IA. Cause and Effect . . . . . . . . . . . . . . 465 1.2. Prerequisites of Selforganization . . . . . . . 467 1.2.3. Evolut ion Must S ta r t f rom R andom Even ts 467 1.2.2. Ins t ruc t ion Requires In format ion . . . . 467 1.2.3. In format ion Originates or Gains Value by S e l e c t i o n . . . . . . . . . . . . . . . 469 1.2.4. Selection Occurs wi th Special Substances under Special Conditions . . . . . . . . 470

/pdf/selforganization-of-matter-and-the-evolution-of-biological-3ms9rkbxjp.pdf

Selforganization of matter and the evolution of biological macromolecules

RNA enzymes or ribozymes can act as endoribonucleases, catalyzing the cleavage of RNA molecules with a sequence specificity of cleavage greater than that of known ribonucleases and approaching that of the DNA restriction endonucleases, thus serving as RNA sequence specific endoribonucleases. An example is a shortened form of the self-splicing ribosomal RNA intervening sequence of Tetrahymena (L-19 IVS RNA). Site-specific mutagenesis of the enzyme active site of the L-19 IVS RNA alters the substrate sequence specificity in a predictable manner, allowing a set of sequence-specific endoribonucleases to be synthesized. Varying conditions allow the ribozyme to act as a polymerase (nucleotidyltransferase), a dephosphorylase (acid phosphatase or phosphotransferase) or a sequence-specific endoribonuclease.

Rna ribozyme polymerases, dephosphorylases, restriction endoribonucleases and methods.

At some stage in the origin of life, an informational polymer must have arisen by purely chemical means. According to one version of the 'RNA world' hypothesis this polymer was RNA, but attempts to provide experimental support for this have failed. In particular, although there has been some success demonstrating that 'activated' ribonucleotides can polymerize to form RNA, it is far from obvious how such ribonucleotides could have formed from their constituent parts (ribose and nucleobases). Ribose is difficult to form selectively, and the addition of nucleobases to ribose is inefficient in the case of purines and does not occur at all in the case of the canonical pyrimidines. Here we show that activated pyrimidine ribonucleotides can be formed in a short sequence that bypasses free ribose and the nucleobases, and instead proceeds through arabinose amino-oxazoline and anhydronucleoside intermediates. The starting materials for the synthesis-cyanamide, cyanoacetylene, glycolaldehyde, glyceraldehyde and inorganic phosphate-are plausible prebiotic feedstock molecules, and the conditions of the synthesis are consistent with potential early-Earth geochemical models. Although inorganic phosphate is only incorporated into the nucleotides at a late stage of the sequence, its presence from the start is essential as it controls three reactions in the earlier stages by acting as a general acid/base catalyst, a nucleophilic catalyst, a pH buffer and a chemical buffer. For prebiotic reaction sequences, our results highlight the importance of working with mixed chemical systems in which reactants for a particular reaction step can also control other steps.

/pdf/synthesis-of-activated-pyrimidine-ribonucleotides-in-207dh19sws.pdf

Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions

All life that is known to exist on Earth today and all life for which there is evidence in the geological record seems to be of the same form — one based on DNA genomes and protein enzymes. Yet there are strong reasons to conclude that DNA- and protein-based life was preceded by a simpler life form based primarily on RNA. This earlier era is referred to as the 'RNA world', during which the genetic information resided in the sequence of RNA molecules and the phenotype derived from the catalytic properties of RNA.

The antiquity of RNA-based evolution

The demonstration that ribosomal peptide synthesis is a ribozyme-catalyzed reaction makes it almost certain that there was once an RNA World. The central problem for origin-of-life studies, therefore, is to understand how a protein-free RNA World became established on the primitive Earth. We first review the literature on the prebiotic synthesis of the nucleotides, the nonenzymatic synthesis and copying of polynucleotides, and the selection of ribozyme catalysts of a kind that might have facilitated polynucleotide replication. This leads to a brief outline of the Molecular Biologists' Dream, an optimistic scenario for the origin of the RNA World. In the second part of the review we point out the many unresolved problems presented by the Molecular Biologists' Dream. This in turn leads to a discussion of genetic systems simpler than RNA that might have “invented” RNA. Finally, we review studies of prebiotic membrane formation.

/pdf/prebiotic-chemistry-and-the-origin-of-the-rna-world-43tk55t5qu.pdf

Prebiotic Chemistry and the Origin of the RNA World

Recent work is reviewed on some reactions that could have occurred on the primitive earth and that could have played a part in the evolution of a self-replicating system. The transition from the primitive atmosphere to the simplest replicating molecules is considered in four stages: (1) the formation of a 'prebiotic soup' of organic precursors, including the purine and pyrimidine bases and the pentose sugars; (2) the condensation of these precursors and inorganic phosphate to form monomeric nucleotides and activated nucleotide derivatives; (3) the polymerization of nucleotide derivatives to oligonucleotides; and (4) the complementary replication of oligonucleotides in a template-directed process that depends on Watson-Crick base pairing.

Prebiotic chemistry and nucleic acid replication

Previous attempts to phosphorylate nucleosides by heating with inorganic phosphate succeeeded only when acid phosphates such as Ca(HPO 4 ) 2 were used. The addition of urea and ammonium chloride to the reaction mixture permits phosphorylation in high yield with neutral or basic phosphates at temperatures in the range of 65° to 100°C. Since the abundant mineral, hydroxylapatite, is a satisfactory substrate for this reaction, we believe that this procedure plausible model for prebiotic phosphorylation.

https://science.sciencemag.org/content/sci/171/3970/490.full.pdf

Urea-Inorganic Phosphate Mixtures as Prebiotic Phosphorylating Agents

Preferential formation of (2'–5')-linked internucleotide bonds in non-enzymatic reactions

The Pb2+ and Zn2+ ions are efficient catalysts for the polycytidylic acid-directed polymerization of an activated guanylic acid derivative, guanosine 5'-phosphorimidazolide The products include oligomers of 30 to 40 units in length The nucleotide residues are predominantly 2'-5' linked when Pb2+ is the catalyst, and predominantly 3'-5' linked in the presence of Zn2+ The significance of these results in the context of the prebiotic evolution of RNA polymerase is discussed

https://science.sciencemag.org/content/sci/208/4451/1464.full.pdf

Efficient metal-ion catalyzed template-directed oligonucleotide synthesis

Adenosine-5'-monophosphorimidazolide reacts efficiently with adenosine derivatives on a polyuridylic acid template, with the formation of internucleotide bonds

R. Lohrmann

Papers

Prebiotic chemistry and nucleic acid replication

Urea-Inorganic Phosphate Mixtures as Prebiotic Phosphorylating Agents

Preferential formation of (2'–5')-linked internucleotide bonds in non-enzymatic reactions

Efficient metal-ion catalyzed template-directed oligonucleotide synthesis

Template-Directed Synthesis with Adenosine-5'-phosphorimidazolide