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227 Views of RNA: Is RNA Unique in Its Chemical Isomer Space?

Cleaves HJ, Meringer M, Goodwin J - Astrobiology (2015)

Bottom Line: However, to date no one-pot reaction has been shown capable of yielding RNA monomers from likely prebiotically abundant starting materials, though this does not rule out the possibility that simpler, more easily prebiotically accessible nucleic acids may have preceded RNA.The resulting structures are then evaluated by using molecular descriptors typically applied in quantitative structure-property relationship (QSPR) studies and predicted physicochemical properties.We conclude that ribonucleosides may have competed with a multitude of alternative structures whose potential proto-biochemical roles and abiotic syntheses remain to be explored.

View Article: PubMed Central - PubMed

Affiliation: 1 Earth-Life Science Institute (ELSI), Tokyo Institute of Technology , Tokyo, Japan .

ABSTRACT
Ribonucleic acid (RNA) is one of the two nucleic acids used by extant biochemistry and plays a central role as the intermediary carrier of genetic information in transcription and translation. If RNA was involved in the origin of life, it should have a facile prebiotic synthesis. A wide variety of such syntheses have been explored. However, to date no one-pot reaction has been shown capable of yielding RNA monomers from likely prebiotically abundant starting materials, though this does not rule out the possibility that simpler, more easily prebiotically accessible nucleic acids may have preceded RNA. Given structural constraints, such as the ability to form complementary base pairs and a linear covalent polymer, a variety of structural isomers of RNA could potentially function as genetic platforms. By using structure-generation software, all the potential structural isomers of the ribosides (BC5H9O4, where B is nucleobase), as well as a set of simpler minimal analogues derived from them, that can potentially serve as monomeric building blocks of nucleic acid-like molecules are enumerated. Molecules are selected based on their likely stability under biochemically relevant conditions (e.g., moderate pH and temperature) and the presence of at least two functional groups allowing the monomers to be incorporated into linear polymers. The resulting structures are then evaluated by using molecular descriptors typically applied in quantitative structure-property relationship (QSPR) studies and predicted physicochemical properties. Several databases have been queried to determine whether any of the computed isomers had been synthesized previously. Very few of the molecules that emerge from this structure set have been previously described. We conclude that ribonucleosides may have competed with a multitude of alternative structures whose potential proto-biochemical roles and abiotic syntheses remain to be explored.

No MeSH data available.


Distribution of possible backbone distance monomer repeats from the enumerated set. Black bars: ester linkages. White bars: diol-mediated linkages connected directly as ethers. Light gray bars: diol linkages assuming incorporation of a phosphate linker. Linkage distance repeat frequencies are summed over the total number of occurrences in the set, i.e., a single structure that can be linked three unique ways is counted three times.
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f7: Distribution of possible backbone distance monomer repeats from the enumerated set. Black bars: ester linkages. White bars: diol-mediated linkages connected directly as ethers. Light gray bars: diol linkages assuming incorporation of a phosphate linker. Linkage distance repeat frequencies are summed over the total number of occurrences in the set, i.e., a single structure that can be linked three unique ways is counted three times.

Mentions: The distribution of backbone atom repeats for both sets is shown in Fig. 7.


227 Views of RNA: Is RNA Unique in Its Chemical Isomer Space?

Cleaves HJ, Meringer M, Goodwin J - Astrobiology (2015)

Distribution of possible backbone distance monomer repeats from the enumerated set. Black bars: ester linkages. White bars: diol-mediated linkages connected directly as ethers. Light gray bars: diol linkages assuming incorporation of a phosphate linker. Linkage distance repeat frequencies are summed over the total number of occurrences in the set, i.e., a single structure that can be linked three unique ways is counted three times.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4523004&req=5

f7: Distribution of possible backbone distance monomer repeats from the enumerated set. Black bars: ester linkages. White bars: diol-mediated linkages connected directly as ethers. Light gray bars: diol linkages assuming incorporation of a phosphate linker. Linkage distance repeat frequencies are summed over the total number of occurrences in the set, i.e., a single structure that can be linked three unique ways is counted three times.
Mentions: The distribution of backbone atom repeats for both sets is shown in Fig. 7.

Bottom Line: However, to date no one-pot reaction has been shown capable of yielding RNA monomers from likely prebiotically abundant starting materials, though this does not rule out the possibility that simpler, more easily prebiotically accessible nucleic acids may have preceded RNA.The resulting structures are then evaluated by using molecular descriptors typically applied in quantitative structure-property relationship (QSPR) studies and predicted physicochemical properties.We conclude that ribonucleosides may have competed with a multitude of alternative structures whose potential proto-biochemical roles and abiotic syntheses remain to be explored.

View Article: PubMed Central - PubMed

Affiliation: 1 Earth-Life Science Institute (ELSI), Tokyo Institute of Technology , Tokyo, Japan .

ABSTRACT
Ribonucleic acid (RNA) is one of the two nucleic acids used by extant biochemistry and plays a central role as the intermediary carrier of genetic information in transcription and translation. If RNA was involved in the origin of life, it should have a facile prebiotic synthesis. A wide variety of such syntheses have been explored. However, to date no one-pot reaction has been shown capable of yielding RNA monomers from likely prebiotically abundant starting materials, though this does not rule out the possibility that simpler, more easily prebiotically accessible nucleic acids may have preceded RNA. Given structural constraints, such as the ability to form complementary base pairs and a linear covalent polymer, a variety of structural isomers of RNA could potentially function as genetic platforms. By using structure-generation software, all the potential structural isomers of the ribosides (BC5H9O4, where B is nucleobase), as well as a set of simpler minimal analogues derived from them, that can potentially serve as monomeric building blocks of nucleic acid-like molecules are enumerated. Molecules are selected based on their likely stability under biochemically relevant conditions (e.g., moderate pH and temperature) and the presence of at least two functional groups allowing the monomers to be incorporated into linear polymers. The resulting structures are then evaluated by using molecular descriptors typically applied in quantitative structure-property relationship (QSPR) studies and predicted physicochemical properties. Several databases have been queried to determine whether any of the computed isomers had been synthesized previously. Very few of the molecules that emerge from this structure set have been previously described. We conclude that ribonucleosides may have competed with a multitude of alternative structures whose potential proto-biochemical roles and abiotic syntheses remain to be explored.

No MeSH data available.