Replication elongates short DNA, reduces sequence bias and develops trimer structure

Article Biochemical Research Methods

Optimized expression of large fragment DNA polymerase I from Geobacillus stearothermophilus in Escherichia coli expression system

Eva Agustriana et al.

Summary: This study focused on the scaling-up production and optimization of expression conditions for Bst DNA polymerase, offering a feasible noncommercial enzyme option for cost-effective detection of COVID-19.

PREPARATIVE BIOCHEMISTRY & BIOTECHNOLOGY (2023)

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Article Chemistry, Multidisciplinary

Experimental Tests of the Virtual Circular Genome Model for Nonenzymatic RNA Replication

Dian Ding et al.

Summary: The virtual circular genome (VCG) model proposes a method for indefinite cycles of nonenzymatic RNA replication during the origin of life. Initial experimental studies of the feasibility of the VCG model have been conducted, investigating factors such as oligonucleotide length, concentration, composition, and temperature on the extent of primer extension. The findings suggest that environmental fluctuations and ongoing in situ activation chemistry are crucial for continuous and accurate VCG replication.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2023)

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Article Multidisciplinary Sciences

Ribozyme-mediated RNA synthesis and replication in a model Hadean microenvironment

Annalena Salditt et al.

Summary: Enzyme-catalyzed replication of nucleic acid sequences is vital for the survival and evolution of biological entities. In this study, we explore a potential system for sustained RNA replication using a derivative of a group I intron as a replicase. We find that heated air-water interfaces exposed to a CO2-rich atmosphere enable RNA replication and synthesis of functional ribozymes, driven by autonomous oscillations in salt concentrations and pH resulting from precipitation of acidified dew droplets.

NATURE COMMUNICATIONS (2023)

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Article Biochemistry & Molecular Biology

Kinetic explanations for the sequence biases observed in the nonenzymatic copying of RNA templates

Dian Ding et al.

Summary: The research findings suggest that while the use of 2-aminoimidazole activated nucleotides for nonenzymatic RNA primer extension increases efficiency, it is still insufficient for copying RNA templates containing all four canonical nucleotides. The study demonstrates significant differences in affinity among the ten 2-aminoimidazole-bridged dinucleotide intermediates, with certain noncanonical nucleotide having the potential to improve sequence dependent differences in affinity and primer extension rate. Imidazolium-bridged intermediates with more uniform binding and reactivity may lead to the ability to copy arbitrary template sequences under prebiotically plausible conditions.

NUCLEIC ACIDS RESEARCH (2022)

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Article Physics, Multidisciplinary

Water cycles in a Hadean CO2 atmosphere drive the evolution of long DNA

Alan Ianeselli et al.

Summary: Detailed microfluidics experiments and numerical simulations have revealed the significant role of dew in the origin of life and the Darwinian evolution of DNA and RNA. Dew can periodically denature the structures of DNA and RNA at low temperatures and promote the replication of long strands over short ones. The experiments simulated the conditions of early Earth and showed that dew creates cycles of humidity, salt, and pH that are favorable for prebiotic replication chemistries.

NATURE PHYSICS (2022)

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Article Biology

Thermodynamic and Kinetic Sequence Selection in Enzyme-Free Polymer Self-Assembly inside a Non-equilibrium RNA Reactor

Tobias Goeppel et al.

Summary: The RNA world hypothesis explains the emergence of living systems on Earth by proposing that RNA molecules acted as carriers of information and catalysts for replication. This study analyzes the dynamics in sequence space to understand the transition from a pre-RNA to an RNA world. The researchers investigate the self-assembly of polymers through templated ligation, taking into account the thermodynamic and kinetic effects of sequence context. They also explore the role of kinetic stalling and symmetry breaking in the selection of self-enhancing sequences.

LIFE-BASEL (2022)

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Article Chemistry, Multidisciplinary

RNA Oligomerisation without Added Catalyst from 2′,3′-Cyclic Nucleotides by Drying at Air-Water Interfaces

Avinash Vicholous Dass et al.

Summary: The study reveals a possible mechanism for the abiotic synthesis of RNA from its monomers, suggesting a plausible entry point for the evolution of life on early Earth.

CHEMSYSTEMSCHEM (2022)

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Article Biology

Rolling-circle and strand-displacement mechanisms for non-enzymatic RNA replication at the time of the origin of life

Andrew S. Tupper et al.

Summary: RNA replication in viruses likely started non-enzymatically before polymerases were selected to speed up the process. Different viruses utilize various replication mechanisms, with some requiring environmental cycling for replication and others not being affected by re-annealing. Rolling-circle replication is expected to occur non-enzymatically and may be a starting point for the evolution of polymerase-catalyzed replication.

JOURNAL OF THEORETICAL BIOLOGY (2021)

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Article Multidisciplinary Sciences

Structured sequences emerge from random pool when replicated by templated ligation

Patrick W. Kudella et al.

Summary: Through templated ligation reactions, the study found that linking short oligomers from a random sequence pool reduces the sequence space of product strands, resulting in long, highly structured sequences with low entropy. This self-selecting ligation reaction can be restarted by only a few majority sequences, providing a favorable starting point for Darwinian evolution in an RNA world scenario.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

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Article Chemistry, Multidisciplinary