution and has been used extensively to analyze oligomers resulting from polymerization of activated nucleotides [17,18]. The gradient was standardized using 5'-AMP as a monomer control and hydrolyzed PolyA to ensure that the salt gradient was optimized for resolving smaller oligomers. A typical reaction mixture was used for the standardization of all reaction parameters, which consisted of 5 mM 5'-AMP and 1 mM POPC. This was subjected to seven DH-RH cycles under acidic conditions using H2SO4 and the samples were analyzed by HPLC. Figure 1 shows the chromatogram for the resultant mixture obtained from this reaction. Multiple peaks were observed in the reaction mixture, some of which were identified based on their retention times with respect to the controls.

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.