Prebiotic routes to nucleosides: a quantum chemical insight into the energetics of the multistep reaction pathways

One of the most controversial questions of the RNA world theory is the formation of nucleosides through the reaction of nucleobases with ribose. The study presented herein discusses the thermodynamics of nucleoside formation under prebiotic conditions through the classical reaction route, which involves ribose and cytosine, as well as through the novel pathway suggested by Powner et al. [Nature 2009 , 459, 239–242]. Our computations show that, in contrast to the classical pathway, the route proposed by Powner et al. perfectly satisfies all conditions of a typical metabolic pathway that occurs in living organisms. In addition, we reveal the reasons that render the reaction of ribose with nucleobases endothermic and, thereby, less plausible under prebiotic conditions. We show that phosphates may play an indispensable role in the glycosylation of nucleobases by making this endothermic reaction step exothermic. In addition, we describe the catalytic role of phosphate anions in the formation of 2‐aminooxazole, which is one of the key steps of the synthetic route reported by Powner et al.     

Simple ethers as models of sugar molecules in calculations of vertical excitation energies of DNA and RNA nucleosides

The ribose and deoxyribose molecules of RNA and DNA nucleosides are substituted with simple model compounds 1-methoxy-2-ethanol and 1-methoxypropane to mimic the effect of binding to sugars on the vertical excitation energies of purine and pyrimidine bases. The (R)-1-methoxy-2-ethanol, CH(3)OC*HCH(2)OH, for model ribose nucleosides and (R)-1-methoxypropane, CH(3)OC*HC(2)H(5), for model deoxyribose nucleosides have minimal structural characteristics of ribose and deoxyribose molecules when attached to nucleic acid purine and pyrimidine bases. The bases are attached to the C1 carbon atom designated by the asterisk. The vertical excitation energies of these model nucleosides are calculated with the time-dependent density functional theory method at the B3LYP level with 6-311++G(d,p) and aug-cc-pVDZ basis sets. The attachment of the ether molecules qualitatively and quantitatively modifies the excited state energy levels of the model nucleosides when compared to the free bases. These changes can affect the deexcitation mechanisms for photoexcited nucleosides.     

Correlation of the C-1′ chemical shifts with the vicinal spin-spin coupling constants of the H-1′ and H-2′ protons in nucleosides. II. 2′-, 3′-, and 5′-O-substituted nucleosides

The existence of a correlation has been established for pyrimidine but not for purine, nucleosides. It is suggested that the change in the chemical shift of the anomeric carbon is a consequence of 1,2-eclipsing interaction between O-2′ and N-1′ in the S type of conformation of the ribose ring. Possible reason for the absence of a correlation in the case of purine nucleosides are discussed. It is shown that the chemical shift of the anomeric carbon can be used in the conformational analysis of the ribose rings of pyrimidine nucleosides.     

Complexes of copper(II) with adenosine or guanosine nucleosides, nucleotides 5'-monophosphate, 2'-deoxynucleosides or 2'-deoxynucleotides 5'-monophosphate in aqueous solution

In this paper copper(II) complex formation in aqueous solution with a series of nucleosides (adenosine or guanosine) or nucleotides 5'-monophosphate is studied by means of potentiometry, visible spectrophotometry and ultraviolet circular dichroism. A chemical model has been formulated for each binary system (at T= 25 degrees C and I = 0.1 M), with particular attention to the interaction in the basic field. A spectrum (both visible absorption and ultraviolet circular dichroism) for each complex with a significant percentage of formation (in the adopted experimental conditions) has been calculated, allowing structural details to be hypothesised. The interaction with deprotonated alcoholic group(s) of the ribose moiety has been found to be fundamental in determining the co-ordination chemistry of each ligand considered while cases of co-operation between the purine and ribose donor(s) were also considered. Confirmations were also obtained by an investigation on the corresponding 2'-deoxy compounds as ligands.     

Phosphoribosyl Pyrophosphate: A Molecular Vestige of the Origin of Life on Minerals

In this contribution, we report the formation under prebiotic conditions of phosphoribosyl pyrophosphate (PRPP) as a molecular precursor in the one‐pot synthesis of a canonical nucleotide, namely adenosine monophosphate (AMP) from its building blocks (KH₂PO₄ or P_i, adenine, and d ‐ribose), on a fumed silica surface. The on‐the‐rocks approach ¹ has been successfully applied to the simultaneous phosphorylation and glycosylation of ribose. The one‐pot formation mechanism of AMP involves a two‐step pathway via an activated intermediate, namely PRPP, obtained by multiple ribose phosphorylations upon mild thermal activation.     

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.     

Chemoenzymatic preparation of nucleosides from furanoses

Chemoenzymatic preparation of ribose, deoxyribose and arabinose 5-phosphates was accomplished. These compounds were tested as starting materials in the enzymatic preparation of natural and modified purine and pyrimidine nucleosides, using an overexpressed Escherichia coli phosphopentomutase.     

Thioguanosine Conversion Enables mRNA-Lifetime Evaluation by RNA Sequencing Using Double Metabolic Labeling (TUC-seq DUAL)

Temporal information about cellular RNA populations is essential to understand the functional roles of RNA. We have developed the hydrazine/NH₄Cl/OsO₄-based conversion of 6-thioguanosine (6sG) into A′, where A′ constitutes a 6-hydrazino purine derivative. A′ retains the Watson–Crick base-pair mode and is efficiently decoded as adenosine in primer extension assays and in RNA sequencing. Because 6sG is applicable to metabolic labeling of freshly synthesized RNA and because the conversion chemistry is fully compatible with the conversion of the frequently used metabolic label 4-thiouridine (4sU) into C, the combination of both modified nucleosides in dual-labeling setups enables high accuracy measurements of RNA decay. This approach, termed TUC-seq DUAL, uses the two modified nucleosides in subsequent pulses and their simultaneous detection, enabling mRNA-lifetime evaluation with unprecedented precision.     

Investigation of the influence of intramolecular electrostatic interactions on the conformational equilibrium in pyrimidine nucleosides by the PMR method

The influence of solvents on the PMR spectra of uridine and cytidine has been studied. Because of intramolecular electrostatic interactions (IEIs) between the 2-keto oxygen and the freely rotating 2-hydroxyl, the position of the conformational equilibrium in the pyrimidine nucleosides but not in purine and deoxy nucleosides, depends substantially on the dielectric constant of the solvent and the size of the partial negative charge on the 2-keto oxygen of the base. It has been shown that an increase in the IEI leads to an increase in the 3′-endo (N) population of the ribose ring and to an increased influence of the temperature on the state of the conformational equilibrium.     

Thioguanosine Conversion Enables mRNA‐Lifetime Evaluation by RNA Sequencing Using Double Metabolic Labeling (TUC‐seq DUAL)

Temporal information about cellular RNA populations is essential to understand the functional roles of RNA. We have developed the hydrazine/NH₄Cl/OsO₄‐based conversion of 6‐thioguanosine (6sG) into A′, where A′ constitutes a 6‐hydrazino purine derivative. A′ retains the Watson–Crick base‐pair mode and is efficiently decoded as adenosine in primer extension assays and in RNA sequencing. Because 6sG is applicable to metabolic labeling of freshly synthesized RNA and because the conversion chemistry is fully compatible with the conversion of the frequently used metabolic label 4‐thiouridine (4sU) into C, the combination of both modified nucleosides in dual‐labeling setups enables high accuracy measurements of RNA decay. This approach, termed TUC‐seq DUAL, uses the two modified nucleosides in subsequent pulses and their simultaneous detection, enabling mRNA‐lifetime evaluation with unprecedented precision.     

Selective derivatization and sequestration of ribose from a prebiotic mix

Observations regarding the catalytic potential of RNA and the role of RNA in biology have formed the basis for the "RNA world" hypothesis, which suggests that a genetic system based on self-replicating polyribonucleotides preceded modern biology. However, attempts to devise a realistic prebiotic synthesis of nucleic acids from simple starting materials have been plagued by problems of poor chemical selectivity, lack of stereo- and regiospecificity, and similar rates of formation and degradation of some of the key intermediates. For example, ribose would have been only a small component of a highly complex mix of sugars resulting from the condensation of formaldehyde in a prebiotic world. In addition, ribose is more reactive and degrades more rapidly compared with most other monosaccharides. This study demonstrates an approach for the preferential sequestration of ribose relative to other sugars that takes advantage of its greater reactivity. Cyanamide reacts especially rapidly with ribose to form a stable bicyclic adduct. This product crystallizes spontaneously in aqueous solution, whereas the corresponding products derived from threose, galactose, glucose, mannose, and each of the other pentoses do not. Furthermore, when employing a racemic mixture of d- and l-ribose, enantiomerically twinned crystals are formed that contain discrete homochiral domains.     

Application of reversed-phase and ion-pair HPLC for investigation of nucleotide metabolism in erythrocytes,reticulocytes and tumour cells

Summary The determination of nucleotides, nucleosides, and nucleobases was carried out in cells of different metabolic complexity: in mature and immature red blood cells, in Ehrlich ascites tumour cells from different proliferation stages, and in other tumour cells. The maturation of reticulocytes to erythrocytes is accompanied by loss of organelles and energy-requiring processes as well as the switch from aerobic to anaerobic ATP production. The profile of purine nucleotides, nucleosides, bases, and pyridine dinucleotides, by reversed-phae HPLC, shows large concentration changes during the maturation of red blood cells. The concentrations of purine mono and triphosphates are two to four times greater in reticulocytes in comparison with erythrocytes; the difference in the concentrations of nucleosides and nucleobases between reticulocytes and erythrocytes is even greater. Application of ion-pair HPLC showed that the Ehrlich ascites cells loose major portions of purine mono-, diand triphosphates between the 7th and 11th day after inoculation. Fast growing solid sarcoma tumours of rats (MV 202 Ner) contain higher amounts of nucleotides than slowly growing tumours of identical cell type.     

Unusual deoxygenation and reactivity studies related to O6-(benzotriazol-1-yl)inosine derivatives

New and unusual developments related to the chemistry of O6-(benzotriazol-1-yl)inosine derivatives are reported. First, a simple, scalable method for their syntheses via the use of PPh3/I2/HOBt has been developed and has been mechanistically investigated by 31P(1H) NMR. Studies were then conducted into a unique oxygen transfer reaction between O6-(benzotriazol-1-yl)inosine nucleosides and bis(pinacolato)diboron (pinB-Bpin) leading to the formation of C-6 (benzotriazol-1-yl)purine nucleoside derivatives and pinB-O-Bpin. This reaction has been investigated by 11B(1H) NMR and compared to pinB-O-Bpin obtained by oxidation of pinB-Bpin. The structures of the C-6 (benzotriazol-1-yl)purine nucleosides have been unequivocally established via Pd-mediated C-N bond formation between bromo purine nucleosides and 1H-benzotriazole. Finally, short and extremely simple synthesis of 1,N6-ethano- and 1,N6-propano-2'-deoxyadenosine are reported in order to demonstrate the synthetic versatility of the O6-(benzotriazol-1-yl)inosine nucleoside derivatives for the assembly of relatively complex compounds.     

Conformational properties of shape modified nucleosides--fleximers

A detailed (1)H NMR conformational study complemented with ab initio computations was performed in solution on fleximer nucleosides 1, 3, and 5 in relation to their natural counterparts. The substitution of the purine nucleobase found in the natural nucleosides with a more flexible two-ring heterocyclic system strongly increased the population of anti conformation around the glycosidic bond. This was accompanied by a large shift toward a north-type sugar conformation, which was explained by the interplay of anomeric, gauche, and steric effects. The formal separation of the bicyclic purine base into its imidazole and pyrimidine moieties allows for formation of a hydrogen bond between the NH(2) and 2'-OH groups and facilitates favorable conjugation between the two heterocyclic rings. Our results show that the interplay of stereoelectronic effects, combined with the flexibility of the nucleobase and possible conjugation effects within the nucleobase, plays a crucial role in the search for shape-mimic nucleosides that will interact with flexible binding sites.     

Precursors of biological cofactors from ultraviolet irradiation of circumstellar/interstellar ice analogues

Biological cofactors include functionalized derivatives of cyclic tetrapyrrole structures that incorporate different metal ions. They build up structural partnerships with proteins, which play a crucial role in biochemical reactions. Porphyrin, chlorin, bacteriochlorin, and corrin are the basic structures of cofactors (heme, chlorophyll, bacteriochlorophyll, siroheme, F 430, and vitamin B12). Laboratory and theoretical work suggest that the molecular building blocks of proteins (alpha-amino acids) and nucleic acids (carbohydrates, purines, and pyrimidines) were generated under prebiotic conditions. On the other hand, experimental data on the prebiotic chemistry of cofactors are rare. We propose to search directly for the pathways of the formation of cofactors in the laboratory. Herein we report on the detection of N-heterocycles and amines in the room-temperature residue obtained after photo- and thermal processing of an interstellar ice analogue under high vacuum at 12 K. Among them, hexahydro-1,3,5-triazine and its derivatives, together with monopyrrolic molecules, are precursors of porphinoid cofactors. Hexahydropyrimidine was also detected. This is the first detection of these compounds in experiments simulating circumstellar/interstellar conditions. Except for 2-aminopyrrole and 2,4-diaminofuran, which were only found in 13C-labeled experiments, all the reported species were detected in both 12C- and 13C-labeled experiments, excluding contamination. The molecules reported here might be present in circumstellar/interstellar grains and cometary dust and could be detected by the Stardust and Rosetta missions.     

A prebiotic role for 8-oxoguanosine as a flavin mimic in pyrimidine dimer photorepair

Redox-active enzyme cofactors derived from ribonucleotides have been called "fossils of the RNA world," suggesting that early catalysts employed modified nucleobases to facilitate redox chemistry in primitive metabolism. Here, we show that the common oxidative damage product 8-oxo-7,8-dihydroguanine (OG), when incorporated into a DNA or RNA strand in proximity to a cyclobutane pyrimidine dimer, can mimic the function of a flavin in photorepair. The OG nucleotide acts catalytically in a mechanism consistent with that of photolyase in which the photoexcited state of the purine donates an electron to a pyrimidine dimer to initiate bond cleavage; subsequent back electron transfer regenerates OG. This unusual example of one form of DNA damage, oxidation, functioning to repair another, photodimerization, may provide insight into the origins of prebiotic redox processes.     

Chemical Etiology of Nucleic Acid Structure: The Pentulofuranosyl Oligonucleotide Systems: The (1′→3′)‐β‐L‐Ribulo, (4′→3′)‐α‐L‐Xylulo,and (1′→3′)‐α‐L‐Xylulo Nucleic Acids

Under potentially prebiotic scenarios, ribose (pentose), the component of RNA is formed in meager amounts, as opposed to ribulose and xylulose (pentuloses). Consequently, replacement of ribose in RNA, with pentulose sugars, gives rise to prospective oligonucleotide candidates that are potentially prebiotic structural variants of RNA that could be formed by the same type of chemical pathways that gave rise to RNA from ribose. The potentially natural alternative (1′→3′)‐ribulo oligonucleotides and (4′→3′)‐ and (1′→3′)‐xylulo oligonucleotides consisting of adenine and thymine were synthesized and found to exhibit no self‐pairing or cross‐pairing with RNA. This signifies that even though pentulose sugars may have been abundant in a prebiotic scenario, the pentulose nucleic acids (NAs), if and when formed, would not have been competitors of RNA, or interfered with the emergence of RNA as a functional informational system. The reason for the lack of base pairing in pentulose NA highlights the contrasting and central role played by the furanosyl ring in RNA and pentulose NA, enabling and optimizing the base pairing in RNA, while impeding it in pentulose NA.     

Investigation of the influence of intramolecular electrostatic interactions on the conformational equilibrium in pyrimidine nucleosides by the PMR method

The influence of solvents on the PMR spectra of uridine and cytidine has been studied. Because of intramolecular electrostatic interactions (IEIs) between the 2-keto oxygen and the freely rotating 2-hydroxyl, the position of the conformational equilibrium in the pyrimidine nucleosides but not in purine and deoxy nucleosides, depends substantially on the dielectric constant of the solvent and the size of the partial negative charge on the 2-keto oxygen of the base. It has been shown that an increase in the IEI leads to an increase in the 3-endo (N) population of the ribose ring and to an increased influence of the temperature on the state of the conformational equilibrium.All-Union Scientific-Research Institute of Applied Biochemistry, Olaine. Translated from Khimiya Prirodnykh Soedinenii, No. 3, pp. 362–366, May–June, 1981.     

Selective Voltammetric and Flow-Injection Determination of Guanosine and Adenosine at a Glassy Carbon Electrode Modified with a Ruthenium Hexachlororuthenate Film

An inorganic film of ruthenium hexachlororuthenate (RuRuCl₆), deposited on the surface of a glassy carbon electrode, exhibits electrocatalytic activity in the oxidation of purine nucleosides, such as guanosine and adenosine. Appropriate operating conditions are found for fabricating a polymer film on the surface of glassy carbon and for recording the maximum electrocatalytic current for the modified electrode. A method for the selective voltammetric determination of guanosine and adenosine in their simultaneous presence at an electrode modified by a RuRuCl₆ film is developed. A procedure is proposed for the amperometric detection of purine nucleosides with this modified electrode under the conditions of flow-injection analysis. The linear dependence of the analytical signal on the concentration of guanosine and adenosine is observed up to 5 × 10^–6 M in the stationary mode and up to 5 × 10^–7 M in the flow system. The proposed method for the selective determination of guanosine and adenosine was tested in the analysis of human urine.