Design of a New Programmable and Dynamic Alternative Genetic System – PRODYGY

Studies of non-enzymatic polymerization with bifunctional boronoribonucléotidiques probes (synthetic entities) are conducted to assess their ability to transfer genetic information. These complex systems are studied by various analytical methods (thermal denaturation, circular dichrosime, NMR, modeling). These studies will be complemented by experiments based on the natural selection of the fittest elements.

The first results have allowed us to highlight the geometric and electronic factors essential to the functioning of the non-enzymatic ligation. These results allowed us to consider studies of non-enzymatic polymerization with bifunctional probes. We are currently investigating the parameters affecting the DNA-templated polymerization.

At the crossroad between chemistry and biology, this project aims to develop systems with effective functional performance. These new synthetic switches represent a resource that could be exploited to transform our ability to interact with biological systems and profoundly change the way we handle, programs and analyze biological systems.

1) M. Smietana,* A.R. Martin, J.-J. Vasseur,
Pure and Applied Chemistry, 2012, 84, 1659-1667.

2) C. El Amri,* A. R. Martin, J.-J. Vasseur, M. Smietana*,
ChemBioChem 2012, 13, 1605-1612.

3) R. Barbeyron, J. Wengel J.-J. Vasseur, M. Smietana*,
Monatshefte fur Chemie–Chemical Monthly, 2013, In press. Invited manuscript, special young investigator issue.

4) J.F. Poisson, M. Smietana
l'Actualité Chimique, 2013, 370, 47.

The synthesis of nucleic acids in living organisms is very precisely controlled. This remarkable fidelity in information transfer is the result of selective polymerization and correction enzymes. In the absence of these enzymes, chemically-controlled DNA synthesis is by contrast poorly efficient and less selective. In this context, the structuring of bio-inspired artificial genetic systems is a field of growing importance. The objective of this approach is to decompose a complex phenomena of life (DNA synthesis) into a set of simple phenomenon with complementary functions themselves interacted. One approach to achieve this goal is the template-directed formation of internucleosidic linkages in the absence of enzymatic or chemical activation. These chemical systems need to provide elements of molecular recognition as well as proof-reading control and reversible covalent bonds are well fitted for this task as they can lead to new materials able to repair themselves or transform in response to their environment. Among the many reversible covalent reactions, boronate esters that are formed dynamically by the reaction of a boronic acid and a cis-diol have not been exploited so far in the nucleic acid field. Usually designed and evaluated as probes for sugar detection, boronic acids can bind 1,2- or 1,3-cis-diol-containing molecules through the reversible formation of 5 or 6-membered cyclic boronate esters without chemical activation. In the presence of water, there is an equilibrium between free boronic acids and boronate esters depending on various parameters: substitution of the diol moiety, substitution of the boronic acid, pH and temperature of the medium, presence of anions, etc… Thus, boronate esters are able to reversibly dissociate and associate and rearrange their molecular components depending on the media. Moreover, boron chemistry seems to have played an important role on early earth as borate minerals was presumably involved in the prebiotic synthesis of ribose.
We recently described the completion of the set of four 2’-deoxy-5’-borononucleotide analogues of natural nucleotide monophosphates. Our goal is to develop a new type of boronic acid-based internucleosidic linkage. Indeed, the boronic acid-diol equilibrium is directional and its reversibility allows the formation of thermodynamically stable architectures. Thus, the incorporation of these analogues into DNA strands and the study of their binding abilities will help our understanding of the encoding of genetic information. Such system might allow the template-directed self-assembly of boronic acid building blocks without chemical activation and should also be the first step towards the conception of an artificial self-replicating genetic code. Controlling the formation of such systems could be relevant for the design of dynamic “smart” nucleic acids-based polymers.
The goal of the present application is the creation of an artificial genetic system based on monomers linked through reversible connections having the capacity to undergo spontaneous and continuous changes in their constitution by exchange, reshuffling, incorporation and decorporation of various monomeric components.