Effects of Monomer and Template Concentration on the Kinetics of Nonenzymatic Template-Directed Oligoguanylate Synthesis

Kanavarioti, Anastassia; Bernasconi, and Claude F.; Baird, Eldon E.

doi:10.1021/ja9807237

Cited by 37 publications

(40 citation statements)

References 38 publications

(36 reference statements)

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“…S7), as less of the active amino form of the primer becomes available, lowering the rate for the first chemical step, as known for the attack of amines on other monomers (31). The pK a of the protonated form of the 3′-amine of 3′-amino-2′,3′-dideoxythymdine is 7.7, as determined by 13 C NMR (SI Appendix, Figs. S11 and S12).…”

Section: Resultsmentioning

confidence: 97%

“…Chemically activated nucleoside monophosphates were shown to oligomerize on template strands in the absence of polymerases (11). Copying is efficient on templates rich in cytidylic acid with monomers featuring organic leaving groups (12,13). Oligomers (substrates experiencing stronger template effects) can undergo several rounds of enzyme-free self-replication, particularly when reversible immobilization is involved (14,15).…”

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confidence: 99%

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Templating efficiency of naked DNA

Kervio

Hochgesand

Steiner

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

111

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Template-directed synthesis of complementary strands is pivotal for life. Nature employs polymerases for this reaction, leaving the ability of DNA itself to direct the incorporation of individual nucleotides at the end of a growing primer difficult to assess. Using 64 sequences, we now find that any of the four nucleobases, in combination with any neighboring residue, support enzyme-free primer extension when primer and mononucleotide are sufficiently reactive, with ≥93% primer extension for all sequences. Between the 64 possible base triplets, the rate of extension for the poorest template, CAG, with A as templating base, and the most efficient template, TCT, with C as templating base, differs by less than two orders of magnitude. Further, primer extension with a balanced mixture of monomers shows ≥72% of the correct extension product in all cases, and ≥90% incorporation of the correct base for 46 out of 64 triplets in the presence of a downstream-binding strand. A mechanism is proposed with a binding equilibrium for the monomer, deprotonation of the primer, and two chemical steps, the first of which is most strongly modulated by the sequence. Overall, rates show a surprisingly smooth reactivity landscape, with similar incorporation on strongly and weakly templating sequences. These results help to clarify the substrate contribution to copying, as found in polymerase-catalyzed replication, and show an important feature of DNA as genetic material.

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Section: Resultsmentioning

confidence: 97%

mentioning

confidence: 99%

Templating efficiency of naked DNA

Kervio

Hochgesand

Steiner

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

111

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“…In the TD reaction, the rate constants of the formation of oligo(G) longer than 2-mer was greater than that of the cleavage of the phosphodiester bond for the TD reaction. The rate constant of oligo(G) formation increased in the following order : (G) 2 5(G) 3 <(G) 4 (Kanavarioti et al 1993(Kanavarioti et al , 1998. According to the trend of the rate constants of oligomerization, the TD reaction and the clay-catalysed reaction follow similar reaction kinetics, while these systems are quite different (Kawamura & Ferris 1994).…”

Section: The Formation Of Phosphodiester Bonds At High Temperaturesmentioning

confidence: 96%

Behaviour of RNA under hydrothermal conditions and the origins of life

Kawamura¹

2004

International Journal of Astrobiology

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The RNA world hypothesis and the hydrothermal origin of life hypothesis are contradictory to each other. Although it is considered that RNA molecules are too labile to maintain life-like systems at high temperatures and there is extensive literature on nucleic acid hydrolysis, the stability and the chemical evolution of RNA have not been sufficiently analysed from the viewpoint of hydrothermal reactions. Based on our experimental data concerning the stability and the prebiotic formation of RNA at high temperatures, two different aspects seem to be important for evaluating whether RNA molecules are too labile. First, the stability of RNA molecules should be evaluated from the comparison of the rate of formation and the rate of degradation of RNA in open systems. Our prebiotic reaction models of phosphodiester bond formation suggest that at high temperatures the accumulation of RNA may be possible. However, an RNA world entirely consisting of RNA molecules is unlikely to occur because the biologically important interactions are not effective for the bare RNA molecules at high temperatures. Second, since enzymes presently mediate most biological reactions, evaluation of the accumulation of RNA should be based on the comparison between the enzymatic and non-enzymatic reaction rates. Hence, the evaluation of the primitive enzymatic reaction rates at high temperatures has been attempted. There is a large difference between the present enzymatic reaction rates at 25-90 xC and the non-enzymatic reaction rates at high temperatures of 200-300 xC. It is thus possible that prebiotic enzyme-like assemblies could have facilitated the accumulation of RNA molecules at hydrothermal vent temperatures.

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“…closely related, therefore, is the formation of poly C-templated 5¢-3¢ G dimers using 2-MeImpG at 5 · 10 -5 s -1 (Kanavarioti et al, 1999) as well as the related 5¢-3¢ addition of paired 2-MeImpG to an oligo-G primer on a poly C template, at 6.9 · 10 -4 s -1 (Kanavarioti et al, 1998). Accordingly, present calculations overlap rates accessible to imidazolide-activated G within 2¢-5¢ and 3¢-5¢ backbones, though the unknown rates for templated 5¢-5¢ reactions would be even more germane.…”

Section: Yarusmentioning

confidence: 99%

Darwinian Behavior in a Cold, Sporadically Fed Pool of Ribonucleotides

Yarus

2012

Astrobiology

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A testable, explicit origin for Darwinian behavior, feasible on a chaotic early Earth, would aid origins discussion. Here I show that a pool receiving unreliable supplies of unstable ribonucleotide precursors can recurrently fill this role. By using numerical integration, the differential equations governing a sporadically fed pool are solved, yielding quantitative constraints for the proliferation of molecules that also have a chemical phenotype. For example, templated triphosphate nucleotide joining is > 10 4 too slow, suggesting that a group more reactive than pyrophosphate activated primordial nucleotides. However, measured literature rates are sufficient if the Initial Darwinian Ancestor (IDA) resembles a 5¢-5¢ cofactor-like dinucleotide RNA, synthesized via activation with a phosphorimidazolide-like group. A sporadically fed pool offers unforeseen advantages; for example, the pool hosts a novel replicator which is predominantly unpaired, even though it replicates. Such free template is optimized for effective selection during its replication. Pool nucleotides are also subject to a broadly based selection that impels the population toward replication, effective selection, and Darwinian behavior. Such a primordial pool may have left detectable modern traces. A sporadically fed ribonucleotide pool also fits a recognizable early Earth environment, has recognizable modern descendants, and suits the early shape of the phylogenetic tree of Earthly life. Finally, analysis points to particular data now needed to refine the hypothesis. Accordingly, a kinetically explicit chemical hypothesis for a terran IDA can be justified, and informative experiments seem readily accessible.

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Effects of Monomer and Template Concentration on the Kinetics of Nonenzymatic Template-Directed Oligoguanylate Synthesis

Cited by 37 publications

References 38 publications

Templating efficiency of naked DNA

Templating efficiency of naked DNA

Behaviour of RNA under hydrothermal conditions and the origins of life

Darwinian Behavior in a Cold, Sporadically Fed Pool of Ribonucleotides

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