Enzymatic Synthesis of Base-Modified Nucleic Acids

Nucleic acids collectively play primordial functions, some of which are still barely understood, in all living organisms. DNA and RNA oligonucleotides have also advanced as pivotal tools in numerous applications such as therapeutic technologies, diagnostics, or material sciences. Chemical modifications, particularly at the level of the nucleobases, are ubiquitous. Indeed, base modifications in natural DNA and RNA are nearly as important as the primary sequences and are involved in numerous biological roles and functions, mainly via epigenetic regulation mechanisms. In synthetic nucleic acids, chemical modifications provide oligonucleotides with improved binding or catalytic activities as well as exogenous reactivities, all of which are largely nonaccessible to canonical DNA or RNA. Nucleobase modifications can be incorporated into oligonucleotides either by standard solid-phase synthesis or by application of a chemoenzymatic method. In this chapter, we will describe how the combination of polymerases and nucleoside triphosphate analogs can be harnessed to synthesize oligonucleotides containing nucleobase modifications. We will highlight the potency of this approach through the description of relevant examples including synthesis of oligonucleotides containing naturally occurring modifications and the selection of functional nucleic acids with improved properties. In the last section of this chapter, more recent applications of this method will be discussed with an emphasis on mRNA-based vaccines and on controlled enzymatic synthesis.