Chemomimesis and Molecular Darwinism in Action: From Abiotic Generation of Nucleobases to Nucleosides and RNA.

Molecular Darwinian evolution is an intrinsic property of reacting pools of molecules resulting in the adaptation of the system to changing conditions. It has no a priori aim. From the point of view of the origin of life, Darwinian selection behavior, when spontaneously emerging in the ensembles of molecules composing prebiotic pools, initiates subsequent evolution of increasingly complex and chemical information.

Nonenzymatic Oligomerization of 3',5'-Cyclic CMP Induced by Proton and UV Irradiation Hints at a Nonfastidious Origin of RNA.

We report that 3',5'-cyclic CMP undergoes nonenzymatic di- and trimerization at 20 °C under dry conditions upon proton or UV irradiation. The reaction involves stacking of the cyclic monomers and subsequent polymerization through serial transphosphorylations between the stacked monomers. Proton- and UV-induced oligomerization of 3',5'-cyclic CMP demonstrates that pyrimidines-similar to purines-might also have taken part in the spontaneous generation of RNA under plausible prebiotic conditions as well as in an extraterrestrial context.

Non-Enzymatic Oligomerization of 3', 5' Cyclic AMP.

Recent studies illustrate that short oligonucleotide sequences can be easily produced from nucleotide precursors in a template-free non-enzymatic way under dehydrating conditions, i.e. using essentially dry materials.

Emergence of the First Catalytic Oligonucleotides in a Formamide-Based Origin Scenario.

50 years after the historical Miller-Urey experiment, the formamide-based scenario is perhaps the most powerful concurrent hypothesis for the origin of life on our planet besides the traditional HCN-based concept. The information accumulated during the last 15 years in this topic is astonishingly growing and nowadays the formamide-based model represents one of the most complete and coherent pathways leading from simple prebiotic precursors up to the first catalytically active RNA molecules. In this work, we overview the major events of this long pathway that have emerged from recent experimental and theoretical studies, mainly concentrating on the mechanistic, methodological, and structural aspects of this research.

From formamide to RNA, the path is tenuous but continuous.

Reactions of formamide (NH2COH) in the presence of catalysts of both terrestrial and meteoritic origin yield, in plausible and variegated conditions, a large panel of precursors of (pre)genetic and (pre)metabolic interest. Formamide chemistry potentially satisfies all of the steps from the very initial precursors to RNA. Water chemistry enters the scene in RNA non-enzymatic synthesis and recombination.

Tetraloop-like geometries could form the basis of the catalytic activity of the most ancient ribooligonucleotides.

The origin of the catalytic activity of ancient oligonucleotides is a largely unexplored field of contemporary science. In the current work we use molecular dynamics simulations to investigate the plausibility of tetraloop-like overhang geometries to initiate transphosphorylation reactions that lead to ligation and terminal cleavage in simple, Watson-Crick (WC) complementary oligoC/oligoG sequences observed experimentally. We show a series of examples of known tetraloop architectures, which can be adopted by the unpaired overhangs of short oligonucleotide sequences for a sufficiently long time to enable chemical reactions that lead to simple ribozyme-like catalytic activity.

Untemplated nonenzymatic polymerization of 3',5'cGMP: a plausible route to 3',5'-linked oligonucleotides in primordia.

The high-energy 3',5' phosphodiester linkages conserved in 3',5' cyclic GMPs offer a genuine solution for monomer activation required by the transphosphorylation reactions that could lead to the emergence of the first simple oligonucleotide sequences on the early Earth. In this work we provide an in-depth characterization of the effect of the reaction conditions on the yield of the polymerization reaction of 3',5' cyclic GMPs both in aqueous environment as well as under dehydrating conditions. We show that the threshold temperature of the polymerization is about 30 °C lower under dehydrating conditions than in solution.

Materials for the onset. A story of necessity and chance.

We review the reactions that take place in the HCN/NH2COH/catalysts system. In a vision of origin-of-life as emergence of new properties in complexity, the effectiveness of HCN/NH2COH chemistry is so robust and variegate to look unreasonable. In a logic close to Occamian simplicity, this chemistry embodies necessity.

From the one-carbon amide formamide to RNA all the steps are prebiotically possible.

Formamide provides the raw material and the reaction leads connecting hydrogen cyanide HCN chemistry with higher complexity molecular structures. Formamide is liquid between 4 and 210 °C and, upon heating in the presence of one of several catalysts, affords nucleic bases, acyclonucleosides, carboxylic acids and aminoacids. In formamide in the presence of a source of phosphate, nucleosides are non-fastidiously phosphorylated in every position of the sugar residue, also yielding cyclic nucleotides.

Genetics first or metabolism first? The formamide clue.

Life is made of the intimate interaction of metabolism and genetics, both built around the chemistry of the most common elements of the Universe (hydrogen, oxygen, nitrogen, and carbon). The transmissible interaction of metabolic and genetic cycles results in the hypercycles of organization and de-organization of chemical information, of living and non-living. The origin-of-life quest has long been split into several attitudes exemplified by the aphorisms "genetics-first" or "metabolism-first".

Generation of RNA molecules by a base-catalysed click-like reaction.

The problem of the abiotic origin of RNA from prebiotically plausible compounds remains unsolved. As a potential partial solution, we report the spontaneous polymerization of 3',5'-cyclic GMP in water, in formamide, in dimethylformamide, and (in water) in the presence of a Brønsted base such as 1,8-diazabicycloundec-7-ene. The reaction is untemplated, does not require enzymatic activities, is thermodynamically favoured and selectively yields 3',5'-bonded ribopolymers containing as many as 25 nucleotides.

Formamide and the origin of life.

The complexity of life boils down to the definition: "self-sustained chemical system capable of undergoing Darwinian evolution" (Joyce, 1994) [1]. The term "self-sustained" implies a set of chemical reactions capable of harnessing energy from the environment, using it to carry out programmed anabolic and catabolic functions. We briefly present our opinion on the general validity of this definition.

May cyclic nucleotides be a source for abiotic RNA synthesis?

Nucleic bases are obtained by heating formamide in the presence of various catalysts. Formamide chemistry also allows the formation of acyclonucleosides and the phosphorylation of nucleosides in every possible position, also affording 2',3' and 3',5' cyclic forms. We have reported that 3',5' cyclic GMP and 3',5' cyclic AMP polymerize in abiotic conditions yielding short oligonucleotides.

On the observable transition to living matter.

In recent developments in chemistry and genetic engineering, the humble researcher dealing with the origin of life finds her(him)self in a grey area of tackling something that even does not yet have a clear definition agreed upon. A series of chemical steps is described to be considered as the life-nonlife transition, if one adheres to the minimalistic definition: life is self-reproduction with variations. The fully artificial RNA system chosen for the exploration corresponds sequence-wise to the reconstructed initial triplet repeats, presumably corresponding to the earliest protein-coding molecules.

Nonenzymatic ligation of an RNA oligonucleotide analyzed by atomic force microscopy.

The products of ligation reaction of a 24 nucleotides long PolyA RNA adsorbed on mica were observed by atomic force microscopy. The occurrence of oligonucleotides at different degrees of polymerization has been quantitatively studied before and after ligation reaction. The microscopy images at the nanoscale show that nonenzymatic ligation of pristine RNA monomers results in the formation of supramolecular aggregates, with prevalence of dimers and tetramers.

Sequence complementarity-driven nonenzymatic ligation of RNA.

We report two reactions of RNA G:C sequences occurring nonenzymatically in water in the absence of any added cofactor or metal ion: (a) sequence complementarity-driven terminal ligation and (b) complementary sequence adaptor-driven multiple tandemization. The two abiotic reactions increase the chemical complexity of the resulting pool of RNA molecules and change the Shannon information of the initial population of sequences.

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 degrees C), in the absence of enzymes or inorganic catalysts. As determined by RNase analyses, the bonds formed were canonical 3',5'-phosphodiester bonds.

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.

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.

Resveratrol and X rays affect gap junction intercellular communications in human glioblastoma cells.

Resveratrol (3,4',5-trihydroxystilbene) is a polyphenol synthesized by a wide variety of plant species in response to injury, UV irradiation and fungal attack. Many studies have revealed a variety of resveratrol intracellular targets whose modulation gives rise to overlapping responses leading to growth arrest and death. Many authors have reported different human cancer cell lines, treated with resveratrol at micromolar concentrations, arrested their proliferative cycle in the G1/S boundary or in the S phase and this cell cycle arrest was followed by apoptotic death.

Molecular complexity favors the evolution of ribopolymers.

We have explored the stability of selected ribo oligomers in water and have determined the physical-chemical conditions in which the key 3'-phosphoester bond is more stable when embedded in the polymer than when present in the monomer. In these conditions, the spontaneous formation and the survival of ribo polymers are potentially favored. A narrow pH range was identified in which complex sequences resist degradation markedly more than monotonous ones, thus potentially favoring the evolution of sequence-based genetic information.