Temperature-dependence of the template-directed synthesis of oligoguanylates

Fakhrai, H.; Inoue, Tan; Orgel, Leslie E.

doi:10.1016/0040-4020(84)85101-7

Cited by 24 publications

(15 citation statements)

References 5 publications

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“…Nevertheless some comments are in order at this point. The trend towards larger bimolecular rate constants with increasing oligomer length is in apparent contrast with results obtained by Fakhrai et al (1984) who found that short and long oligonucleotides exhibited similar reactivity. However this contradiction is only superficial.…”

Section: Elongation In the Presence Of The Templatecontrasting

confidence: 84%

“…One is that beyond a certain length the oligomers are expected to have a strong binding affinity to the template, assuring dominance of the template-directed reaction over possible solution pathways. The other is that the reactivity of the otigomers should become virtually independent of n, as suggested by Fakhrai et al (1984).…”

Section: Fi42iimentioning

confidence: 93%

“…A further complication would be that the initiation occurs both on the template and in solution, with the relative contribution of the two pathways being strongly temperature dependent. For example, the dimer is an effective initiator for the template-directed chain growth at 0 °C, but not at 37 °C, where the presence of the trimer is required (Fakhrai et al, 1984).…”

Section: Fi42iimentioning

confidence: 99%

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Kinetic analysis of the template effect in ribooligoguanylate elongation

Kanavarioti

White

1987

Origins Life Evol Biosphere

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We have undertaken a complete kinetic analysis of the template-directed oligoguanylate synthesis originated in Orgel's laboratory (Inoue and Orgel, 1982). The reaction of guanosine 5'-phospho-2-methylimidazolide, 2-MelmpG, with ribooligoguanylates all 3'-5' linked, designated n3 with n = 7-12, was studied in the presence/absence of the complementary template polycytidylic acid, poly(C). Conditions were chosen where poly(C) and 2-MelmpG are in large excess over the oligoguanylate. In the absence of the template at 37 degrees C the reaction leads to three isomeric oligomers that are elongated by one monomer unit. They are the 3'-5' linked, (n + 1)3, the 2'-5' linked, (n + 1)2, and the pyrophosphate product, (n + 1)p, formed in an approximate ratio 1:2:5. In the presence of the template the reaction is 20-fold faster and yields products n + 1, n + 2, n + 3 etc. as long as 2-MelmpG is available. Most importantly the formation of the natural, 3'-5' linked isomer, is enhanced selectively by 140-fold at 37 degrees C. Qualitative observations allow the conclusion that this enhancement is temperature dependent and increases with decreasing temperature. For example, at 1 degree C only the 3'-5' linked isomers were detected. Initial rates for the disappearance of the n3 oligoguanylate were determined at 1, 23, and 37 degrees C. It was found that the pseudo-first order rate constant for oligoguanylate elongation was linearly proportional to the 2-MelmpG concentration. This implies that the reaction complex poly(C).n3.2-MelmpG does not accumulate under the reaction conditions, a conclusion which is also supported by infrared data (Miles and Frazier, 1982). The implication of the above results with respect to chemical evolution is that lower temperatures, i.e., close to freezing, enhance the regioselectivity of these template-directed reactions and that one way to improve replication models may be sought in finding conditions that favor stable reaction complexes.

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Section: Elongation In the Presence Of The Templatecontrasting

confidence: 84%

Section: Fi42iimentioning

confidence: 93%

Section: Fi42iimentioning

confidence: 99%

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Kinetic analysis of the template effect in ribooligoguanylate elongation

Kanavarioti

White

1987

Origins Life Evol Biosphere

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“…A complex of oligo(A) and poly(U) investigated by the temperature dependence of ultraviolet absorption is more stable than an inverse complex consisting of oligo(U) and poly(A) [34,351. Furthermore, non-enzymatic template-dependent polymerisation of activated purine mononucleotides is possible [4,5], whereas analogous oligomerisation of pyrimidines was not reported. These effects are due to the improved stacking ability of purines which allows formation of weak complexes of monomeric purines and polypyrimidines [36], as the helical arrangement of the single strand leads to a substantial overlap of monomeric purines and the bases of single-stranded oligopyrimidines.…”

Section: Complexes Of Hairpin and Assemblermentioning

confidence: 97%

Complexes of DNA hairpins and a single‐stranded oligonucleotide detected by affinity chromatography and mung bean nuclease cleavage

Baumann

Lehmann

Schwellnus³

et al. 1987

European Journal of Biochemistry

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The emergence of a simple translation device consisting of an assembler strand (primordial mRNA) and RNA hairpins (primordial tRNA) is presumed to be an important step leading to the origin of life. The assumption of a non-enzymatic interaction of primordial tRNA and mRNA is experimentally approached. DNA hairpins containing five or more adenosine residues in the loop are able to bind to complementary oligonucleotides covalently bound to cellulose. The exact number of base pairs formed between the hairpins and the assembler strand is determined by two methods applied to DNA hairpin/assembler complexes. The melting temperature of a complex is measured and the cleavage pattern by nuclease from mung bean is determined. The loop of the smallest hairpin able to bind consists of five adenosine residues and only three base pairs are formed. This supports the idea of a primordial recognition similar to the contemporary codon-anticodon interaction.The emergence of a simple translation device is a crucial step in the process leading to the origin of life. A proposed translation device [l] consists of interacting oligoribonucleotides. The occurrence of short oligoribonucleotides seems reasonable, since the synthesis of chemically activated ribonucleotides under almost primordial conditions [2], their oligomerisation [3] and their template-directed enzyme-free polymerisation [4, 51 have been demonstrated. The model for self-organisation of matter needs oligoribonucleotides with a hairpin structure acting as primeval tRNA and a singlestranded polynucleotide functioning as primeval mRNA. This single-stranded assembler is thought to bind the hairpin molecules by formation of three base pairs with the loop nucleosides thus arranging the hairpins in a distinct sequence. The base-pairing interactions are thought to be stabilized additionally by lateral forces between the helical parts of the hairpin oligonucleotides occurring at a high Mg2 + concentration. The search for conditions leading to stable binding of hairpins to single strands by base triplets is of interest and a presupposition for intended formation of the peptide bond.In order to investigate the proposed base-pairing ability, two sets of molecules containing either thymidine or deoxyadenosine in the loop region both with an identical helical region as shown in Fig. 1 were synthesized 16 size of the loop was varied with regard to a possible primordial codon-anticodon interaction. The binding ability of the hairpins to complementary homooligonucleotides chemically bound to a solid support was investigated. This method had been originally used for the study of complexes of singlestranded oligonucleotides [8, 91. In order to investigate the steric arrangement of the particular loop nucleosides in free and complexed hairpin oligonucleotides, the single-strandspecific nuclease from mung bean was used as a structural probe [lo, 111. The best known similar nuclease S1 from Aspergillus oryzae had been used as a structural tool to reveal special features of tRNA [12, 131. MAT...

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“…Preceding self-replication, changes in the rate of nucleotide condensation would be driven by genome-independent forces. They evidently include a dependence on template length (Fakhrai et al 1984;Kanavarioti and Bernasconi 1990) and on the selfinteraction energy (determined by a subgenomic sequence) minimizing duplex formation (unpublished resuits). Present findings suggest that, as in Darwinian evolution, pre-self-replication systems will be observed to follow a path of least action over time.…”

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confidence: 99%

A fitness principle for pre-Darwinian evolution based on selection of the least action path

Davis

1996

J Mol Evol

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Optimization of fitness through the action of natural selection can be extended to serve as a principle governing evolution in its pre-self-replication stage, when these concepts are interpreted in a more general way. Although replicase copying errors are then above the threshold for formation of a consensus sequence, nucleotide condensation still proceeds, and the mean condensation rate coefficient will still depend quantitatively on the efficiency of all available templates. A superior template will therefore increase the mean condensation rate coefficient, despite low replicase fidelity and formation of a cluster of product sequences. Any elevation in this mean would also be reasonably stable, when the cluster of sequences formed can retain sufficient homology with template to preserve those (subgenome) segments responsible for its copying efficiency. With the tendency for nucleotide condensation to occur by the fastest-available reaction path, even when complete sequence doubling is unlikely, achieving the highest possible effective condensation rate coefficient provides a selection principle that can apply to pre-Darwinian processes as well as to Darwinian evolution (Davis 1978a(Davis , 1991a. Since this implies that the effective condensation activation free energy has the lowest possible value, the principle reveals that evolution has traced a path of least action, reflecting minimization of this energy term over an interval extending from its early pre-self-replication stages.Natural selection is known to operate on competitively replicating RNA molecules during evolution in vitro (Kramer et al. 1974). Consistent with the fundamental theorem of natural selection, the mean polymer formation rate coefficient increased at a rate equal to the variance in rate coefficients for these RNA species (Davis 1978a(Davis ,b, 1991a. This finding implies that frequency changes among competing RNA species occur in a direction that maximizes increases in their mean propagation rate (Kimura 1958;Davis 1978aDavis , 1991a Shahshahani 1979). After rescaling Fisher's theorem (1930) from polymer propagation to monomer incorporation (Davis 1994), replicative fitness can be equated with the apparent rate coefficient for nucleotide condensation, in a pseudo-first-order reaction. This step generalizes fitness from a measure of comparative doubling rates--as used, for instance, in the kinetic model of Eigen and co-workers (Eigen and Biebricher 1988)--to one concerning the effective activation barrier for a reaction with multiple, competing paths. In this form, it may extend to pre-self-replication events. The maximum principle then requires that the reaction system evolve, at any instant, in a direction that minimizes its effective activation free energy.An action, S, based on a difference between the expectation value for effective activation free energy, (F~), and its minimum value, F~min , in a mixed population of self-propagating polymers,(1) has been found to be minimized over the interval (0, "r) of evolution. This follows ...

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Temperature-dependence of the template-directed synthesis of oligoguanylates

Cited by 24 publications

References 5 publications

Kinetic analysis of the template effect in ribooligoguanylate elongation

Kinetic analysis of the template effect in ribooligoguanylate elongation

Complexes of DNA hairpins and a single‐stranded oligonucleotide detected by affinity chromatography and mung bean nuclease cleavage

A fitness principle for pre-Darwinian evolution based on selection of the least action path

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