Formamide-based prebiotic synthesis of nucleobases: a kinetically accessible reaction route

Synthesis of nucleobases in nonaqueous environments is an alternative way for the emergence of terrestrial life, which could solve the fundamental problem connected to the hydrolytic instability of nucleic acid components in an aqueous environment. In this contribution, we present a plausible reaction route for the prebiotic synthesis of nucleobases in formamide, which does not require participation of the formamide trimer and aminoimidazole-carbonitrile intermediates. The computed activation energy of the proposed pathway is noticeably higher than that of the HCN-based synthetic route, but it is still feasible under the experimental conditions of the Saladino synthesis. We show that, albeit both the pyrimidine and purine ring formation utilizes the undissociated form of formamide, the dehydration product of formamide, HCN, may also play a key role in the mechanism. The rate determining step of the entire reaction path is the cyclization of the diaza-pentanimine precursor. The subsequent formation of the imidazole ring proceeds with a moderate activation energy. Our calculations thus demonstrate that the experimentally suggested reaction path without the involvement of aminoimidazole-carbonitrile intermediates is also a viable alternative for the nonaqueous synthesis of nucleobases.     

Direct Prebiotic Pathway to DNA Nucleosides

It is assumed that RNA played a key role in the origin of life, and the transition to more complex but more stable DNA for continuous information storage and replication requires the development of a ribonucleotide reductase to obtain the deoxyribonucleotides from ribonucleotides. This step, as well as an alternative path from abiotic molecules to DNA‐based life is completely unknown. Shown here is the formation of deoxyribonucleosides under relevant prebiotic conditions in water in high regio‐ and stereoselectivity, from all canonical purine and pyrimidine bases, by condensation with acetaldehyde and sugar‐forming precursors. Thus, a continuous path to deoxyribonucleosides, starting from simple, prebiotically available molecules has been discovered. Furthermore, the deoxyapionucleosides (DApiNA) were identified as a potential DNA progenitor. The results suggest that the DNA world evolved much earlier than previously assumed.     

The search for a potentially prebiotic synthesis of nucleotides via arabinose-3-phosphate and its cyanamide derivative

For the RNA world hypothesis to be accepted, the constitutional self-assembly of RNA will have to be demonstrated. Conceptually, the simplest route to RNA involves nucleotide polymerisation. Activated pyrimidine nucleotides can be derived from arabinose-3-phosphate under potentially prebiotic conditions, but the prebiotic synthesis of this sugar phosphate has not hitherto been investigated. The results of synthetic approaches involving phosphorylation, phosphate migration and 2,3-C--C bond construction are described herein.     

Synthesis of Prebiotic Building Blocks by Photochemistry

Ultraviolet(UV) light is a very competent energy source for the synthesis of prebiotic building blocks on early Earth. In aqueous solution, hydrated electron is produced by irradiating ferrocyanide/cuprous cyanide/hydrosulfide by 254 nm UV light. Hydrated electron is a powerful reducing reagent driving the formation of prebiotic building blocks under prebiotically plausible conditions. Here we summarize the photoredox synthesis of prebiotic related building blocks from hydrogen cyanide(HCN) and other prebiotically related molecules. These results indicate biological related building blocks can be generated on the surface of early Earth.     

Spontaneous emergence of membrane-forming protoamphiphiles from a lipid–amino acid mixture under wet–dry cycles

Dynamic interplay between peptide synthesis and membrane assembly would have been crucial for the emergence of protocells on the prebiotic Earth. However, the effect of membrane-forming amphiphiles on peptide synthesis, under prebiotically plausible conditions, remains relatively unexplored. Here we discern the effect of a phospholipid on peptide synthesis using a non-activated amino acid, under wet–dry cycles. We report two competing processes simultaneously forming peptides and N-acyl amino acids (NAAs) in a single-pot reaction from a common set of reactants. NAA synthesis occurs via an ester–amide exchange, which is the first demonstration of this phenomenon in a lipid–amino acid system. Furthermore, NAAs self-assemble into vesicles at acidic pH, signifying their ability to form protocellular membranes under acidic geothermal conditions. Our work highlights the importance of exploring the co-evolutionary interactions between membrane assembly and peptide synthesis, having implications for the emergence of hitherto uncharacterized compounds of unknown prebiotic relevance.

Synthesis of lipoamino acids via ester–amide exchange under prebiotically plausible wet-dry cycling conditions that results in vesicles at acidic pH.     

Structure-function Relationships in Human Hypoxanthine-guanine Phosphoribosyltransferase （HGPRT） by Random Mutagenesis

Introduction Hypoxanthine guaninephosphoribosyltransferase(HGPRT,EC2.4.2.8)isakeyenzymeofthepurine salvagepathway,whichallowsrecyclingofpurinebases intoDNAandRNA.Itiswidelydistributedinnature andhasbeenstudiedbothinprokaryotesandeu karyotes.Inhumans,acomp…     

A Prebiotic Synthesis of Pterins

The genesis of life on Earth is a hypothesis of evolutionary science that can be, at least partially, tested experimentally. The prebiotic synthesis of cofactors or coenzymes is a poorly explored issue, likely because their formation under plausible prebiotic conditions is not clear. In this sense, it has been proposed that the cofactors are “molecular fossils” of an early phase of life. In contrast, Eschenmoser and Loewenthal suggested a prebiotic hydrocyanic origin of cofactor building blocks. In the present paper, the formation of a set of pterins from cyanide polymerizations is demonstrated, showing that the main structure of some cofactors can be prebiotically formed. Indeed, it was observed that aqueous aerosols additionally increase the relative composition for pterins in the insoluble NH₄CN polymers synthesized. The novel identification of pterins in NH₄CN polymers, together with the previous detection of other important biomonomers, indicates that cyanide polymerizations were essential in the early state of prebiotic chemistry.     

Activation chemistry drives the emergence of functionalised protocells

The complexity of the simplest conceivable cell suggests that the chemistry of prebiotic mixtures needs to be explored to understand the intricate network of prebiotic reactions that led to the emergence of life. Early cells probably relied upon compatible and interconnected chemistries to link RNA, peptides and membranes. Here we show that several types of vesicles, composed of prebiotically plausible mixtures of amphiphiles, spontaneously form and sustain the methyl isocyanide-mediated activation of amino acids, peptides and nucleotides. Activation chemistry also drives the advantageous conversion of reactive monoacylglycerol phosphates into inert cyclophospholipids, thus supporting their potential role as major constituents of protocells. Moreover, activation of prebiotic building blocks within fatty acid-based vesicles yields lipidated species capable of localising to and functionalising primitive membranes. Our findings describe a potentially prebiotic scenario in which the components of primitive cells undergo activation and provide new species that might have enabled an increase in the functionality of protocells.

The complexity of the simplest conceivable cell suggests that the chemistry of prebiotic mixtures needs to be explored to understand the intricate network of prebiotic reactions that led to the emergence of life.     

Eutectic phase polymerization of activated ribonucleotide mixtures yields quasi-equimolar incorporation of purine and pyrimidine nucleobases

The RNA world hypothesis requires a plausible mechanism by which RNA itself (or precursor RNA-like polymers) can be synthesized nonenzymatically from the corresponding building blocks. Simulation experiments have exploited chemically reactive mononucleotides as monomers. Solutions of such monomers in the prebiotic environment were likely to be very dilute, but in experimental simulations of polymerization reactions dilute solutions of activated mononucleotides in the millimolar range hydrolyze extensively, and only trace amounts of dimers and trimers are formed. We report here that random medium-size RNA analogues with mixed sequences (5- to 17-mers with traces of longer products) can be synthesized in ice eutectic phases that are produced when dilute solutions of activated monomers and catalysts (Mg(II) and Pb(II)) are frozen and maintained at -18 degrees C for periods up to 38 days. Under these conditions, the monomers are concentrated as eutectics in an ice matrix. Hydrolysis of the activated mononucleotides was suppressed at low-temperature ranges, and polymerization was enhanced with yields up to 90%. Analysis of the mixed oligomers established that incorporation of both purine and pyrimidine bases proceeded at comparable rates and yields. These results suggest that ice deposits on the early Earth could have facilitated the synthesis of short- and medium-size random sequence RNA analogues and thereby provided a microenvironment suitable for the formation of biopolymers or their precursors.     

Copying of RNA Sequences without Pre‐Activation

Template‐directed incorporation of nucleotides at the terminus of a growing complementary strand is the basis of replication. For RNA, this process can occur in the absence of enzymes, if the ribonucleotides are first converted to an active species with a leaving group. Thus far, the activation required a separate chemical step, complicating prebiotically plausible scenarios. Here we show that a combination of a carbodiimide and an organocatalyst induces near‐quantitative incorporation of any of the four ribonucleotides. Upon in situ activation, adenosine monophosphate was found to also form oligomers in aqueous solution. So, both de novo strand formation and sequence‐specific copying can occur without an artificial synthetic step.     

Anionic N-Fries rearrangement of N-alkyl-2-iodo anilides induced by iodine-magnesium exchange: application for synthesis of strained 1,2,3-trisubstituted indoles

A superior, mild, high-yielding one-pot process for rapid access to oxo anilides has been developed that involves three cascade reactions: iodine-magnesium exchange, regiospecific ortho N-Fries rearrangement, and in situ trapping of the formed aniline anion. Coupled with McMurry cyclization, the two-step process allows ready synthesis of strained 1,2,3-trisubstituted indoles regioselectively.     

Photooxidation of nucleic acids on metal oxides: physico-chemical and astrobiological perspectives

Photocatalytic oxidation of nucleic acid components on aqueous metal oxides (TiO(2), α-FeOOH, and α-Fe(2)O(3)) has been studied. The oxidation of purine nucleotides results in the formation of the purine radical cations and sugar-phosphate radicals, whereas the oxidation of pyrimidine nucleotides other than thymine results in the oxidation of only the sugar-phosphate. The oxidation of the thymine (and to a far less extent for the 5-methylcytosine) derivatives results in deprotonation from the methyl group of the base. Some single stranded (ss) oligoribonucleotides and wild-type ss RNA were oxidized at purine sites. In contrast, double stranded (ds) oligoribonucleotides and DNA were not oxidized. These results account for observations suggesting that cellular ds DNA is not damaged by exposure to photoirradiated TiO(2) nanoparticles inserted into the cell, whereas ss RNA is extensively damaged. The astrobiological import of our observations is that the rapid degradation of monomer nucleotides make them poor targets as biosignatures, whereas duplex DNA is a better target as it is resilient to oxidative diagenesis. Another import of our studies is that ds DNA (as opposed to ss RNA) appears to be optimized to withstand oxidative stress both due to the advantageous polymer morphology and the subtle details of its radical chemistry. This peculiarity may account for the preference for DNA over RNA as a "molecule of life" provided that metal oxides served as the template for synthesis of polynucleotides, as suggested by Orgel and others.     

Synthesis of N2-arylaminopyrimidine-5-carbonitrile derivatives via SNAr amination reaction

An efficient and high-yielding synthesis of N~2-arylaminopyrimidine-5-carbonitrile derivatives starting from arylamines and 2-methylthio-pyrimidine-5-carbonitriIe derivatives has been developed in the presence of cesium carbonate as basic reagent.This new protocol showed high chemical tolerance for a range of functional groups,and only the methylthio substituent on C2 of the pyrimidine ring was replaced with arylamine derivatives under the reaction conditions.     

Preparation of homologs of oligoribouridylic acid by selective partial hydrolysis of RNA

The preparation of oligouridylic acids was achieved by the stepwise partial hydrolysis of RNA using enzymatical and chemical methods of degradation followed by chromatographic purification steps. After RNA is submitted first to RNase T1 and after that to RNase U2 it is cleaved into oligopyrimidine nucleotides carrying purine nucleotides only at their 3'-terminal. By chemical deamination the pyrimidine sequences are converted to oligouridine sequences. After enzymatical dephosphorylation of the oligouridylic acids their 3'-terminal purine nucleosides are eliminated by a periodate-lysine treatment. The phosphate groups remaining at the 3'-terminal of the resulting oligouridylic acids are enzymatically removed. As a result of the partial hydrolysis the mean recoveries of the particular homologues are U2-U7 93% and U8 86% adding up to about 0.5% of the amount of RNA used as starting material.     

Prebiotic Cell Membranes that Survive Extreme Environmental Pressure Conditions

Attractive candidates for compartmentalizing prebiotic cells are membranes comprised of single‐chain fatty acids. It is generally believed that life may have originated in the depth of the protoocean, that is, under high hydrostatic pressure conditions, but the structure and physical–chemical properties of prebiotic membranes under such conditions have not yet been explored. We report the temperature‐ and pressure‐dependent properties of membranes composed of prebiotically highly‐plausible lipids and demonstrate that prebiotic membranes could not only withstand extreme temperatures, but also serve as robust models of protocells operating in extreme pressure environments. We show that pressure not only increases the stability of vesicular systems but also limits their flexibility and permeability to solutes, while still keeping the membrane in an overall fluid‐like and thus functional state.     

Gas-phase acidity studies of multiple sites of adenine and adenine derivatives

The acidities of multiple sites in the purine nucleobase adenine (1) and adenine alkyl derivatives 9-ethyladenine (2), 3-methyladenine (3), 1-methyladenine (4), and N,N-dimethyladenine (5) have been investigated for the first time, using computational and experimental methods to provide an understanding of adenine reactivity. We have previously measured two acidic sites on adenine, with the N9 site being 19 kcal mol(-)(1) more acidic than the N10 site (333 +/- 2 versus 352 +/- 4 kcal mol(-)(1), respectively). In this work, we have established that 9-ethyladenine has two sites more acidic than water: the N10 (352 +/- 4 kcal mol(-)(1)) and the C8 (374 +/- 2 kcal mol(-)(1)). We have likewise measured two acidities for 3-methyladenine, the N10 (347 +/- 4 kcal mol(-)(1)) and the C2 (370 +/- 3 kcal mol(-)(1)). For 1-methyladenine and N,N-dimethyladenine, we measure the N9H acidity to be 331 +/- 2 and 333 +/- 2 kcal mol(-)(1), respectively. We believe that the bracketing of only one site for the latter species is a kinetic effect, which we discuss further in the paper. Computationally, we have found the interesting result that some of the vinylic C-H sites in these purine bases are predicted to be much more acidic than water (DeltaH(acid) = 390.7 kcal mol(-)(1)) in the gas phase, on the order of 373 kcal mol(-)(1). The acidic vinylic C-H sites are always adjacent to an N-R group, and this pattern is maintained regardless of whether the site is on the five- or six-membered ring of the purine. Vinylic C-H sites elsewhere on the purine have calculated acidities of about 400 kcal mol(-)(1). The differing acidities are interpreted through electrostatic potential calculations. We also relate our results to the intriguing biochemical decarboxylation of orotate ribose monophosphate, which involves a vinylic anion adjacent to an N-R group; this decarboxylation is the last step in the de novo biosynthesis of pyrimidine nucleotides, and the enzyme that catalyzes the reaction, orotate ribose monophosphate decarboxylase, has been the subject of intense study recently, as its mechanism remains elusive.     

L-ProT catalyzed highly regioselective N-alkoxyalkylation of purine rings with vinyl ethers

An efficient and regioselective synthesis of N-9 alkoxyalkylated purine nucleoside derivatives was achieved via the N-alkoxyalkylation of purine rings with vinyl ethers catalyzed by L-ProT.The advantages of this protocol include good to excellent yield,mild reaction condition,and simple manipulation.A plausible mechanism for the transformation was given.     

Molecular Mechanism of Diaminomaleonitrile to Diaminofumaronitrile Photoisomerization: An Intermediate Step in the Prebiotic Formation of Purine Nucleobases

The photoinduced isomerization of diaminomaleonitrile (DAMN) to diaminofumaronitrile (DAFN) was suggested to play a key role in the prebiotically plausible formation of purine nucleobases and nucleotides. In this work we analyze two competitive photoisomerization mechanisms on the basis of state‐of‐the‐art quantum‐chemical calculations. Even though it was suggested that this process might occur on the triplet potential‐energy surface, our results indicate that the singlet reaction channel should not be disregarded either. In fact, the peaked topography of the S₁/S₀ conical intersection suggests that the deexcitation should most likely occur on a sub‐picosecond timescale and the singlet photoisomerization mechanism might effectively compete even with a very efficient intersystem crossing. Such a scenario is further supported by the relatively small spin–orbit coupling of the S₁ and T₂ states in the Franck–Condon region, which does not indicate a very effective triplet bypass for this photoreaction. Therefore, we conclude that the triplet reaction channel in DAMN might not be as prominent as was previously thought.     

Synthesis and Triple‐Helix‐Stabilization Properties of Branched Oligonucleotides Carrying 8‐Aminoadenine Moieties

The synthesis of several branched oligonucleotides, i.e., of the parallel hairpins 5 – 8 and the Y‐shaped 9 is described, together with their use in the formation of pyrimidine?pyrimidine?purine triple helices. Special attention was paid to the optimization of the assembly of the second strand from asymmetric branching molecules. The presence of 8‐aminoadenine moieties in the Watson? Crick purine strand and 2′‐O‐methyl‐RNA in the Hoogsteen pyrimidine strand produced strong stabilization of the triplex.     

Total synthesis of the opioid agonistic indole alkaloid mitragynine and the first total syntheses of 9-methoxygeissoschizol and 9-methoxy-Nb-methylgeissoschizol

An enantiospecific method for the synthesis of 4-methoxytryptophan has been developed via a regiospecific Larock heteroannulation and employed for the first total syntheses of 9-methoxygeissoschizol and 9-methoxy-Nb-methylgeissoschizol, as well as the total synthesis of the opioid agonistic alkaloid mitragynine. The asymmetric Pictet-Spengler reaction and a Ni(COD)2-mediated cyclization served as key steps.