Enhancement of peptide bond formation by polyribonucleotides on clay surfaces in fluctuating environments

White, David; Erickson, Jeffrey C.

doi:10.1007/bf01792420

Cited by 26 publications

(10 citation statements)

References 30 publications

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“…Beljanski et al (1968) identified a protein synthesizing system from Alcaligenesfaecalis that seems to utilize these esters as intermediates. Furthermore, a number of models for the origin of peptide synthesis and the genetic code involve internal-2'-aminoacyl esters of RNA Ikehara et al 1977;Nelsestuen 1978;Usher 1980;Dounce 1981;White and Erickson 1981). Our novel observation of stereoselective aminoacylation at the internal site suggests that these models should be studied more closely.…”

Section: Discussionmentioning

confidence: 81%

Stereoselective aminoacylation of a dinucleoside monophosphate by the imidazolides ofDl-alanine and N-(tert-butoxycarbonyl)-Dl-alanine

Profy

Usher

1984

J Mol Evol

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The aminoacylation of diinosine monophosphate (IpI) was studied. When the acylating agent was the imidazolide of N-(tert-butoxycarbonyl)-DL-alanine, a 40% enantiomeric excess of the L isomer was incorporated at the internal 2' site and the positions of equilibrium for the 2' in equilibrium with 3' migration reaction differed for the D and L enantiomers. The reactivity of the nucleoside hydroxyl groups decreased in the order 2'(3') greater than internal 2' greater than 5', and the extent of reaction was affected by the concentration of the imidazole buffer (pH 7.1). In contrast, reaction of IpI with the imidazolide of unprotected DL-alanine led to an excess of the D isomer at the internal 2' site, while reaction with the N-carboxy anhydride of DL-alanine proceeded without detectable stereoselection. The relevance of these results to the evolution of optical activity and the origin of genetically directed protein synthesis is discussed.

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Section: Discussionmentioning

confidence: 81%

Stereoselective aminoacylation of a dinucleoside monophosphate by the imidazolides ofDl-alanine and N-(tert-butoxycarbonyl)-Dl-alanine

Profy

Usher

1984

J Mol Evol

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“…These surfaces have been experimentally shown to provide favorable conditions for possible prebiotic chemical reactions [25-27] (see also refs. [28-30], see refs.…”

Section: Discussionmentioning

confidence: 99%

The evolution of strand preference in simulated RNA replicators with strand displacement: Implications for the origin of transcription

et al. 2008

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BackgroundThe simplest conceivable example of evolving systems is RNA molecules that can replicate themselves. Since replication produces a new RNA strand complementary to a template, all templates would eventually become double-stranded and, hence, become unavailable for replication. Thus the problem of how to separate the two strands is considered a major issue for the early evolution of self-replicating RNA. One biologically plausible way to copy a double-stranded RNA is to displace a preexisting strand by a newly synthesized strand. Such copying can in principle be initiated from either the (+) or (-) strand of a double-stranded RNA. Assuming that only one of them, say (+), can act as replicase when single-stranded, strand displacement produces a new replicase if the (-) strand is the template. If, however, the (+) strand is the template, it produces a new template (but no replicase). Modern transcription exhibits extreme strand preference wherein anti-sense strands are always the template. Likewise, replication by strand displacement seems optimal if it also exhibits extreme strand preference wherein (-) strands are always the template, favoring replicase production. Here we investigate whether such strand preference can evolve in a simple RNA replicator system with strand displacement.ResultsWe first studied a simple mathematical model of the replicator dynamics. Our results indicated that if the system is well-mixed, there is no selective force acting upon strand preference per se. Next, we studied an individual-based simulation model to investigate the evolution of strand preference under finite diffusion. Interestingly, the results showed that selective forces "emerge" because of finite diffusion. Strikingly, the direction of the strand preference that evolves [i.e. (+) or (-) strand excess] is a complex non-monotonic function of the diffusion intensity. The mechanism underlying this behavior is elucidated. Furthermore, a speciation-like phenomenon is observed under certain conditions: two extreme replication strategies, namely replicase producers and template producers, emerge and coexist among competing replicators.ConclusionFinite diffusion enables the evolution of strand preference, the direction of which is a non-monotonic function of the diffusion intensity. By identifying the conditions under which strand preference evolves, this study provides an insight into how a rudimentary transcription-like pattern might have emerged in an RNA-based replicator system.ReviewersThis article was reviewed by Eugene V Koonin, Rob Kinght and István Scheuring (nominated by David H Ardell). For the full reviews, please go to the Reviewers' comments section.

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“…Si-OH groups at clay particle edges are free to interact with amino acid carboxyl groups, leading to condensation reaction and ester formation. Such a reaction has been proposed to be an activation mechanism of amino acids for peptide bond formation (Jewett and Lawless 1981;White and Erickson 1981;Collins et al 1988;Basiuk et al 1991). In case of SWa-1 clay, the negative layer charge is localized on tetrahedra (Table 1).…”

Section: Glycine Reactionmentioning

confidence: 97%

The effect of smectite composition on the catalysis of peptide bond formation

Bujdák

Rode

1996

J Mol Evol

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Clay-catalyzed glycine and diglycine oligomerizations were performed as drying/wetting cycles at 80 degrees C. Two trioctahedral smectites (hectorite and saponite), three pure montmorillonites, a ferruginous smectite, an Fe(II)-rich smectite, and three smectites containing goethite admixture were used as catalysts. Highest peptide bond formation was found with trioctahedral smectites. About 7% of glycine was converted to diglycine and diketopiperazine on hectorite after 7 days. In the case of dioctahedral smectites, highest yields were achieved using clays with a negative-layer charge localized in the octahedral sheets (up to 2% of converted glycine after 7 days). The presence of Fe(II) in clay is reflected in a higher efficiency in catalyzing amino acid dimerization (about 3.5% of converted glycine after 7 days). The possible significance of the results for prebiotic chemistry is discussed.

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Enhancement of peptide bond formation by polyribonucleotides on clay surfaces in fluctuating environments

Cited by 26 publications

References 30 publications

Stereoselective aminoacylation of a dinucleoside monophosphate by the imidazolides ofDl-alanine and N-(tert-butoxycarbonyl)-Dl-alanine

Stereoselective aminoacylation of a dinucleoside monophosphate by the imidazolides ofDl-alanine and N-(tert-butoxycarbonyl)-Dl-alanine

The evolution of strand preference in simulated RNA replicators with strand displacement: Implications for the origin of transcription

The effect of smectite composition on the catalysis of peptide bond formation

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