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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.


Mass profile of HRMS analysis obtained for Cyc7 sample of a typical reaction mixture of 5'-AMP and POPC. Chemical identities of the various peaks are tabulated in Table 1.
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life-05-00065-f007: Mass profile of HRMS analysis obtained for Cyc7 sample of a typical reaction mixture of 5'-AMP and POPC. Chemical identities of the various peaks are tabulated in Table 1.

Mentions: Since HPLC analysis demonstrated formation of oligomers during the DH-RH reaction in sufficient yields, mass analysis was performed to further characterize these oligomers. Aqueous phase from Cyc7 reaction mixtures, containing 5 mM 5'-AMP + 1 mM POPC, were used for mass determination. MALDI was initially performed on these samples. However, the material did not get ionized as expected. Possible reasons could be the presence of salt in the mixtures, as the starting material used was a sodium salt of 5'-AMP. Attempts to use C18 Zip-Tips (EMD Millipore) for reducing the salt content were not effective as it also resulted in loss of shorter oligomers in the process. Therefore, HRMS was employed for mass analysis of aqueous phases from the aforementioned mixture. Though the liquid chromatography element failed to resolve individual oligomeric peaks, it did eliminate the salt, resulting in mass profiles of whole reaction mixtures, as shown in Figure 7. Table 1 shows the theoretically calculated mass for the various oligomeric species formed in the reaction along with the actual observed masses obtained from HRMS analysis.


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)

Mass profile of HRMS analysis obtained for Cyc7 sample of a typical reaction mixture of 5'-AMP and POPC. Chemical identities of the various peaks are tabulated in Table 1.
© Copyright Policy
Related In: Results  -  Collection

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

life-05-00065-f007: Mass profile of HRMS analysis obtained for Cyc7 sample of a typical reaction mixture of 5'-AMP and POPC. Chemical identities of the various peaks are tabulated in Table 1.
Mentions: Since HPLC analysis demonstrated formation of oligomers during the DH-RH reaction in sufficient yields, mass analysis was performed to further characterize these oligomers. Aqueous phase from Cyc7 reaction mixtures, containing 5 mM 5'-AMP + 1 mM POPC, were used for mass determination. MALDI was initially performed on these samples. However, the material did not get ionized as expected. Possible reasons could be the presence of salt in the mixtures, as the starting material used was a sodium salt of 5'-AMP. Attempts to use C18 Zip-Tips (EMD Millipore) for reducing the salt content were not effective as it also resulted in loss of shorter oligomers in the process. Therefore, HRMS was employed for mass analysis of aqueous phases from the aforementioned mixture. Though the liquid chromatography element failed to resolve individual oligomeric peaks, it did eliminate the salt, resulting in mass profiles of whole reaction mixtures, as shown in Figure 7. Table 1 shows the theoretically calculated mass for the various oligomeric species formed in the reaction along with the actual observed masses obtained from HRMS analysis.

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.