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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.


Comparison of Cyc1 and Cyc10 chromatograms from 5'-rMP reaction on DNA Pac PA200 column obtained using a fluorescence detector (λex = 365 nm and λem = 425 nm). Polymerization takes place immediately after one cycle of DH-RH at pH 2, as is evident from the multiple peaks obtained (blue trace). Greater polymerization resulting in longer oligomers seems to occur when 5'-rMP monomers are subjected to 10 DH-RH; such cycles as indicated in the black trace. The green arrow denotes the retention time of 5'-AMP on the same gradient for comparison.
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life-05-00065-f008: Comparison of Cyc1 and Cyc10 chromatograms from 5'-rMP reaction on DNA Pac PA200 column obtained using a fluorescence detector (λex = 365 nm and λem = 425 nm). Polymerization takes place immediately after one cycle of DH-RH at pH 2, as is evident from the multiple peaks obtained (blue trace). Greater polymerization resulting in longer oligomers seems to occur when 5'-rMP monomers are subjected to 10 DH-RH; such cycles as indicated in the black trace. The green arrow denotes the retention time of 5'-AMP on the same gradient for comparison.

Mentions: Since loss of base seems to be a predominant outcome under these reaction conditions, formation of oligomers with only sugar-phosphate backbones was investigated. Such sugar-phosphate polymers are interesting in themselves as they provide preformed polymeric templates that could be used to form informational polymers by addition of suitable bases. Given this interesting and prebiotically plausible scenario, 5'-rMP was subjected to DH-RH cycles under the aforementioned conditions, optimized for 5'-NMPs. Since the molecules lack a nucleobase, their detection or even the product analysis with spectrophotometric methods was challenging. However, weak intrinsic fluorescence was observed in samples, which potentially resulted from prolonged heating of sugars. It is important to note that the rMP monomer by itself does not show any such fluorescence. Using simultaneous excitation-emission analysis, the following wavelengths were shown to be the most relevant for detecting the rMP reaction products: λex = 360–370 nm and λem = 420–430 nm. The reaction mixtures could now be analyzed with HPLC using a fluorescence detector. Multiple peaks were observed even in lower cycles, which resembled peaks that were obtained for nucleotide polymerization (Figure 8). Since assignment of individual peaks was not trivial, the HPLC peaks obtained from 5'-NMP polymerization were used as a proxy to temporarily assign oligomer length for peaks seen in the 5'-rMP reactions. As mentioned earlier, the rMP monomer alone could not be used as a control as it shows no fluorescence.


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)

Comparison of Cyc1 and Cyc10 chromatograms from 5'-rMP reaction on DNA Pac PA200 column obtained using a fluorescence detector (λex = 365 nm and λem = 425 nm). Polymerization takes place immediately after one cycle of DH-RH at pH 2, as is evident from the multiple peaks obtained (blue trace). Greater polymerization resulting in longer oligomers seems to occur when 5'-rMP monomers are subjected to 10 DH-RH; such cycles as indicated in the black trace. The green arrow denotes the retention time of 5'-AMP on the same gradient for comparison.
© Copyright Policy
Related In: Results  -  Collection

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

life-05-00065-f008: Comparison of Cyc1 and Cyc10 chromatograms from 5'-rMP reaction on DNA Pac PA200 column obtained using a fluorescence detector (λex = 365 nm and λem = 425 nm). Polymerization takes place immediately after one cycle of DH-RH at pH 2, as is evident from the multiple peaks obtained (blue trace). Greater polymerization resulting in longer oligomers seems to occur when 5'-rMP monomers are subjected to 10 DH-RH; such cycles as indicated in the black trace. The green arrow denotes the retention time of 5'-AMP on the same gradient for comparison.
Mentions: Since loss of base seems to be a predominant outcome under these reaction conditions, formation of oligomers with only sugar-phosphate backbones was investigated. Such sugar-phosphate polymers are interesting in themselves as they provide preformed polymeric templates that could be used to form informational polymers by addition of suitable bases. Given this interesting and prebiotically plausible scenario, 5'-rMP was subjected to DH-RH cycles under the aforementioned conditions, optimized for 5'-NMPs. Since the molecules lack a nucleobase, their detection or even the product analysis with spectrophotometric methods was challenging. However, weak intrinsic fluorescence was observed in samples, which potentially resulted from prolonged heating of sugars. It is important to note that the rMP monomer by itself does not show any such fluorescence. Using simultaneous excitation-emission analysis, the following wavelengths were shown to be the most relevant for detecting the rMP reaction products: λex = 360–370 nm and λem = 420–430 nm. The reaction mixtures could now be analyzed with HPLC using a fluorescence detector. Multiple peaks were observed even in lower cycles, which resembled peaks that were obtained for nucleotide polymerization (Figure 8). Since assignment of individual peaks was not trivial, the HPLC peaks obtained from 5'-NMP polymerization were used as a proxy to temporarily assign oligomer length for peaks seen in the 5'-rMP reactions. As mentioned earlier, the rMP monomer alone could not be used as a control as it shows no fluorescence.

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.