The assembly of ancient informational polymers from nucleotide precursors is the central challenge of life's origin on our planet. Among the possible solutions, dry polymerization of 3',5'-cyclic guanosine monophosphate (3',5'-cGMP) has been proposed as a candidate to create oligonucleotides of 15-20 units in length. However, the reported sensitivity of the reaction to the presence of cations raised questions of whether this chemistry could be relevant in a geological context. The experiments in this study show that the presence of cations is not restrictive as long as the reaction is conducted in an acidic environment, in contrast to previous reports that suggested optimal conditions at pH 9.

• Keywords
• cGMP, nonenzymatic polymerization, nucleotides, prebiotic chemistry,
• MeSH
• Cyclic GMP * MeSH
• Catalysis MeSH
• Oligonucleotides MeSH
• Polymerization MeSH
• RNA * MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Cyclic GMP * MeSH
• Oligonucleotides MeSH
• RNA * MeSH

Template-free nonenzymatic polymerization of 3',5' cyclic nucleotides is an emerging topic of the origin of life research. In the last ten years, a number of papers have been published addressing various aspects of this process. These works evoked a vivid discussion among scientists working in the field of prebiotic chemistry. The aim of the current review is to answer the most frequently raised questions related to the detection and characterization of oligomeric products as well as to the geological context of this chemistry.

• Keywords
• cyclic nucleotides, polymerization, prebiotic chemistry,
• Publication type
• Journal Article MeSH
• Review MeSH

RNase J1 is the major 5'-to-3' bacterial exoribonuclease. We demonstrate that in its absence, RNA polymerases (RNAPs) are redistributed on DNA, with increased RNAP occupancy on some genes without a parallel increase in transcriptional output. This suggests that some of these RNAPs represent stalled, non-transcribing complexes. We show that RNase J1 is able to resolve these stalled RNAP complexes by a "torpedo" mechanism, whereby RNase J1 degrades the nascent RNA and causes the transcription complex to disassemble upon collision with RNAP. A heterologous enzyme, yeast Xrn1 (5'-to-3' exonuclease), is less efficient than RNase J1 in resolving stalled Bacillus subtilis RNAP, suggesting that the effect is RNase-specific. Our results thus reveal a novel general principle, whereby an RNase can participate in genome-wide surveillance of stalled RNAP complexes, preventing potentially deleterious transcription-replication collisions.

• Keywords
• RNAP, RNase J1, stalling, torpedo, transcription-replication collision,
• MeSH
• Bacillus subtilis enzymology   genetics   MeSH
• Bacterial Proteins metabolism   MeSH
• RNA, Bacterial genetics   metabolism   MeSH
• DNA-Directed RNA Polymerases metabolism   MeSH
• Exoribonucleases metabolism   MeSH
• Transcription, Genetic MeSH
• RNA, Messenger genetics   metabolism   MeSH
• Gene Expression Regulation, Bacterial MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Bacterial Proteins MeSH
• RNA, Bacterial MeSH
• DNA-Directed RNA Polymerases MeSH
• Exoribonucleases MeSH
• RNA, Messenger MeSH

Molecular Darwinian evolution is an intrinsic property of reacting pools of molecules resulting in the adaptation of the system to changing conditions. It has no a priori aim. From the point of view of the origin of life, Darwinian selection behavior, when spontaneously emerging in the ensembles of molecules composing prebiotic pools, initiates subsequent evolution of increasingly complex and innovative chemical information. On the conservation side, it is a posteriori observed that numerous biological processes are based on prebiotically promptly made compounds, as proposed by the concept of Chemomimesis. Molecular Darwinian evolution and Chemomimesis are principles acting in balanced cooperation in the frame of Systems Chemistry. The one-pot synthesis of nucleosides in radical chemistry conditions is possibly a telling example of the operation of these principles. Other indications of similar cases of molecular evolution can be found among biogenic processes.

• Keywords
• Chemomimesis, Molecular Darwinism, origin of life, systems chemistry,
• Publication type
• Journal Article MeSH
• Review MeSH

A short history of Campbell's primordial soup: In this essay we try to disclose some of the historical connections between the studies that have contributed to our current understanding of the emergence of catalytic RNA molecules and their components from an inanimate matter.

• Keywords
• RNA, nucleosides, nucleotides, oligonucleotides, prebiotic chemistry,
• MeSH
• Nucleosides chemistry   MeSH
• Nucleotides chemistry   MeSH
• Prebiotics * MeSH
• Ribosomes metabolism   MeSH
• RNA, Catalytic metabolism   MeSH
• RNA metabolism   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Review MeSH
• Names of Substances
• Nucleosides MeSH
• Nucleotides MeSH
• Prebiotics * MeSH
• RNA, Catalytic MeSH
• RNA MeSH