Origin of Informational Polymers

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119

138

The synthesis of RNA chains from 3,5-cAMP and 3,5-cGMP was observed. The RNA chains formed in water, at moderate temperatures (40 -90°C), in the absence of enzymes or inorganic catalysts. As determined by RNase analyses, the bonds formed were canonical 3,5-phosphodiester bonds. The polymerizations are based on two reactions not previously described: 1) oligomerization of 3, 5-cGMP to ϳ25-nucleotide-long RNA molecules, and of 3,5-cAMP to 4-to 8-nucleotide-long molecules. Oligonucleotide A molecules were further extended by reciprocal terminal ligation to yield RNA molecules up to >120 nucleotides long and 2) chain extension by terminal ligation of newly polymerized products of 3,5-cGMP on preformed oligonucleotides. The enzyme-and template-independent synthesis of long oligomers in water from prebiotically affordable precursors approaches the concept of spontaneous generation of (pre)genetic information.The origin of informational polymers is not understood. The RNA polymerization process has been studied for five decades, the results showing that from preactivated precursors polymers of several tens can be obtained, as reviewed previously (1). These pioneering studies provide the proof-of-principle that RNA precursors can self-assemble yielding linear polymers. However, the prebiotic validity of a process based on complex preactivation procedures is limited (1, 2), and the problem of defining a prebiotically plausible chemical and thermodynamic scenario for the synthesis and accumulation of informational polymers remains open. The core of the problem is the standard state Gibbs free energy change (3, 4) stating that condensation reactions are very inefficient in water. Given that extant polymerizations occur in water, this is a major difficulty, only partially solved by the fact that these processes at present occur inside the active site of enzymes where water activity may be drastically reduced. The other part of the extant solution, fruit of evolution, is the use of biologically highly preactivated triphosphate nucleotides (3). In primordia, RNA molecules had no enzymes to catalyze their chain-wise growth, and highly activated precursors can be considered as prebiotic only with difficulty.We reasoned that for a pre-enzymatic polymerization to occur the solution must have relied on a simple and robust process. Ideally, such a process should have been based on compounds that were reactive yet relatively stable, chemically not too elaborate to allow their efficient production, and not too dissimilar from the products of their polymerization to minimize the chemical cost of the process.It was observed that phosphorylation of nucleosides occurs in formamide simply in the presence of a source of organic or inorganic phosphate at temperatures at which both the reactants and the products are stable (5). Phosphorylation occurs in every possible position of the nucleoside sugar moiety resulting, both for purine and pyrimidine nucleosides, in the production of 2Ј-, 3Ј-, 5Ј-, 2Ј,3Ј-cyclic, and 3Ј,5Ј-cyclic XMPs 3 (5). Th...

Section: Resultsmentioning

confidence: 99%

Generation of Long RNA Chains in Water

Costanzo

Pino

Ciciriello

et al. 2009

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119

138

“…By simple heating in the presence of common catalysts, formamide yields a complete set of nucleic bases (48 -51), acyclonucleosides (52), creates conditions in which phosphoester bonds in polymers are more stable than in the monomers (14,53), and favors the formation of micelles (54,55). The novel property of formamide described here, efficient phosphorylation of nucleosides from minerals, provides one more missing link in the identification of a single unifying chemical frame for the self-organization of nucleic polymers in prebiotic conditions.…”

Section: Discussionmentioning

confidence: 99%

Nucleoside Phosphorylation by Phosphate Minerals

Costanzo

Saladino

Crestini

et al. 2007

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118

126

2؉ (PO 4 ) 2 (OH) 4 ).Based on their behavior in the formamide-driven nucleoside phosphorylation reaction, these minerals can be characterized as: 1) inactive, 2) low level phosphorylating agents, or 3) active phosphorylating agents. Instances were detected (Libethenite and Hydroxylapatite) in which phosphorylation occurs on the mineral surface, followed by release of the phosphorylated compounds. Libethenite and Cornetite markedly protect the ␤-glycosidic bond. Thus, activated nucleic monomers can form in a liquid non-aqueous environment in conditions compatible with the thermodynamics of polymerization, providing a solution to the standard-state Gibbs free energy change (⌬G°') problem, the major obstacle for polymerizations in the liquid phase in plausible prebiotic scenarios.In prebiotic scenarios biopolymers can be thought of as condensation products of abiotically formed monomers. Polymers (polysaccharides, peptides, and polynucleotides) will not spontaneously form in an aqueous solution from their monomers because of the standard-state Gibbs free-energy change (⌬G°'), as critically reviewed in Ref.(1). Thermodynamic considerations impose that amino acid polymerization or the formation of phosphodiester or glycosidic linkages will be spontaneous only under highly dehydrating conditions. Thus, either (i) life did not arise in aqueous environments, or (ii) pre-genetic polymerizations required activated monomers.In the polymerization process of nucleic acids extant organisms activate the monomers by converting them to phosphorylated derivatives and then utilize the favorable free energy of phosphate hydrolysis to drive the reaction. Does this present day process mimic spontaneously occurring prebiotic reactions, thus representing a sort of biochemiomimesis descending from ancient pathways, or should it be considered a fully novel cellular invention?The Source of Phosphate Is a Problem-Early studies on the condensation of water-soluble phosphates to polyphosphates and on the phosphorylation, condensation, or polymerization of biomolecules with polyphosphates have been reviewed (2, 3). Most of the phosphorus in the early Earth would have been in the form of water-insoluble minerals like apatites. Therefore, the origin of the water-soluble (poly)phosphates required for prebiotic evolution has long been a mystery (2). Yamagata et al. (3) showed that volcanic activity produces water-soluble phosphates through partial hydrolysis of P 4 O 10 , providing at least a partial solution to their origin. However, as pointed out, phosphates from hydrolysis of polyphosphate would precipitate to the sea bed as insoluble salts.The phosphorylation of biological molecules has been explored through several different routes. Phosphonic acids have been proposed as a source of biophosphates (4). For the phosphorylation of nucleosides, two early reports described the preparation of uridine phosphates by heating uridine with inorganic phosphates in an aqueous environment (5) and the effects of condensing agents on this reaction (6). ...

“…The protective effect exerted by formamide is probably due to the formation of an extensive and highly organized hydrogen bond network shielding the removal of nucleobases (9,16,17). Because of the high directionality of the hydrogen bond, the position of the phosphate moiety (5Ј-versus 3Ј-phosphate) is also a relevant stereo electronic parameter to be considered, 5Ј-AMP being more stable than 3Ј-AMP.…”

Section: Comparison Of the Bond Stabilities In Ribo-and In 2ј-deoxyrimentioning

confidence: 99%

Origin of Informational Polymers

Saladino

Crestini

Ciciriello

et al. 2006

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We have measured the stabilities of the bonds that are critical for determining the half-life of ribonucleotides and the ␤-glycosidic and 3-and 5-phosphoester bonds. Stabilities were measured under a wide range of temperatures and water/formamide ratios. The stability of phosphodiester bonds in oligoribonucleotides was determined in the same environments. The comparison of bond stabilities in the monomer versus the polymer forms of the ribo compounds revealed that physico-chemical conditions exist in which polymerization is thermodynamically favored. These conditions were compared with those determining a similar behavior for 2-deoxyribonucleosides, deoxyribonucleotides, and deoxyribooligonucleotides and were shown to profoundly differ. The implications of these facts on the origin of informational polymers are discussed.Minimal requirements for informational polymers to have originated under prebiotic conditions are a unitary chemical frame for the synthesis of nucleobases and a favorable thermodynamic energy balance for the polymerization of nucleotides to oligonucleotides.A Formamide-based Unitary Chemistry-To gather into a single reaction milieu all the precursors necessary for the assembly of the first informational polymers, a unitary chemical frame is needed. A series of observations suggest that formamide (NH 2 CHO) chemistry might have provided such a frame.To summarize the evidence: the one-carbon compound formamide is a highly versatile building block for the syntheses of all the necessary precursor nucleic bases. We have reported (Refs. 1-4 and references therein) the synthesis of purine, N 9 -formylpurine, adenine, N 9 , N6-diformyladenine, hypoxanthine, cytosine, hydroxypyrimidine, 4(3H)-pyrimidinone, uracil, 5,6-dihydrouracil, thymine, 5-hydroxymethyluracil, AICA (5-aminoimidazole-4-carboxamide), FAICA (5-formylaminoimidazole-4-carboxamide), and urea. These compounds are obtained from formamide heated in the presence of simple inorganic catalysts such as silica, alumina, zeolites, CaCO 3 , TiO 2 , common clays, kaolin, montmorillonites, olivines, and cosmic dust analogues of olivines. In all cases and for each catalyst several compounds were simultaneously formed, as summarized in Ref. 4.The richest yields were obtained in the presence of clays, TiO 2 , and cosmic dust analogues. Guanine is conspicuously absent, but a possible efficient substitute in base pairing might have been provided by hypoxanthine. Notably, formamide also yields purine acyclonucleosides through a formose-like condensation of N-formyl derivatives (2), providing a solution to the long-standing problem of the lack of reactivity between nucleobases and ribose or 2Ј-deoxyribose. In addition, formamide is an efficient activator of nucleoside transphosphorylation (Refs. 5-7), 2 further supporting its possible relevance in the prebiotic polymerization reactions that did lead to pregenetic informational macromolecules.Formamide is easily formed by hydrolysis of HCN and is stable in liquid form over a wide range of temperatures (2.5-2...