Selective Chemical Reactions for Nucleic Acid Sequencing and DNA-Encoded Library Synthesis

Part One: The ability to map methylation sites in the human genome and epitranscriptome has transformed our understanding of how these modifications govern and influence a host of cellular processes and human diseases. Amongst the most widely studied methylations is N6-methyladenine, known as 6mA in DNA and m6A in RNA. While traditional methods to sequence these modifications have depended on antibody pulldowns, chemistry-based approaches are often less sequence dependent, can work on either DNA or RNA, and thus can provide a robust, inexpensive, and universal sequencing approach. In part one of this thesis, the first chemistry-based single-nucleotide resolution sequencing method for the detection of N6-adenine methylation sites in DNA and RNA is presented. This method takes advantage of the chemoselective deamination of unmodified adenines under acidic nitrite conditions, resulting in a (d)A to (d)G transition, while leaving methylated adenine sites unaffected. As changes in N6-adenine methylation of RNA and DNA have been implicated in a range of human diseases, especially cancers, the method has been rapidly adopted by researchers globally as an affordable and straightforward sequencing approach to assist in understanding the role and impact of the epigenome and epitranscriptome on human health. The ability of this method to detect other nucleotide modifications was also evaluated and described. Part Two: DNA-encoded libraries (DELs) comprise millions to billions of small-molecules covalently linked to a unique DNA barcode that can be read using standard next-generation sequencing (NGS). This technology has revolutionized the field of drug discovery as a method to rapidly identify small molecules that can serve as novel leads for drug development. The success of a drug discovery campaign involving a DEL depends on the chemical diversity presented within the DEL; methods that can generate DELs with new molecular architectures and with greater chemical diversity are critically needed to advance drug discovery efforts both within industry and academia. To this end, the use of photoredox chemistry as a facile method to generate DELs with drug-like properties is presented as part two of this thesis. An efficient approach for the photoredox-catalysed hydroaminoalkylation between on-DNA secondary N-substituted (hetero)arylamines and vinylarenes is explored as a method to generate DELs with known bioactive architectures. The developed reaction proceeds efficiently with a broad and well-explored substrate scope, working best with electron poor to neutral vinylarenes. This method is well suited for the construction of DELs enabling an expansion of drug-like chemical space.