Fabiana Ciciriello

Generation of Long RNA Chains in Water

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 ∼25-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.

Synthesis and Degradation of Nucleobases and Nucleic Acids by Formamide in the Presence of Montmorillonites

We describe the role of formamide, a product of the hydrolysis of hydrogen cyanide, as precursor of several components of nucleic acids under prebiotic conditions. When formamide is heated in the presence of montmorillonites, the efficient one‐pot synthesis of purine, adenine, cytosine, and uracil is obtained. Along with these nucleobases, several components of the inosine pathway are obtained: 5‐aminoimidazole‐4‐carboxamide, 5‐formamidoimidazole‐4‐carboxamide and hypoxanthine. This almost complete catalogue of nucleic acid precursors is accompanied by N9‐formylpurine, which, containing a masked glycosidic bond in its formyl moiety, is a plausible precursor of purine acyclonucleosides. In addition, montmorillonites differentially affect the rate of degradation of nucleobases when embedded in 2′‐deoxyoligonucleotides; namely, montmorillonites protect adenine and guanine from the degradative action of formamide, while thymine degradation is enhanced. The oligonucleotide backbone reactivity to formamide is also affected; this shows that the interaction with montmorillonites modifies the rate of abstraction of the Hα and Hβ protons on the sugar moieties.

From formamide to RNA: the roles of formamide and water in the evolution of chemical information

In pursuing the origin of informational polymers, we followed the assumption that their spontaneous formation could only have occurred: (i) if all the components were present at the same site and in the same reaction, and (ii) if the thermodynamics of the processes involved favored a polymerized over a monomeric state of the precursors. A plausible scenario satisfying both assumptions is provided.

Formamide as the main building block in the origin of nucleic acids

The simplest molecules grouping the four most common elements of the universe H,C,O and N (with the exception of the biologically inert He) are isocyanate HNCO and formamide H2NCOH. Reasons for the availability of formamide on prebiotic Earth are presented. We review evidence showing that formamide in the presence of largely available catalysts and by moderate heating yields the complete set of nucleic bases necessary for the formation of nucleic acids. Formamide also favours the formation of acyclonucleosides and the phosphorylation and trans-phosphorylation of nucleosides, thus providing a plausible chemical frame for the passage from a simple one-carbon compound to nucleic polymers. Physico-chemical conditions exist in which formamide favours the stability of the phosphoester bonds in nucleic polymers relative to that of the same bonds in monomers. Starting from a formamide-laden environment subject only to the laws of chemistry, a hypothesis is outlined sketching the passage towards an aqueous world in which Darwinian rules apply.

Synthesis and degradation of nucleic acid components by formamide and cosmic dust analogues

We show the unprecedented one‐pot synthesis of a large suite of pyrimidines (including cytosine and uracil) and purines from formamide in the presence of cosmic‐dust analogues (CDAs) of olivines. Since the major problem in the origin of informational macromolecules is the instability of their precursors, we also investigate the stabilizing effect of CDAs on the intrinsic instability of oligonucleotides in formamide.

Nonenzymatic RNA Ligation in Water

We describe the nonenzymatic ligation of RNA oligomers in water. Dimers and tetramers are formed in a time-, pH-, and temperature-dependent reaction. Ligation efficiency depends on oligonucleotide length and sequence and is strongly enhanced by adenine-based nucleotide cofactors. Ligation of short RNA fragments could have liberated the prebiotic polymerization systems from the thermodynamically demanding task of reaching a (pre)genetically meaningful size by stepwise addition of one precursor monomer at the time.

Origin of informational polymers: Differential stability of phosphoester bonds in ribomonomers and ribooligomers

We have measured the stabilities of the bonds that are critical for determining the half-life of ribonucleotides and the β-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.

Origin of Informational Polymers: The Concurrent Roles of Formamide and Phosphates

Formamide chemistry provides a unitary system by gathering all of the precursors needed to synthesise pregenetic informational polymers in a single milieu. This is not observed with HCN chemistry. With common catalysts, formamide affords all of the precursor nucleobases, photochemically condenses into acyclonucleosides, favours transphosphorylation and enhances micellar aggregation of surfactants. Also, formamide provides a set of physicochemical conditions that thermodynamically favour the polymeric state of nucleotides over the monomers. In the origin‐of‐informational‐polymers scenario, formamide acts in every step, the least characterised being the set of its reactions with phosphates. On this matter, we report two complementary sets of results: 1) the synthesis of prebiotic precursors from formamide, which are catalysed by soluble and mineral phosphates—we observed the formation of rich mixtures that include uracil, 9H‐purine, cytosine, dihydrouracil, hypoxanthine, adenosine, urea, parabanic acid, the amino acid N‐formylglycine and the peptide‐condensing agent carbodiimide; and 2) the protection of ribo‐ and deoxyribophosphoester bonds by phosphates. The relevance of these effects with respect to the origin of informational polymers is discussed.

About a Formamide-Based Origin of Informational Polymers: Syntheses of Nucleobases and Favourable Thermodynamic Niches for Early Polymers

Formamide NH2CHO chemistry provides a unitary frame into which several pieces of the origin-of-life puzzle may be adjusted. Synthetic processes were uncovered which, starting from formamide and prebiotically easily available common catalysts, yield all the necessary nucleic bases precursors, including acyclonucleosides. Formamide allows phosphorylations and trans-phosphorylations, favours the micellar aggregation of surfactants and, most importantly, determines conditions in which the formation of nucleic polymers is thermodynamically favoured. In the detected conditions, the phosphoester bonds are more stable in the polymeric than in the monomeric form, thus allowing formation and survival of informational nucleic polymers.

A Novel Synthesis of Biomolecular Precursors

We discuss the role of formamide, a product of hydrolysis of hydrogen cyanide (HCN), as precursor of relevant components of nucleic acids in prebiotic conditions and describe the efficient synthesis of purine, adenine, cytosine, thymine, and 5-hydroxymethyluracil. The remarkable formation of some purine acyclonucleosides is also reported, providing a possible solution to the problem of the elusive origin of nucleosides under prebiotic conditions. The role of catalysts as CaCO3, silica, alumina, TiO2 and others in enhancing and variegating the yields of these compounds is described. In addition, formamide acts as a selective agent in the degradation of bases, nucleosides and DNA oligomers. Taken together, these observations reveal a formamide-based synthesis/degradation cycle whose properties provide an equilibration mechanism for the pool of prebiotic precursors.