Abstract: The instant specification provides novel assays and systems for determining off-target effects of base editors. These assays and systems may comprise bacterial and/or eukaryotic cell systems and may be used to determine off-target editing frequencies, including Cas9-independent off-target editing frequencies. Also provided herein are novel base editors, wherein the base editors have reduced Cas9-independent off-target editing frequencies while maintaining high on-target editing efficiencies. Further provided are methods of contacting a nucleic acid molecule with these base editors to obtain reduced off-target editing frequencies, and in particular reduced Cas9-independent off-target editing events. Further provided are methods of treatment comprising administering these base editors to a subject. Also provided are pharmaceutical compositions comprising the base editors described herein, and nucleic acids, vectors, cells, and kits useful for the generation of these base editors.

Abstract: The present disclosure provides for base editors which satisfy a need in the art for installation of targeted transversions of thymine (T) to adenine (A), or correspondingly, trans versions of adenine (A) to thymine (T). The nucleobase editor domains include a nucleic acid programmable DNA binding protein and an adenosine methyltransferase domain. The base editors may be engineered through the use of continuous or non-continuous evolution systems, such as phage-assisted continuous evolution (PACE). In particular, the present disclosure provides for evolved adenine-to-thymine (or thymine-to-adenine) base editor variants that overcome deficiencies in the art for base editors that can install single-base A:T to T:A transversion mutations. In some embodiments, methods for targeted nucleic acid editing are provided. In some embodiments, pharmaceutical compositions comprising, and vectors and kits for the generation of, targeted base editors are provided.

Abstract: Some aspects of this disclosure provide strategies, systems, reagents, methods, and kits that are useful for the targeted editing of nucleic acids, including editing a single site within the genome of a cell or subject, e.g., within the human genome. The disclosure provides fusion proteins of nucleic acid programmable DNA binding proteins (napDNAbp), e.g., Cas9 or variants thereof, and nucleic acid editing proteins such as cytidine deaminase domains (e.g., novel cytidine deaminases generated by ancestral sequence reconstruction), and adenosine deaminases that deaminate adenine in DNA. Aspects of the disclosure relate to fusion proteins (e.g., base editors) that have improved expression and/or localize efficiently to the nucleus. In some embodiments, base editors are codon optimized for expression in mammalian cells. In some embodiments, base editors include multiple nuclear localization sequences (e.g., bipartite NLSs), e.g., at least two NLSs.