Ramanarayanan Krishnamurthy

Ester‐Mediated Amide Bond Formation Driven by Wet–Dry Cycles: A Possible Path to Polypeptides on the Prebiotic Earth

Although it is generally accepted that amino acids were present on the prebiotic Earth, the mechanism by which α-amino acids were condensed into polypeptides before the emergence of enzymes remains unsolved. Here, we demonstrate a prebiotically plausible mechanism for peptide (amide) bond formation that is enabled by α-hydroxy acids, which were likely present along with amino acids on the early Earth. Together, α-hydroxy acids and α-amino acids form depsipeptides—oligomers with a combination of ester and amide linkages—in model prebiotic reactions that are driven by wet–cool/dry–hot cycles. Through a combination of ester–amide bond exchange and ester bond hydrolysis, depsipeptides are enriched with amino acids over time. These results support a long-standing hypothesis that peptides might have arisen from ester-based precursors.

Spontaneous Prebiotic Formation of a β-Ribofuranoside That Self-Assembles with a Complementary Heterocycle

The RNA World hypothesis is central to many current theories regarding the origin and early evolution of life. However, the formation of RNA by plausible prebiotic reactions remains problematic. Formidable challenges include glycosidic bond formation between ribose and the canonical nucleobases, as well as the inability of nucleosides to mutually select their pairing partners from a complex mixture of other molecules prior to polymerization. Here we report a one-pot model prebiotic reaction between a pyrimidine nucleobase (2,4,6-triaminopyrimidine, TAP) and ribose, which produces TAP-ribose conjugates in high yield (60-90%). When cyanuric acid (CA), a plausible ancestral nucleobase, is mixed with a crude TAP+ribose reaction mixture, micrometer-length supramolecular, noncovalent assemblies are formed. A major product of the TAP+ribose reaction is a β-ribofuranoside of TAP, which we term TARC. This nucleoside is also shown to efficiently form supramolecular assemblies in water by pairing and stacking with CA. These results provide a proof-of-concept system demonstrating that several challenges associated with the prebiotic emergence of RNA, or pre-RNA polymers, may not be as problematic as widely believed.

Formation of glycolaldehyde phosphate from glycolaldehyde in aqueous solution

Amidotriphosphate (0.1 M) in aqueous solution at near neutral pH in the presence of magnesium ions (0.25 M) converts glycolaldehyde (0.025 M) within days at room temperature into glycolaldehyde phosphate in (analytically) nearly quantitative yields (76% in isolated product). This robust phosphorylation process was observed to proceed at concentrations as low as 30 μM glycolaldehyde and 60 μM phosphorylation reagent under otherwise identical conditions. In sharp contrast, attempts to achieve a phosphorylation of glycolaldehyde with cyclotriphosphate (‘trimetaphosphate’) as phosphorylating reagent were unsuccessful. Mechanistically, the phosphorylation of glycolaldehyde with amidotriphosphate is an example of intramolecular delivery of the phosphate group.

Role of pK(a) of nucleobases in the origins of chemical evolution.

The formation of canonical base pairs through Watson–Crick hydrogen bonding sits at the heart of the genetic apparatus. The specificity of the base pairing of adenine with thymine/uracil and guanine with cytosine preserves accurate information for the biochemical blueprint and replicates the instructions necessary for carrying out biological function. The chemical evolution question of how these five canonical nucleobases were selected over various other possibilities remains intriguing. Since these and alternative nucleobases would have been available for chemical evolution, the reasons for the emergence of this system appear to be primarily functional. While investigating the base-pairing properties of structural nucleic acid analogs, we encountered a relationship between the pKa of a series of nonstandard (and canonical) nucleobases and the pH of the aqueous medium. This relationship appeared to correspond with the propensity of these molecules to self-assemble via Watson–Crick-type base-pairing interactions. A simple correlation of the “magnitude of the difference between the pKa and pH” (pKa–pH correlation) enables a general prediction of which types of heterocyclic recognition elements form hydrogen-bonded base pairs in aqueous media. Using the pKa–pH relationship, we can rationalize why nature chose the canonical nucleobases in terms of hydrophobic and hydrophilic interactions, and further extrapolate its significance within the context of chemical evolution. The connection between the physicochemical properties of bioorganic compounds and the interactions with their aqueous environment directly affects structure and function, at both a molecular and a supramolecular level. A general structure–function pattern emerges in biomolecules and biopolymers in aqueous media near neutral pH. A pKa – pH < 2 generally prompts catalytic functions, central to metabolism, but a difference in pKa – pH > 2 seems to result in the emergence of structure, central to replication. While this general trend is observed throughout extant biology, it could have also been an important factor in chemical evolution.

A Unified Mechanism for Abiotic Adenine and Purine Synthesis in Formamide

The synthesis of purines through dehydration and condensation of formamide is a potential abiotic source of nucleobases. It has been reported since the 1950s that heating formamide to near boiling generates purine in high yield (> 70%). The scope of this formamide condensation has been broadened by the identification of multiple biologically relevant products, including nucleobases and amino acid derivatives, from both neat andmineral-doped formamide. Mechanistic pathways to purines have been proposed, though there are significant variations between routes leading to related products. Herein, data is presented suggesting a common pathway for the abiotic syntheses of both purine and adenine from formamide; the proposed route is also highly reminiscent of the biosynthesis of purine nucleobases (Scheme 1). This is the first evidence suggesting that a glycine derivative is a critical intermediate in purine synthesis from formamide, and that this glycine backbone forms a scaffold for purine ring production in the same orientation as in purine ring biosynthesis. Parallels between nucleobase biosynthesis and plausible abiotic syntheses may allude to the origins of this metabolic pathway. Abiotic nucleobases and their analogues have been identified in meteorites, spark discharge experiments, and hydrogen cyanide (HCN) condensation reactions. Typical laboratory procedures call for one to 15m HCN in aqueous ammonia at 25–70 8C. Analyses of the nonphotochemical, mechanistic route fromHCN to adenine have been conducted by Or , Orgel, and Ferris. Briefly, diaminomaleonitrile (DAMN), a relatively stable HCN tetramer, has been identified as an important intermediate. It provides the ring junction scaffold that subsequently closes to an imidazole and then a bicyclic purine, through reaction with cyanide-derived formamidine (Scheme 2). In aqueous

Spontaneous formation and base pairing of plausible prebiotic nucleotides in water

The RNA World hypothesis presupposes that abiotic reactions originally produced nucleotides, the monomers of RNA and universal constituents of metabolism. However, compatible prebiotic reactions for the synthesis of complementary (that is, base pairing) nucleotides and mechanisms for their mutual selection within a complex chemical environment have not been reported. Here we show that two plausible prebiotic heterocycles, melamine and barbituric acid, form glycosidic linkages with ribose and ribose-5-phosphate in water to produce nucleosides and nucleotides in good yields. Even without purification, these nucleotides base pair in aqueous solution to create linear supramolecular assemblies containing thousands of ordered nucleotides. Nucleotide anomerization and supramolecular assemblies favour the biologically relevant β-anomer form of these ribonucleotides, revealing abiotic mechanisms by which nucleotide structure and configuration could have been originally favoured. These findings indicate that nucleotide formation and selection may have been robust processes on the prebiotic Earth, if other nucleobases preceded those of extant life.

A Plausible Simultaneous Synthesis of Amino Acids and Simple Peptides on the Primordial Earth

Following his seminal work in 1953, Stanley Miller conducted an experiment in 1958 to study the polymerization of amino acids under simulated early Earth conditions. In the experiment, Miller sparked a gas mixture of CH4, NH3, and H2O, while intermittently adding the plausible prebiotic condensing reagent cyanamide. For unknown reasons, an analysis of the samples was not reported. We analyzed the archived samples for amino acids, dipeptides, and diketopiperazines by liquid chromatography, ion mobility spectrometry, and mass spectrometry. A dozen amino acids, 10 glycine-containing dipeptides, and 3 glycine-containing diketopiperazines were detected. Millers experiment was repeated and similar polymerization products were observed. Aqueous heating experiments indicate that Strecker synthesis intermediates play a key role in facilitating polymerization. These results highlight the potential importance of condensing reagents in generating diversity within the prebiotic chemical inventory.

Mineral induced formation of pentose-2,4-bisphosphates

Formation of rac.-pentose-2,4-bisphosphates is demonstrated, starting from glycolaldehyde phosphate and glyceraldehyde-2-phosphate, and induced by mixed valence double layer metal hydroxide minerals. The reactions proceed from dilute aqueous reactant solutions (1.5 mM) at near neutral pH. Conditions have been established, where ribose-2,4- bisphosphate is the major product (∼48%) among the pentose-2,4-bisphosphates, which are formed with up to 25% yield.

Exploratory Experiments on the Chemistry of the “Glyoxylate Scenario”: Formation of Ketosugars from Dihydroxyfumarate

In the context of a “glyoxylate scenario” of primordial metabolism,1 the reactions of dihydroxyfumarate (DHF) with reactive small molecule aldehydes (e.g., glyoxylate, formaldehyde, glycolaldehyde, and glyceraldehyde) in water were investigated and shown to form dihydroxyacetone, tetrulose, and the two pentuloses, with almost quantitative conversion. The practically clean and selective formation of ketoses in these reactions, with no detectable admixture of aldoses, stands in stark contrast to the formose reaction, where a complex mixture of linear and branched aldoses and ketoses are produced. These results suggest that the reaction of DHF with aldehydes could constitute a reasonable pathway for the formation of carbohydrates and allow for alternative potential prebiotic scenarios to the formose reaction to be considered.

1 Before RNA and After: Geophysical and Geochemical Constraints on Molecular Evolution

1. INTRODUCTION This chapter offers a description of some of the physical and chemical settings for the origin of life on Earth. Considering the topic of this book, particular attention is given to the conditions for a precursor RNA World; an ab initio system based on phosphate-sugar backbone structures in linear polymers and currently with nitrogen bases as recognition molecules. Both the appeal and the uncertainties in the assumption of an RNA World are obvious. The biochemical advantage of this model has geochemical and cosmochemical complements such as the abundance in the universe of simple aldehydes, “the sugar of space.” With their relatively high oxidation state, the aldehydes are compatible with plausible models of early terrestrial atmospheres dominated by CO 2 , H 2 O, N 2 , and small mixing fractions of CO, CH 4 and other reductants. Further suggestions of an RNA World come from observed and inferred sources of active oligophosphates and from concentration mechanisms based on the molecular charge conferred by phosphate esters. Finally, the facile formation of ribose phosphate has been successfully modeled under mild aqueous conditions in the laboratory. Obstacles to progress in prebiotic synthesis leading to the inception of an RNA World yet remain. The concentration of neutral molecules such as formaldehyde and glycolaldehyde required to permit the phosphorylation and sugar phosphate formation found in the laboratory remains an impediment to modeling molecular evolution. Furthermore, the oligomerization of nucleosides or nucleotides without the aid of artificial activating groups, and the synthesis and attachment of nitrogen bases in a formaldehyde environment...