Kinetic Monitoring of Self-Replicating Systems through Measurement of Fluorescence Resonance Energy Transfer

Schöneborn, Holger; Bülle, Jan; Kiedrowski, Günter von

doi:10.1002/1439-7633(20011203)2:12<922::aid-cbic922>3.0.co;2-u

Cited by 20 publications

(9 citation statements)

References 44 publications

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“…A full annotation of the algorithms is available in the supplementary material. Figure 4 describes how the IRPR, PPP, and MPP values were calculated using realistic reaction kinetics and free energies obtained from empirical studies (Cantor and Schimmel 1980;Turner 2000;Reynaldo et al 2000;Rohatgi et al 1996;Schoneborn et al 2001;SantaLucia 1998;Xia et al 1998). The p-bond formation and breakage rates were modeled on phosphoramidate bonds, although due to the timescale separation between h-bond and p-bond dynamics, the same overall behavior is expected irrespective of the absolute values of p-bond formation and breakage rates (see supplementary material).…”

Section: Methodsmentioning

confidence: 99%

A Stochastic Model of Nonenzymatic Nucleic Acid Replication: “Elongators” Sequester Replicators

2007

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Abstract. The origin of nucleic acid template replication is a major unsolved problem in science. A novel stochastic model of nucleic acid chemistry was developed to allow rapid prototyping of chemical experiments designed to discover sufficient conditions for template replication. Experiments using the model brought to attention a robust property of nucleic acid template populations, the tendency for elongation to outcompete replication. Externally imposed denaturation-renaturation cycles did not reverse this tendency. For example, it has been proposed that fast tidal cycling could establish a TCR (tidal chain reaction) analogous to a PCR (polymerase chain reaction) acting on nucleic acid polymers, allowing their self-replication. However, elongating side-reactions that would have been prevented by the polymerase in the PCR still occurred in the simulation of the TCR. The same finding was found with temperature and monomer cycles. We propose that if cycling reactors are to allow template replication, oligonucleotide phenotypes that are capable of favorably altering the flux ratio between replication and elongation, for example, by facilitating sequence-specific cleavage within templates, are necessary; accordingly the minimal replicase ribozyme may have possessed restriction functionality.

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Section: Methodsmentioning

confidence: 99%

A Stochastic Model of Nonenzymatic Nucleic Acid Replication: “Elongators” Sequester Replicators

2007

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“…The field of self-replication has evolved from the duplication of small nucleotide sequences [547][548][549][550][551][552][553]613 to anabolic autocatalysis, e.g. RNA enzymes undergo self-sustained replication in the absence of proteins.…”

Section: Self-replicatorsmentioning

confidence: 99%

Supramolecular catalysis. Part 2: artificial enzyme mimics

et al. 2014

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The design of artificial catalysts able to compete with the catalytic proficiency of enzymes is an intense subject of research. Non-covalent interactions are thought to be involved in several properties of enzymatic catalysis, notably (i) the confinement of the substrates and the active site within a catalytic pocket, (ii) the creation of a hydrophobic pocket in water, (iii) self-replication properties and (iv) allosteric properties. The origins of the enhanced rates and high catalytic selectivities associated with these properties are still a matter of debate. Stabilisation of the transition state and favourable conformations of the active site and the product(s) are probably part of the answer. We present here artificial catalysts and biomacromolecule hybrid catalysts which constitute good models towards the development of truly competitive artificial enzymes.

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“…FRET experiments are frequently used to follow chemical or biochemical processes, but have rarely 14 been practiced for monitoring the progress of self-replication, due primarily to the fact that attaching dyes to relatively small molecules can dramatically affect their structure and template reactivity. Accordingly, DNA and peptide replication experiments were followed ex situ by HPLC after quenching aliquots from the experiment solution, [15][16][17] and replication of small organic molecules was followed mainly by NMR.…”

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confidence: 99%