Nonenzymatic ligation of short-chained 2'-5'- or 3'-5'-linked oligoribonucleotides on 2'-5'- or 3'-5'-linked complementary templates

Enzyme-free ligation of dimers and trimers to RNA primers

The template-directed formation of phosphodiester bonds between two nucleic acid components is a pivotal process in biology. To induce such a reaction in the absence of enzymes is a challenge. This challenge has been met for the extension of a primer with mononucleotides, but the ligation of short oligonucleotides (dimers or trimers) has proven difficult. Here we report a method for ligating dimers and trimers of ribonucleotides using in situ activation in aqueous buffer. All 16 different dimers and two trimers were tested. Binding studies by NMR showed low millimolar dissociation constants for complexes between representative dimers and hairpins mimicking primer-template duplexes, confirming that a weak template effect is not the cause of the poor ligating properties of these short oligomers. Rather, cyclization was found to compete with ligation, with up to 90% of dimer being converted to the cyclic form during the course of an assay. This side reaction is strongly sequence dependent and more pronounced for dimers than for trimers. Under optimized reaction conditions, high yields were observed with strongly pairing purines at the 3'-terminus. These results show that short oligomers of ribonucleotides are competent reactants in enzyme-free copying.

Nonenzymatic Polymerization into Long Linear RNA Templated by Liquid Crystal Self-Assembly

Self-synthesizing materials, in which supramolecular structuring enhances the formation of new molecules that participate to the process, represent an intriguing notion to account for the first appearance of biomolecules in an abiotic Earth. We present here a study of the abiotic formation of interchain phosphodiester bonds in solutions of short RNA oligomers in various states of supramolecular arrangement and their reaction kinetics. We found a spectrum of conditions in which RNA oligomers self-assemble and phase separate into highly concentrated ordered fluid liquid crystal (LC) microdomains. We show that such supramolecular state provides a template guiding their ligation into hundred-bases long chains. The quantitative analysis presented here demonstrates that nucleic acid LC boosts the rate of end-to-end ligation and suppresses the formation of the otherwise dominant cyclic oligomers. These results strengthen the concept of supramolecular ordering as an efficient pathway toward the emergence of the RNA World in the primordial Earth.

Non-enzymatic recombination of RNA: Ligation in loops

BACKGROUND

While the RNA world hypothesis is widely accepted, it is still far from complete: the existence of self-replicating ribozyme, consisting of potentially hundreds of nucleotides, is a core assumption for the majority of RNA world models. The appearance of such long RNA molecules under prebiotic conditions is not self-evident. Recombination seems to be a plausible way of creating RNA diversity, resulting in the appearance of functional RNAs, capable of self-replicating.

METHODS

We report here on the study of recombination process modelled with two 96 nts RNA fragments. Detection of recombination products was performed with RT-PCR followed by TA-cloning and Sanger sequencing.

RESULTS

A wide range of recombinant products was detected. We found that (i) the most efficient ligation was observed for RNA species forming bulges or internal loops, with ligation partners located within the loop; (ii) a strong preference was observed for formation of a few types of major products with a large variety of minor products; (iii) ligation could occur with participation of either 2',3'-cyclophosphate or 5'-ppp; (iv) the presence of key reaction components, i.e. 5'ppp-RNAs, enabled the formation of additional types of product; (v) molecular dynamics simulations of one of the most abundant products suggests that the ligation results in a preferable formation of 2'-5'- rather than 3'-5'-linkages.

CONCLUSIONS

The study demonstrates regularities of new RNA molecules formation with non-enzymatic recombination process.

GENERAL SIGNIFICANCE

Our findings provide new data supporting the RNA World hypothesis and show the way of new RNA sequences emergence under prebiotic conditions.

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". Recently, the opposition between these approaches has been solved by more unitary theoretical and experimental frames taking into account energetic, evolutionary, proto-metabolic and environmental aspects. Nevertheless, a unitary and simple chemical frame is still needed that could afford both the precursors of the synthetic pathways eventually leading to RNA and to the key components of the central metabolic cycles, possibly connected with the synthesis of fatty acids. In order to approach the problem of the origin of life it is therefore reasonable to start from the assumption that both metabolism and genetics had a common origin, shared a common chemical frame, and were embedded under physical-chemical conditions favourable for the onset of both. The singleness of such a prebiotically productive chemical process would partake of Darwinian advantages over more complex fragmentary chemical systems. The prebiotic chemistry of formamide affords in a single and simple physical-chemical frame nucleic bases, acyclonucleosides, nucleotides, biogenic carboxylic acids, sugars, amino sugars, amino acids and condensing agents. Thus, we suggest the possibility that formamide could have jointly provided the main components for the onset of both (pre)genetic and (pre)metabolic processes. As a note of caution, we discuss the fact that these observations only indicate possible solutions at the level of organic substrates, not at the systemic chemical level.

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. The polymerizations are based on two reactions not previously described: 1) oligomerization of 3', 5'-cGMP to approximately 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.

Darwinian chemistry: towards the synthesis of a simple cell

The total synthesis of a simple cell is in many ways the ultimate challenge in synthetic biology. Outlined eight years ago in a visionary article by Szostak et al. (J. W. Szostak, D. P. Bartel and P. L. Luisi, Nature, 2001, 409, 387), the chances of success seemed remote. However, recent progress in nucleic acid chemistry, directed evolution and membrane biophysics have brought the prospect of a simple synthetic cell with life-like properties such as growth, division, heredity and evolution within reach. Success in this area will not only revolutionize our understanding of abiogenesis but provide a fertile test-bed for models of prebiotic chemistry and early evolution. Last but not least, a robust "living" protocell may provide a versatile and safe chassis for embedding synthetic devices and systems.

Nonenzymatic recombination of RNA: possible mechanism for the formation of novel sequences

We report on the formation of novel RNA molecules in a recombination-like, nonenzymatic reaction proceeding in the complex of partially complementary RNA-oligonucleotides under very simple conditions. Analysis of the isolated products demonstrated that at least 5% of the formed linkages are of the (natural) 3',5'-phosphodiester type. We suggest that similar reactions could contribute to the development of the 'RNA world', but could also proceed in vivo within variously structured RNA or RNA complexes containing loops, bulges, or dangling ends, providing an emergence of novel RNA sequences.