Postsynthetic Modification of Nucleic Acids and Generation of Nucleoside Supramolecular Synthons by Palladium-Mediated Reactions

Abstract

Probing the structure of nucleic acids is paramount in understanding their recognition properties and ensuing functions. Nucleic acids are commonly studied by biophysical techniques like fluorescence, NMR, EPR and X-ray crystallography, to name a few. The majority of these techniques use DNA and RNA oligonucleotides (ONs) labeled with appropriate biophysical probes as components of nucleic acids do not contain intrinsic labels such as fluorophores, NMR isotopes, paramagnetic and heavy atoms that are suitable for efficient analysis. Labeled ONs are commonly synthesized by either solid-phase ON synthesis or enzymatic methods. While solid-phase protocol is a convenient approach to construct site-specifically labeled ON sequences, longer nucleic acids are made by using nucleic acid processing enzymes such as polymerases and nucleotide transferase. In case of chemical method, certain modified amidites show poor coupling efficiency or they do not survive harsh conditions employed in solid-phase method. On the other hand, enzymatic incorporation works under mild conditions, but in several instance the unnatural substrates are not well accepted by the enzymes. Hence, there is constant demand for the development of new labeling strategies that will provide access to a wide variety of labeled ONs. This doctoral dissertation describes the (i) development of a modular postsynthetic modification method to label DNA/RNA ONs and (ii) generation of nucleoside supramolecular synthons by using palladium-mediated cross-coupling reactions. In the first part, we illustrate the development of a Pd-mediated posttranscriptional Suzuki‒Miyaura cross-coupling reaction to label RNA with various biophysical probes. This method is highly chemoselective and offers direct access to RNA ONs labeled with commonly used fluorescent and affinity tags and new fluorogenic environment-sensitive nucleoside probes in a ligand-controlled stereoselective fashion. Further, we explored the influence of nucleic acid conformations on the Suzuki‒Miyaura cross-coupling reaction using polymorphic G-quadruplex forming sequences as the study model. We observed that the cross-coupling reaction works in a conformation-dependent manner and conformational selectivity of the reaction decreased in the order of – GQ topology > single-stranded DNA and no reaction with double-stranded DNA. In the second part of the doctoral dissertation, we describe the utility of Pd-mediated cross-coupling reaction to develop environment-sensitive fluorescent deoxyguanosine nucleolipids. These fluorescent nucleolipids support gel formation and show interesting chemo- and thermo-responsive behaviour upon self-assembling. Taken together, the results presented in this thesis highlight the potential of Pd-mediated cross-coupling reactions in generating functionalized nucleic acids for biophysical analysis and supramolecular assemblies for material applications.