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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.


Computed MOI (top) and cross-sectional molecular shadows (bottom) of the 962 energy-minimized output adenosine-analog stereoisomers, shown in descending order from left to right of the pairwise metrics for the three major axes (i.e., X+Y, Y+Z, Z+X). The stereoisomers of the ribofuranosides are shown as open red circles. D and L β-ribofuranosyladenosine are represented as a solid red circle. Color graphics are available at www.liebertonline.com/ast.
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f8: Computed MOI (top) and cross-sectional molecular shadows (bottom) of the 962 energy-minimized output adenosine-analog stereoisomers, shown in descending order from left to right of the pairwise metrics for the three major axes (i.e., X+Y, Y+Z, Z+X). The stereoisomers of the ribofuranosides are shown as open red circles. D and L β-ribofuranosyladenosine are represented as a solid red circle. Color graphics are available at www.liebertonline.com/ast.

Mentions: Among the many properties computed that do not appear to be restricted to the riboside structures, some properties appear to be relatively special in the case of the ribosides. A comparison of the computed moments of inertia (MOI) and molecular shadows of the adenosine isomers along the three principle axes of each molecule is shown in Fig. 8. The MOI is a measure of the distribution of mass about the center of gravity and thus to some degree a measure of the relative “compactness” of the density distribution of a molecule, while the shadow is similarly, but in a sense inversely, a measure of the relative “expansiveness” of the molecule.


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

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

Computed MOI (top) and cross-sectional molecular shadows (bottom) of the 962 energy-minimized output adenosine-analog stereoisomers, shown in descending order from left to right of the pairwise metrics for the three major axes (i.e., X+Y, Y+Z, Z+X). The stereoisomers of the ribofuranosides are shown as open red circles. D and L β-ribofuranosyladenosine are represented as a solid red circle. Color graphics are available at www.liebertonline.com/ast.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f8: Computed MOI (top) and cross-sectional molecular shadows (bottom) of the 962 energy-minimized output adenosine-analog stereoisomers, shown in descending order from left to right of the pairwise metrics for the three major axes (i.e., X+Y, Y+Z, Z+X). The stereoisomers of the ribofuranosides are shown as open red circles. D and L β-ribofuranosyladenosine are represented as a solid red circle. Color graphics are available at www.liebertonline.com/ast.
Mentions: Among the many properties computed that do not appear to be restricted to the riboside structures, some properties appear to be relatively special in the case of the ribosides. A comparison of the computed moments of inertia (MOI) and molecular shadows of the adenosine isomers along the three principle axes of each molecule is shown in Fig. 8. The MOI is a measure of the distribution of mass about the center of gravity and thus to some degree a measure of the relative “compactness” of the density distribution of a molecule, while the shadow is similarly, but in a sense inversely, a measure of the relative “expansiveness” of the molecule.

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.