Reaction of cytidine nucleotides with cyanoacetylene: support for the intermediacy of nucleoside-2',3'-cyclic phosphates in the prebiotic synthesis of RNA

On the prebiotic selection of nucleotide anomers: A computational study

Present-day known predominance of the β- over the α-anomers in nucleosides and nucleotides emerges from a thermodynamic analysis of their assembly from their components, i.e. bases, sugars, and a phosphate group. Furthermore, the incorporation of uracil into RNA and thymine into DNA rather than the other way around is also predicted from the calculations. An interplay of kinetics and thermodynamics must have driven evolutionary selection of life's building blocks. In this work, based on quantum chemical calculations, we focus on the latter control as a tool for “natural selection”.

Questions and Answers Related to the Prebiotic Production of Oligonucleotide Sequences from 3',5' Cyclic Nucleotide Precursors

Template-free nonenzymatic polymerization of 3',5' cyclic nucleotides is an emerging topic of the origin of life research. In the last ten years, a number of papers have been published addressing various aspects of this process. These works evoked a vivid discussion among scientists working in the field of prebiotic chemistry. The aim of the current review is to answer the most frequently raised questions related to the detection and characterization of oligomeric products as well as to the geological context of this chemistry.

Addressing regio- and stereo-specificity challenges in the synthesis of nucleoside 2',3'-cyclic monophosphate analogs - a rapid and facile synthesis of nucleoside-2',3'-O,O-phosphoro-thioate or -selenoate, and elucidation of the origin of the rare specificity

A new facile, rapid, stereo- and regio-selective one-pot synthesis of nucleoside-2',3'-O,O-phosphorothioate and selenoate analogs has been developed. This method avoids the need for protection strategies and chiral reagents, chiral metal catalysts, or chiral separations. This synthetic method has been applied to all natural nucleosides (U/A/G/C/T). Furthermore, we have deciphered the origin of the stereo- and regio-selectivity of the reaction.

Ionization photophysics and spectroscopy of cyanoacetylene

Photoionization of cyanoacetylene was studied using synchrotron radiation over the non-dissociative ionization excitation range 11-15.6 eV, with photoelectron-photoion coincidence techniques. The absolute ionization cross-section and spectroscopic aspects of the parent ion were recorded. The adiabatic ionization energy of cyanoacetylene was measured as 11.573 ± 0.010 eV. A detailed analysis of photoelectron spectra of HC3N involves new aspects and new assignments of the vibrational components to excitation of the A(2)Σ(+) and B(2)Π states of the cation. Some of the structured autoionization features observed in the 11.94 to 15.5 eV region of the total ion yield (TIY) spectrum were assigned to two Rydberg series converging to the B(2)Π state of HC3N(+). A number of the measured TIY features are suggested to be vibrational components of Rydberg series converging to the C(2)Σ(+) state of HC3N(+) at ≈17.6 eV and others to valence shell transitions of cyanoacetylene in the 11.6-15 eV region. The results of quantum chemical calculations of the cation electronic state geometries, vibrational frequencies and energies, as well as of the C-H dissociation potential energy profiles of the ground and electronic excited states of the ion, are compared with experimental observations. Ionization quantum yields are evaluated and discussed and the problem of adequate calibration of photoionization cross-sections is raised.

Non-canonical 3'-5' extension of RNA with prebiotically plausible ribonucleoside 2',3'-cyclic phosphates

Ribonucleoside 2′,3′-cyclic phosphates (N>p’s) are generated by multiple prebiotically plausible processes and are credible building blocks for the assembly of early RNA oligomers. While N>p’s can be polymerized into short RNAs by non-enzymatic processes with variable efficiency and regioselectivity, no enzymatic route for RNA synthesis had been described. Here we report such a non-canonical 3′-5′ nucleotidyl transferase activity. We engineered a variant of the hairpin ribozyme to catalyze addition of all four N>p’s (2′,3′-cyclic A-, G-, U-, and CMP) to the 5′-hydroxyl termini of RNA strands with 5′ nucleotide addition enhanced in all cases by eutectic ice phase formation at −7 °C. We also observed 5′ addition of 2′,3′-cyclic phosphate-activated β-nicotinamide adenine dinucleotide (NAD>p) and ACA>p RNA trinucleotide, and multiple additions of GUCCA>p RNA pentamers. Our results establish a new mode of RNA 3′-5′ extension with implications for RNA oligomer synthesis from prebiotic nucleotide pools.

Primitive genetic polymers

Since the structure of DNA was elucidated more than 50 years ago, Watson-Crick base pairing has been widely speculated to be the likely mode of both information storage and transfer in the earliest genetic polymers. The discovery of catalytic RNA molecules subsequently provided support for the hypothesis that RNA was perhaps even the first polymer of life. However, the de novo synthesis of RNA using only plausible prebiotic chemistry has proven difficult, to say the least. Experimental investigations, made possible by the application of synthetic and physical organic chemistry, have now provided evidence that the nucleobases (A, G, C, and T/U), the trifunctional moiety ([deoxy]ribose), and the linkage chemistry (phosphate esters) of contemporary nucleic acids may be optimally suited for their present roles-a situation that suggests refinement by evolution. Here, we consider studies of variations in these three distinct components of nucleic acids with regard to the question: Is RNA, as is generally acknowledged of DNA, the product of evolution? If so, what chemical and structural features might have been more likely and advantageous for a proto-RNA?

Chemoselective multicomponent one-pot assembly of purine precursors in water

The recent development of a sequential, high-yielding route to activated pyrimidine nucleotides, under conditions thought to be prebiotic, is an encouraging step toward the greater goal of a plausible prebiotic pathway to RNA and the potential for an RNA world. However, this synthesis has led to a disparity in the methodology available for stepwise construction of the canonical pyrimidine and purine nucleotides. To address this problem, and further explore prebiotically accessible chemical systems, we have developed a high-yielding, aqueous, one-pot, multicomponent reaction that tethers masked-sugar moieties to prebiotically plausible purine precursors. A pH-dependent three-component reaction system has been discovered that utilizes key nucleotide synthons 2-aminooxazole and 5-aminoimidazoles, which allows the first divergent purine/pyrimidine synthesis to be proposed. Due to regiospecific aminoimidazole tethering, the pathway allows N9 purination only, thus suggesting the first prebiotically plausible mechanism for regiospecific N9 purination.

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.

On the prebiotic synthesis of ribonucleotides: photoanomerisation of cytosine nucleosides and nucleotides revisited

Recent work has emphasised the importance of D-ribose aminooxazoline 1 in the synthesis of cytidine ribonucleosides under potentially prebiotic conditions. Upon treatment with cyanoacetylene, 1 is transformed into alpha-D-cytidine (alpha-2), and if an efficient means of anomerising this nucleoside or a derivative thereof were to be found, then the synthesis of one of the key beta-D-nucleosides required to make RNA would be realised. Photoanomerisation of alpha-2 has previously been described, but the yield was extremely low. Therefore, the present study was initiated to determine whether this low yield was the result of a low conversion or competing reaction pathways.

RNA: prebiotic product, or biotic invention?

Spectacular advances in structural and molecular biology have added support to the 'RNA world' hypothesis, and provide a mandate for chemistry to explain how RNA might have been generated prebiotically on the early earth. Difficulties in achieving a prebiotically plausible synthesis of RNA, however, have led many to ponder the question posed in the title of this paper. Herein, we review recent experimental work on the assembly of potential RNA precursors, focusing on methods for stereoselective C-C bond construction by aldolisation and related processes. This chemistry is presented in the context of a broader picture of the potential constitutional self-assembly of RNA. Finally, the relative accessibility of RNA and alternative nucleic acids is considered.