UC San Diego

The most recent base editors, the adenine base editors (ABEs), catalyzes the conversionof A•T→G•C base pairs at precise genomic loci and were developed using extensive protein engineering and evolution starting from a RNA-editing enzyme, TadA. Given its unique trajectory from an RNA-editing enzyme into an efficient and precise DNA-editing base editor and considering that expansion of the current base editing arsenal would require similar engineering efforts, understanding the molecular design principles for base editor design can help accelerate the field of genome editing. This thesis aims to learn these principles through computational simulations as well as bioinformatics analyses of ABEs as the prototypical base editor. First, we explore the onset of DNA-editing activity in TadA due to the first ever mutation discovered in its evolutionary journey into becoming the ABEs. Using molecular dynamics simulations we uncover the structural and functional roles played by this initial mutation. We demonstrate that this critical first mutation enhances the binding affinity of TadA towards DNA and verify its significance through in silico and in vivo reversion analyses. Subsequently, we show that this critical first mutation is capable of enhancing not just the DNA-editing activity of TadA but also its undesirable native RNA-editing functionality. In an attempt to discover mutations that can suppress the native RNA-editing of TadA and to rationalize the effect of all the reported ABE mutations simultaneously, we developed a sequence- based bioinformatics classifier. This classifier relies on evolutionary information learned from naturally-occurring proteins and can aid the laboratory-evolution of novel base editors. Finally, we determine the significance of the remote mutations that happen far away from the active site of TadA. Using molecular modeling and large-scale simulations of entire ABE-DNA complex we show that these remote mutations modulate the conformation of terminal end of the TadA and thus help broadening its DNA-editing substrate-specificity while also suppressing its native RNA-editing activity.