Self-assembling sequence-adaptive peptide nucleic acids.

Several classes of nucleic acid analogs have been reported, but no synthetic informational polymer has yet proven responsive to selection pressures under enzyme-free conditions. Here, we introduce an oligomer family that efficiently self-assembles by means of reversible covalent anchoring of nucleobase recognition units onto simple oligo-dipeptide backbones [thioester peptide nucleic acids (tPNAs)] and undergoes dynamic sequence modification in response to changing templates in solution. The oligomers specifically self-pair with complementary tPNA strands and cross-pair with RNA and DNA in Watson-Crick fashion.

The implausibility of metabolic cycles on the prebiotic Earth.

It has been suggested that complex reaction cycles, analogous to metabolic cycles, operated on the primitive Earth prior to the origin of genetic systems, but severe difficulties arise when these proposals are scrutinized from the standpoint of chemical plausibility.

Protein disulfide oxidoreductases and the evolution of thermophily: was the last common ancestor a heat-loving microbe?

Protein disulfide oxidoreductases (PDOs) are redox enzymes that catalyze dithiol-disulfide exchange reactions. Their sequences and structure reveal the presence of two thioredoxin fold units, each of which is endowed with a catalytic site CXXC motif. PDOs are the outcome of an ancient gene duplication event.

Molecular evolution of peptide methionine sulfoxide reductases (MsrA and MsrB): on the early development of a mechanism that protects against oxidative damage.

Methionine sulfoxide reductases, enzymes that reverse the oxidation of methionine residues, have been described in a wide range of species. The reduction of the diastereoisomers of oxidized methionine is catalyzed by two different monomeric methionine sulfoxide reductases (MsrA and MsrB) and is best understood as an evolutionary response to high levels of oxygen either in the Earth's atmosphere or possibly in more localized environments. Phylogenetic analyses of these proteins suggest that their distribution is the outcome of a complex history including many paralogy and lateral gene transfer events.

Amino acid dependent formation of phosphate anhydrides in water mediated by carbonyl sulfide.

Carbonyl sulfide (COS), a component of volcanic gas emissions and interstellar gas clouds, is shown to be an efficient condensing agent in the context of phosphate chemistry in aqueous solutions. We report that high-energy aminoacyl-phosphate anhydrides and aminoacyl adenylates are generated in solutions containing amino acids, COS, and the corresponding phosphate molecule. We further show that the mixed anhydrides of amino acids and inorganic phosphate are phosphorylating agents, producing pyrophosphate in better than 30% yield in the presence of Ca2+ precipitates.

Carbonyl sulfide-mediated prebiotic formation of peptides.

Almost all discussions of prebiotic chemistry assume that amino acids, nucleotides, and possibly other monomers were first formed on the Earth or brought to it in comets and meteorites, and then condensed nonenzymatically to form oligomeric products. However, attempts to demonstrate plausibly prebiotic polymerization reactions have met with limited success. We show that carbonyl sulfide (COS), a simple volcanic gas, brings about the formation of peptides from amino acids under mild conditions in aqueous solution.

Prebiotic adenine revisited: eutectics and photochemistry.

Recent studies support an earlier suggestion that, if adenine was formed prebiotically on the primitive earth, eutectic freezing of hydrogen cyanide solutions is likely to have been important. Here we revisit the suggestion that the synthesis of adenine may have involved the photochemical conversion of the tetramer of hydrogen cyanide in eutectic solution to 4-amino-5-cyano-imidazole. This would make possible a reaction sequence that does not require the presence of free ammonia.

Prebiotic chemistry and the origin of the RNA world.

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.

Q & A.

Leslie Orgel is a Professor and Senior Fellow at the Salk Institute in La Jolla, California, and an Adjunct Professor at the University of California at San Diego. The first part of his career was devoted to the theoretical inorganic chemistry of transition metal ions. This led to the publication of a book on Ligand-Field Theory.

Some consequences of the RNA world hypothesis.

It is now generally accepted that our familiar biological world was preceded by an RNA world in which ribosome-catalyzed, nucleic-acid coded protein synthesis played no part. If the RNA world was the first biological world there is little that one can learn from biochemistry about prebiotic chemistry, except that the formation and polymerization of nucleotides were once prebiotic processes. If the RNA world was not the first biological world, the above conclusion may not be justified, and one can speculate that the monomers of earlier genetic polymers might be recognizable as important biochemicals.

Thiol-mediated degradation of DNA adsorbed on a colloidal gold surface.

When [P]-labeled DNA is adsorbed on colloidal gold from a 130mmol dm solution of KHPO, it can subsequently be eluted with cold DNA without undergoing detectable degradation. Similarly, DNA can be incubated in solution in the presence or absence of colloidal gold with high concentrations of -mercaptoethanol or hexane-1-thiol without significant degradation. However, when adsorbed DNA is eluted from gold with solutions of one of the thiols, it is recovered as a mixture of mononucleotides and short oligomers.

Is cyanoacetylene prebiotic?

Cyanoacetylene is an earlier intermediate in a proposed prebiotic synthesis of cytosine, while cyanoacetaldehyde is a later intermediate. There is no scientific basis for the claim that cyanoacetaldehyde is more plausibly prebiotic than cyanoacetylene in this context.

Synthesis of adenine from HCN tetramer and ammonium formate.

Adenine is formed in about 18% yield when HCN tetramer is heated with ammonium formate at 110 degrees C. The prebiotic significance of this reaction is discussed.

Sequence dependent N-terminal rearrangement and degradation of peptide nucleic acid (PNA) in aqueous solution.

The stability of the PNA (peptide nucleic acid) thymine monomer ¿N-[2-(thymin-1-ylacetyl)]-N-(2-aminoaminoethyl)glycine¿ and those of various PNA oligomers (5-8-mers) have been measured at room temperature (20 degrees C) as a function of pH. The thymine monomer undergoes N-acyl transfer rearrangement with a half-life of 34 days at pH 11 as analyzed by 1H NMR; and two reactions, the N-acyl transfer and a sequential degradation, are found by HPLC analysis to occur at measurable rates for the oligomers at pH 9 or above. Dependent on the amino-terminal sequence, half-lives of 350 h to 163 days were found at pH 9.

Nonenzymatic synthesis of RNA and DNA oligomers on hexitol nucleic acid templates: the importance of the A structure.

Hexitol nucleic acid (HNA) is an analogue of DNA containing the standard nucleoside bases, but with a phosphorylated 1,5-anhydrohexitol backbone. HNA oligomers form duplexes having the nucleic acid A structure with complementary DNA or RNA oligomers. The HNA decacytidylate oligomer is an efficient template for the oligomerization of the 5'-phosphoroimidazolides of guanosine or deoxyguanosine.

Nonenzymatic oligomerization reactions on templates containing inosinic acid or diaminopurine nucleotide residues.

The template-directed oligomerization of nucleoside-5'-phosphoro-2-methyl imidazolides on standard oligonucleotide templates has been studied extensively. Here, we describe experiments with templates in which inosinic acid (I) is substituted for guanylic acid, or 2,6-diaminopurine nucleotide (D) for adenylic acid. We find that the substitution of I for G in a template is strongly inhibitory and prevents any incorporation of C into internal positions in the oligomeric products of the reaction.

A comparison of RNA with DNA in template-directed synthesis.

Nonenzymatic template-directed copying of RNA sequences rich in cytidylic acid using nucleoside 5'-(2-methylimidazol-1-yl phosphates) as substrates is substantially more efficient than the copying of corresponding DNA sequences. However, many sequences cannot be copied, and the prospect of replication in this system is remote, even for RNA. Surprisingly, wobble-pairing leads to much more efficient incorporation of G opposite U on RNA templates than of G opposite T on DNA templates.

Efficient transfer of information from hexitol nucleic acids to RNA during nonenzymatic oligomerization.

Hexitol nucleic acids (HNAs) are DNA analogues that contain the standard nucleoside bases attached to a phosphorylated 1,5-anhydrohexitol backbone. We find that HNAs support efficient information transfer in nonensymatic template-directed reactions. HNA heterosequences appeared to be superior to the corresponding DNA heterosequences in facilitating synthesis of complementary oligonucleotides from nucleoside-5'-phosphoro-2-methyl imidazolides.

Formation of oligonucleotide-PNA-chimeras by template-directed ligation.

DNA sequences have previously been reported to act as templates for the synthesis of PNA, and vice versa. A continuous evolutionary transition from an informational replicating system based on one polymer to a system based on the other would be facilitated if it were possible to form chimeras, that is molecules that contain monomers of both types. Here we show that ligation to form chimeras proceeds efficiently both on PNA and on DNA templates.

The origin of life--how long did it take?

We do not understand the steps leading from the abiotic early earth to the RNA world. Consequently, we cannot estimate the time required for the origins of life. Attempts to circumvent this essential difficulty are based on misunderstandings of the nature of the problem.

Polymerization of beta-amino acids in aqueous solution.

We have compared carbonyl diimidazole (CDI) and 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDAC) as activating agents for the oligomerization of negatively-charged alpha- and beta-amino acids in homogeneous aqueous solution. alpha-Amino acids can be oligomerized efficiently using CDI, but not by EDAC. beta-Amino acids can be oligomerized efficiently using EDAC, but not by CDI.