Electron-induced origins of prebiotic building blocks of sugars: mechanism of self-reactions of a methanol anion dimer

Karsili, Tolga N. V.; Fennimore, Mark A.; Matsika, Spiridoula

doi:10.1039/c8cp00148k

Cited by 3 publications

(3 citation statements)

References 50 publications

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“…We also included ethylene glycol (EG) in our studies, in addition to PEGs of various MWs (PEG 200, PEG 400, PEG 1000, PEG 8000). EG can be synthesized abiotically 22,23 and is one the larger molecules detected in interstellar medium. 24,25 We first screened various concentrations of EG, PEG 200, PEG 400, PEG 1000, and PEG 8000 to identify optimal crowding conditions for ligase 1 activity in the presence of 1 mM Mg 2+ and 100 mM Tris-HCl, pH 8 (Fig.…”

Section: Resultsmentioning

confidence: 99%

Molecular crowding facilitates ribozyme-catalyzed RNA assembly

DasGupta

Zhang

Szostak

2023

Preprint

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Catalytic RNAs or ribozymes are considered to be central to primordial biology. Most ribozymes require moderate to high concentrations of divalent cations such as Mg2+ to fold into their catalytically competent structures and perform catalysis. However, undesirable effects of Mg2+ such as hydrolysis of reactive RNA building blocks and degradation of RNA structures are likely to undermine its beneficial roles in ribozyme catalysis. Further, prebiotic cell-like compartments bounded by fatty acid membranes are destabilized in the presence of Mg2+, making ribozyme function inside prebiotically relevant protocells a significant challenge. Therefore, we sought to identify conditions that would enable ribozymes to retain activity in low concentrations of Mg2+. Inspired by the ability of ribozymes to function inside crowded cellular environments with <1 mM free Mg2+, we tested molecular crowding as a potential mechanism to lower the Mg2+ concentration required for ribozyme-catalyzed RNA assembly. Here, we show that the ribozyme-catalyzed ligation of phosphorimidazolide RNA substrates is significantly enhanced in the presence of the artificial crowding agent polyethylene glycol. We also found that molecular crowding preserves ligase activity under denaturing conditions such as alkaline pH and the presence of urea. We also show that crowding-induced stimulation of RNA-catalyzed RNA assembly is not limited to phosphorimidazolide ligation but extends to the RNA-catalyzed polymerization of nucleoside triphosphates. RNA-catalyzed RNA ligation is also stimulated by the presence of prebiotically relevant small molecules such as ethylene glycol, ribose, and amino acids, consistent with a role for molecular crowding in primordial ribozyme function and more generally, in the emergence of RNA-based cellular life.

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Section: Resultsmentioning

confidence: 99%

Molecular crowding facilitates ribozyme-catalyzed RNA assembly

DasGupta

Zhang

Szostak

2023

Preprint

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“…We also included ethylene glycol (EG) in our studies in addition to PEGs of various MWs (PEG 200, PEG 400, PEG 1000, PEG 8000). EG can be synthesized abiotically , and is one the larger molecules detected in interstellar medium. , We first screened various concentrations of EG, PEG 200, PEG 400, PEG 1000, and PEG 8000 to identify optimal crowding conditions for ligase 1 activity in the presence of 1 mM Mg 2+ and 100 mM Tris-HCl, pH 8 (Figure S1). We observed remarkable ligation rescue in the presence of EG and both low- and high-MW PEGs.…”

Section: Resultsmentioning

confidence: 99%

Molecular Crowding Facilitates Ribozyme-Catalyzed RNA Assembly

2023

View full text Add to dashboard Cite

Catalytic RNAs or ribozymes are considered to be central to primordial biology. Most ribozymes require moderate to high concentrations of divalent cations such as Mg2+ to fold into their catalytically competent structures and perform catalysis. However, undesirable effects of Mg2+ such as hydrolysis of reactive RNA building blocks and degradation of RNA structures are likely to undermine its beneficial roles in ribozyme catalysis. Further, prebiotic cell-like compartments bounded by fatty acid membranes are destabilized in the presence of Mg2+, making ribozyme function inside prebiotically relevant protocells a significant challenge. Therefore, we sought to identify conditions that would enable ribozymes to retain activity at low concentrations of Mg2+. Inspired by the ability of ribozymes to function inside crowded cellular environments with <1 mM free Mg2+, we tested molecular crowding as a potential mechanism to lower the Mg2+ concentration required for ribozyme-catalyzed RNA assembly. Here, we show that the ribozyme-catalyzed ligation of phosphorimidazolide RNA substrates is significantly enhanced in the presence of the artificial crowding agent polyethylene glycol. We also found that molecular crowding preserves ligase activity under denaturing conditions such as alkaline pH and the presence of urea. Additionally, we show that crowding-induced stimulation of RNA-catalyzed RNA assembly is not limited to phosphorimidazolide ligation but extends to the RNA-catalyzed polymerization of nucleoside triphosphates. RNA-catalyzed RNA ligation is also stimulated by the presence of prebiotically relevant small molecules such as ethylene glycol, ribose, and amino acids, consistent with a role for molecular crowding in primordial ribozyme function and more generally in the emergence of RNA-based cellular life.

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“…The low energy electron (LEE) impact fragmentation of small hydrocarbon molecules are of fundamental importance in understanding the origin and evolution of complex organic molecules in the universe. [1][2][3] Among the various LEE impact fragmentation channels, the near-threshold channels are the most interesting ones. They are rich sources of highly reactive molecular precursors for advanced molecules.…”

Section: Introductionmentioning

confidence: 99%

Origin of Resonant Character in the Electron Impact Two‐Body Neutral‐Fragmentation of Methane

et al. 2022

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The observation of peaks in the threshold region of two-body neutral fragmentation of methane molecule, i. e., CH 4 !CH 3 + H, by low energy electron (LEE) impact has been an enigma. The prevailing explanation that this resonant behavior is due to excitation energy transfer is unsatisfactory since this process is not expected to show peaks in the cross-sections unless there is the involvement of electron-molecule resonances. Our firstprinciples calculations now reveal that the observed peaks could be explained as due to the formation of negative ion resonances, which dominantly dissociate into two neutral fragments and a free-electron. This case of methane is a pointer to the possibility that such reactions contribute significantly to neutral radical production from molecules by LEE impact in comparison to dissociative electron attachment, and in general could play a significant role in electron-based chemical control.

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Electron-induced origins of prebiotic building blocks of sugars: mechanism of self-reactions of a methanol anion dimer

Cited by 3 publications

References 50 publications

Molecular crowding facilitates ribozyme-catalyzed RNA assembly

Molecular crowding facilitates ribozyme-catalyzed RNA assembly

Molecular Crowding Facilitates Ribozyme-Catalyzed RNA Assembly

Origin of Resonant Character in the Electron Impact Two‐Body Neutral‐Fragmentation of Methane

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