Photochemistry of 2-thiooxazole: a plausible prebiotic precursor to RNA nucleotides

Bertram, Lauren; Roberts, Samuel J.; Powner, Matthew W.; Szabla, Rafał

doi:10.1039/d2cp03167a

Cited by 4 publications

(3 citation statements)

References 77 publications

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“…NAMD is an effective tool for studying the correlation between nuclear motion and nonadiabatic transitions along electronic states and has been successfully used in various excited-state dynamics studies. 14,18,[28][29][30][31][32] For large molecules, the NAMD simulation approach combines the classical description of the nuclei to the quantum mechanical description of the electrons (nonadiabatic mixed quantum-classical dynamics), considering all vibrational coordinates. NAMD simulations do not impose limitations or preferences on the reaction pathways, allowing all possible mechanisms to be evaluated equally.…”

Section: Introductionmentioning

confidence: 99%

Ultrafast photoisomerization mechanism of azaborine revealed by nonadiabatic molecular dynamics simulations

Jeong

Park

Kim

et al. 2023

Phys. Chem. Chem. Phys.

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Section: Introductionmentioning

confidence: 99%

Ultrafast photoisomerization mechanism of azaborine revealed by nonadiabatic molecular dynamics simulations

Jeong

Park

Kim

et al. 2023

Phys. Chem. Chem. Phys.

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“…Quartz and clays were used in this research [ 120 , 121 , 122 , 123 , 124 , 125 , 126 , 127 , 128 , 129 , 130 ]. Other groups studied the formation of nucleotides using MD simulations [ 131 , 132 , 133 ], but to our knowledge, these are the first simulations to study the interaction between nucleotides and substrates. Our initial hypothesis was that the presence of substrates has a catalytic effect on the formation of pre-polymers that show

–

hydrogen bonds between nucleotides.…”

Section: Discussionmentioning

confidence: 99%

The Formation of RNA Pre-Polymers in the Presence of Different Prebiotic Mineral Surfaces Studied by Molecular Dynamics Simulations

Dujardin

Himbert

Rheinstädter

2022

Life

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We used all-atom Molecular Dynamics (MD) computer simulations to study the formation of pre-polymers between the four nucleotides in RNA (AMP, UMP, CMP, GMP) in the presence of different substrates that could have been present in a prebiotic environment. Pre-polymers are C3′–C5′ hydrogen-bonded nucleotides that have been suggested to be the precursors of phosphodiester-bonded RNA polymers. We simulated wet–dry cycles by successively removing water molecules from the simulations, from ~60 to 3 water molecules per nucleotide. The nine substrates in this study include three clay minerals, one mica, one phosphate mineral, one silica, and two metal oxides. The substrates differ in their surface charge and ability to form hydrogen bonds with the nucleotides. From the MD simulations, we quantify the interactions between different nucleotides, and between nucleotides and substrates. For comparison, we included graphite as an inert substrate, which is not charged and cannot form hydrogen bonds. We also simulated the dehydration of a nucleotide-only system, which mimics the drying of small droplets. The number of hydrogen bonds between nucleotides and nucleotides and substrates was found to increase significantly when water molecules were removed from the systems. The largest number of C3′–C5′ hydrogen bonds between nucleotides occurred in the graphite and nucleotide-only systems. While the surface of the substrates led to an organization and periodic arrangement of the nucleotides, none of the substrates was found to be a catalyst for pre-polymer formation, neither at full hydration, nor when dehydrated. While confinement and dehydration seem to be the main drivers for hydrogen bond formation, substrate interactions reduced the interactions between nucleotides in all cases. Our findings suggest that small supersaturated water droplets that could have been produced by geysers or springs on the primitive Earth may play an important role in non-enzymatic RNA polymerization.

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“…5 UV irradiation has been considered as one of the major chemical selection pressures available on early Earth. [6][7][8][9][10] For instance, it is well documented that canonical pyrimidine ribonucleosides, cytidine 1 and uridine 2, can reversibly form their photohydrates [11][12][13] 3 and 4 in dilute aqueous solution under UV irradiation, and cytidine 1 can be photochemically converted to uridine 2 in the process (Fig. 1).…”

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confidence: 99%

Prebiotic synthesis of dihydrouridine by photoreduction of uridine in formamide

Xu,

Janicki,

Szabla

et al. 2024

Chem. Commun.

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Photochemistry of 2-thiooxazole: a plausible prebiotic precursor to RNA nucleotides

Abstract: Potentially prebiotic chemical reactions leading to RNA nucleotides involve periods of UV irradiation, which are necessary to promote selectivity and destroy biologially irrelevant side products. Nevetheless, UV light has only...

Cited by 4 publications

References 77 publications

Ultrafast photoisomerization mechanism of azaborine revealed by nonadiabatic molecular dynamics simulations

Ultrafast photoisomerization mechanism of azaborine revealed by nonadiabatic molecular dynamics simulations

The Formation of RNA Pre-Polymers in the Presence of Different Prebiotic Mineral Surfaces Studied by Molecular Dynamics Simulations

Prebiotic synthesis of dihydrouridine by photoreduction of uridine in formamide

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