Effect of terminal 3′-hydroxymethyl modification of an RNA primer on nonenzymatic primer extension

Pal, Ayan; Das, Rajat S.; Zhang, Weicheng; Lang, Megan W.; McLaughlin, Larry W.; Szostak, Jack W.

doi:10.1039/c6cc06925h

Cited by 5 publications

(4 citation statements)

References 29 publications

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“…This difference in sugar conformation could affect the position of the 5′-phosphate of the nucleotide adjacent to the 3′-end of the primer, potentially explaining the observed rate differences. Previous studies indicate that the nature of the 3′-end of the primer can strongly influence the rate of subsequent nonenzymatic primer extension 33 ; up to a 300 fold decrease in the rate of primer extension has been observed for a mismatched base pair vs. a Watson-Crick base pair at the 3′-end of the primer 13 . We therefore evaluated the effect on nonenzymatic primer extension of replacing the ribonucleotide at the 3′-end of the primer with either a 2′-deoxynucleotide or an arabinonucleotide.…”

Section: Results and Discussion Primer Extension With Monomersmentioning

confidence: 99%

A model for the emergence of RNA from a prebiotically plausible mixture of ribonucleotides, arabinonucleotides and 2’-deoxynucleotides

Kim

Zhou

O’Flaherty

et al. 2019

Preprint

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The abiotic synthesis of ribonucleotides is thought to have been an essential step towards the emergence of the RNA world. However, it is likely that the prebiotic synthesis of ribonucleotides was accompanied by the simultaneous synthesis of arabinonucleotides, 2′-deoxyribonucleotides, and other variations on the canonical nucleotides. In order to understand how relatively homogeneous RNA could have emerged from such complex mixtures, we have examined the properties of arabinonucleotides and 2′-deoxyribonucleotides in nonenzymatic template-directed primer extension reactions. We show that nonenzymatic primer extension with activated arabinonucleotides is much less efficient than with activated ribonucleotides, and furthermore that once an arabinonucleotide is incorporated, continued primer extension is strongly inhibited. As previously shown, 2′-deoxyribonucleotides are also less efficiently incorporated in primer extension reactions, but the difference is more modest. Experiments with mixtures of nucleotides suggest that the coexistence of ribo- and arabino-nucleotides does not impede the copying of RNA templates. Moreover, chimeric oligoribonucleotides containing 2′-deoxy- or arabino-nucleotides are effective templates for RNA synthesis. We propose that the initial genetic polymers were random sequence chimeric oligonucleotides formed by untemplated polymerization, but that template copying chemistry favored RNA synthesis; multiple rounds of replication may have led to pools of oligomers composed mainly of RNA.

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Section: Results and Discussion Primer Extension With Monomersmentioning

confidence: 99%

A model for the emergence of RNA from a prebiotically plausible mixture of ribonucleotides, arabinonucleotides and 2’-deoxynucleotides

Kim

Zhou

O’Flaherty

et al. 2019

Preprint

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“…These results have been extended to ligation reactions by the Krishnamurthy group and our own recent assembly of an active ribozyme via a series of 3′N–5′P ligation reactions. , While the α-amino group of aminoacylated RNA should be more nucleophilic than the hydroxyl group of RNA, it was unclear whether the different location of the α-amino group or the increased steric bulk in the reaction center would diminish the rate of primer extension or ligation reactions. Indeed, replacing the 3′-hydroxyl group with a hydroxymethyl group completely abolished reactivity . Together, these results inspired us to test whether the reaction of the free amino group of 2′(3′)-aminoacylated RNA with phosphorimidazolide-activated nucleotides would result in enhanced rates of RNA copying, and whether such amino acid-bridged oligonucleotides could act as templates for cycles of replication (Figure B).…”

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confidence: 99%

“…Indeed, replacing the 3′-hydroxyl group with a hydroxymethyl group completely abolished reactivity. 18 Together, these results inspired us to test whether the reaction of the free amino group of 2′(3′)-aminoacylated RNA with phosphorimidazolide-activated nucleotides would result in enhanced rates of RNA copying, and whether such amino acid-bridged oligonucleotides could act as templates for cycles of replication (Figure 1B).…”

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confidence: 99%

A Potential Role for Aminoacylation in Primordial RNA Copying Chemistry

et al. 2021

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Aminoacylated tRNAs are the substrates for ribosomal protein synthesis in all branches of life, implying an ancient origin for aminoacylation chemistry. In the 1970s, Orgel and colleagues reported potentially prebiotic routes to aminoacylated nucleotides and their RNA-templated condensation to form amino acid-bridged dinucleotides. However, it is unclear whether such reactions would have aided or impeded nonenzymatic RNA replication. Determining whether aminoacylated RNAs could have been advantageous in evolution prior to the emergence of protein synthesis remains a key challenge. We therefore tested the ability of aminoacylated RNA to participate in both templated primer extension and ligation reactions. We find that at low magnesium concentrations that favor fatty acid-based protocells, these reactions proceed orders of magnitude more rapidly than when initiated from the cis-diol of unmodified RNA. We further demonstrate that amino acid-bridged RNAs can act as templates in a subsequent round of copying. Our results suggest that aminoacylation facilitated non-enzymatic RNA replication, thus outlining a potentially primordial functional link between aminoacylation chemistry and RNA replication.

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“…Previous studies indicate that the nature of the 3′-end of the primer can strongly influence the rate of subsequent nonenzymatic primer extension; 37 up to a 300 fold decrease in the rate of primer extension has been observed for a mismatched base pair vs a Watson−Crick base pair at the 3′-end of the primer. 14 We therefore evaluated the effect on nonenzymatic primer extension of replacing the ribonucleotide at the 3′-end of the primer with either a 2′-deoxynucleotide or an arabinonucleotide.…”

Section: Resultsmentioning

confidence: 99%

A Model for the Emergence of RNA from a Prebiotically Plausible Mixture of Ribonucleotides, Arabinonucleotides, and 2′-Deoxynucleotides

et al. 2020

Self Cite

View full text Add to dashboard Cite

The abiotic synthesis of ribonucleotides is thought to have been an essential step toward the emergence of the RNA world. However, it is likely that the prebiotic synthesis of ribonucleotides was accompanied by the simultaneous synthesis of arabinonucleotides, 2′-deoxyribonucleotides, and other variations on the canonical nucleotides. In order to understand how relatively homogeneous RNA could have emerged from such complex mixtures, we have examined the properties of arabinonucleotides and 2′-deoxyribonucleotides in nonenzymatic template-directed primer extension reactions. We show that nonenzymatic primer extension with activated arabinonucleotides is much less efficient than with activated ribonucleotides, and furthermore that once an arabinonucleotide is incorporated, continued primer extension is strongly inhibited. As previously shown, 2′-deoxyribonucleotides are also less efficiently incorporated in primer extension reactions, but the difference is more modest. Experiments with mixtures of nucleotides suggest that the coexistence of riboand arabinonucleotides does not impede the copying of RNA templates. Moreover, chimeric oligoribonucleotides containing 2′deoxy-or arabinonucleotides are effective templates for RNA synthesis. We propose that the initial genetic polymers were random sequence chimeric oligonucleotides formed by untemplated polymerization, but that template copying chemistry favored RNA synthesis; multiple rounds of replication may have led to pools of oligomers composed mainly of RNA.

show abstract

Effect of terminal 3′-hydroxymethyl modification of an RNA primer on nonenzymatic primer extension

Cited by 5 publications

References 29 publications

A model for the emergence of RNA from a prebiotically plausible mixture of ribonucleotides, arabinonucleotides and 2’-deoxynucleotides

A model for the emergence of RNA from a prebiotically plausible mixture of ribonucleotides, arabinonucleotides and 2’-deoxynucleotides

A Potential Role for Aminoacylation in Primordial RNA Copying Chemistry

A Model for the Emergence of RNA from a Prebiotically Plausible Mixture of Ribonucleotides, Arabinonucleotides, and 2′-Deoxynucleotides

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