Thermal, Autonomous Replicator Made from Transfer RNA

Krammer, Hubert; Möller, Friederike M.; Braun, Dieter

doi:10.1103/physrevlett.108.238104

Cited by 15 publications

(26 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Thermally triggered replication (PCR) is compatible with thermal trapping: In previous work, DNA was replicated with a polymerase every 30 s in a laser-driven thermal molecule trap (16). Also the protein-free replication of codon information can be approached by using truncated tRNA molecules in a thermal oscillation (17). Other physical nonequilibrium mechanisms to drive replication have also been explored, such as a mechanical disequilibrium-induced pattern of replication in larger DNA complexes (33).…”

Section: Discussionmentioning

confidence: 99%

“…In the laboratory, thermal molecule traps have previously been demonstrated to support accumulation of biomolecules (12,13), formation of cell-like lipid vesicles (14), and concurrent replication and trapping with a polymerase (15,16). Additionally, a replication of codon information using tRNA is compatible with the temperature cycling in a thermal molecule trap (17).…”

mentioning

confidence: 99%

See 1 more Smart Citation

Escalation of polymerization in a thermal gradient

Mast

Schink

Gerland

et al. 2013

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

Self Cite

153

159

View full text Add to dashboard Cite

For the emergence of early life, the formation of biopolymers such as RNA is essential. However, the addition of nucleotide monomers to existing oligonucleotides requires millimolar concentrations. Even in such optimistic settings, no polymerization of RNA longer than about 20 bases could be demonstrated. How then could self-replicating ribozymes appear, for which recent experiments suggest a minimal length of 200 nt? Here, we demonstrate a mechanism to bridge this gap: the escalated polymerization of nucleotides by a spatially confined thermal gradient. The gradient accumulates monomers by thermophoresis and convection while retaining longer polymers exponentially better. Polymerization and accumulation become mutually self-enhancing and result in a hyperexponential escalation of polymer length. We describe this escalation theoretically under the conservative assumption of reversible polymerization. Taking into account the separately measured thermophoretic properties of RNA, we extrapolate the results for primordial RNA polymerization inside a temperature gradient in pores or fissures of rocks. With a dilute, nanomolar concentration of monomers the model predicts that a pore length of 5 cm and a temperature difference of 10 K suffice to polymerize 200-mers of RNA in micromolar concentrations. The probability to generate these long RNAs is raised by a factor of >10 600 compared with polymerization in a physical equilibrium. We experimentally validate the theory with the reversible polymerization of DNA blocks in a laser-driven thermal trap. The results confirm that a thermal gradient can significantly enlarge the available sequence space for the emergence of catalytically active polymers. molecular evolution | nonequilibrium | RNA world | (nonenzymatic) emergence of RNA | hydrothermal vents P olymers are the vital building blocks of all known life forms. According to the central dogma of molecular biology (1), DNA stores the information for how and when to build proteins, which for their part carry out catalytic tasks like the polymerization of DNA. How this self-perpetuating cycle has started is unknown. The RNA-world hypothesis posits that RNA molecules were the central players in prebiotic evolution, because they exhibit both a catalytic function similar to that of proteins and the information storage capabilities of DNA (2). However, how could such an RNA world have emerged from the prebiotic soup?A key element of the RNA world is a ribozyme that catalyzes RNA replication. Directed in vitro evolution and engineering have shown that such ribozymes exist, but require a length of 200 bases or more, even in favorable high-salt conditions (3). Starting from chemical nonequilibrium conditions with millimolar concentrations of energy-rich nucleotides (4-6) and with the help of catalytic surfaces (7), only the formation of much shorter polynucleotides on the order of 20 bases was demonstrated in the laboratory. Slow kinetics and cleavage due to hydrolysis limit the formation of long polynucleotides and finally lead...

show abstract

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Escalation of polymerization in a thermal gradient

Mast

Schink

Gerland

et al. 2013

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

Self Cite

153

159

View full text Add to dashboard Cite

show abstract

“…In these studies, species are typically represented by DNA or RNA. Variations result from mutations in the nucleotide sequences, and these sequences are reproduced through a template-based process [17,18,[20][21][22][23][24][25][26][27][28][29]. This process requires some form of energy input into the system, which can be achieved by the action of enzymes, or by cyclically changing physical parameters like temperature or hydration [30,31].…”

Section: Introductionmentioning

confidence: 99%

Unbounded growth patterns of reproducing, competing polymers—similarities to biological evolution

et al. 2016

View full text Add to dashboard Cite

Since the origin of life the interplay between reproduction, variation, and selection has been driving the emergence of new species. The evolution of the Earth's biosphere appears to innovate unceasingly instead of coming to a stall. Here, we introduce a model system of linear molecules where new polymers appear by spontaneous ligation. The polymers proliferate following a template-based mechanism. Our combined experimental and theoretical study shows that for sufficiently rapid autocatalysis the reproduction process selects particular lengths-while ever longer polymers emerge. We suggest similarities to biological evolution.

show abstract

“…This fact is often overlooked in hypotheses about the origin of life, as pointed out by kováĉc et al [2]. Exponential replication of RNA duplexes, fed by hairpins derived from an alanine tRNA and driven by externally imposed thermal cycling between 10 and 40°C, was achieved by Krammer et al [3]. They proposed that, in the primordial soup, thermal cycling may have been provided by laminar convection between hot and cold regions in millimetre-sized rock pores [4], and that the substrate oligonucleotides could be concentrated by thermophoretic trapping.…”

Section: Introductionmentioning

confidence: 99%

Hydrogen peroxide thermochemical oscillator as driver for primordial RNA replication

Ball

Brindley

2014

Preprint

View full text Add to dashboard Cite

This paper presents and tests a previously unrecognized mechanism for driving a replicating molecular system on the prebiotic earth. It is proposed that cell-free RNA replication in the primordial soup may have been driven by self-sustained oscillatory thermochemical reactions. To test this hypothesis, a well-characterized hydrogen peroxide oscillator was chosen as the driver and complementary RNA strands with known association and melting kinetics were used as the substrate. An open flow system model for the self-consistent, coupled evolution of the temperature and concentrations in a simple autocatalytic scheme is solved numerically, and it is shown that thermochemical cycling drives replication of the RNA strands. For the ( justifiably realistic) values of parameters chosen for the simulated example system, the mean amount of replicant produced at steady state is 6.56 times the input amount, given a constant supply of substrate species. The spontaneous onset of sustained thermochemical oscillations via slowly drifting parameters is demonstrated, and a scheme is given for prebiotic production of complementary RNA strands on rock surfaces.

show abstract

Thermal, Autonomous Replicator Made from Transfer RNA

Cited by 15 publications

References 34 publications

Escalation of polymerization in a thermal gradient

Escalation of polymerization in a thermal gradient

Unbounded growth patterns of reproducing, competing polymers—similarities to biological evolution

Hydrogen peroxide thermochemical oscillator as driver for primordial RNA replication

Contact Info

Product

Resources

About