Adenosine deamination is one of the most prevalent post-transcriptional modifications in mRNA and is catalyzed by ADAR1 and ADAR2 in humans. ADAR1 and ADAR2 have different substrate selectivity, which is believed to mainly originate from the proteins' deaminase domains (hADAR1d and hADAR2d, respectively). RNA-seq of the Saccharomyces cerevisiae transcriptome subjected to ADAR-catalyzed RNA editing identified substrates with common secondary structure features preferentially edited by hADAR1d over hADAR2d. The relatively small size and efficient reaction of one of these substrates suggested it could be useful for further study of the hADAR1d reaction. Indeed, a short hairpin stem from the S. cerevisiae HER1 mRNA was efficiently deaminated by hADAR1d and used to generate an hADAR1d-specific fluorescent reporter of editing activity. Using substrates preferred by either hADAR1d or hADAR2d in vitro, we found that a chimeric protein bearing an RNA-binding loop from hADAR2d grafted onto hADAR1d showed ADAR2-like selectivity. Finally, a high-throughput mutagenesis analysis (Sat-FACS-Seq) of conserved residues in an RNA-binding loop of hADAR1d revealed essential amino acids for function, advancing our understanding of RNA recognition by this domain.

Base editing is a genome editing strategy that induces specific single nucleotide changes within genomic DNA. Two major DNA base editors, Cytosine base editors (CBEs) and Adenine base editors (ABEs), have been developed that consist of a Cas9 protein linked to a deaminase enzyme that catalyzes targeted base conversion directed by a sgRNA. This strategy has been used widely for precise genome editing because, unlike CRISPR-Cas nuclease-based genome editing systems, this strategy does not create double strand DNA breaks (DSBs) that often result in high levels of undesirable indels. However, recent papers have reported that DNA base editors can cause substantial off-target editing in both genomic DNA and RNA. The off-target editing described in these studies is primarily guide RNA-independent arising from promiscuous reactivity of the deaminase enzymes used in DNA base editors. In this perspective, we discuss the development of DNA base editors, the guide RNA independent off-target activity reported in recent studies, and strategies that improve the selectivity of DNA base editors.

Adenosine Deaminases that act on RNA (ADARs) are enzymes that catalyze adenosine to inosine conversion in dsRNA, a common form of RNA editing. Mutations in the human ADAR1 gene are known to cause disease and recent studies have identified ADAR1 as a potential therapeutic target for a subset of cancers. However, efforts to define the mechanistic effects for disease associated ADAR1 mutations and the rational design of ADAR1 inhibitors are limited by a lack of structural information. Here, we describe the combination of high throughput mutagenesis screening studies, biochemical characterization and Rosetta-based structure modeling to identify unique features of ADAR1. Importantly, these studies reveal a previously unknown zinc-binding site on the surface of the ADAR1 deaminase domain which is important for ADAR1 editing activity. Furthermore, we present structural models that explain known properties of this enzyme and make predictions about the role of specific residues in a surface loop unique to ADAR1.

Adenosine deaminases acting on RNA (ADARs) are RNA editing enzymes that catalyze the hydrolytic deamination of adenosine (A) to inosine (I) in dsRNA. In humans, two catalytically active ADARs, ADAR1 and ADAR2, perform this A-to-I editing event. The growing field of nucleotide base editing has highlighted ADARs as promising therapeutic agents while multiple studies have also identified ADAR1’s role in cancer progression. However, the potential for site-directed RNA editing as well as the rational design of inhibitors is being hindered by the lack of detailed molecular understanding of RNA recognition by ADAR1. Here, we designed short RNA duplexes containing the nucleoside analog, 8-azanebularine (8-azaN), to gain insight into molecular recognition by the human ADAR1 catalytic domain. From gel shift and in vitro deamination experiments, we validate ADAR1 catalytic domain’s duplex secondary structure requirement and present a minimum duplex length for binding (14 bp, with 5 bp 5′ and 8 bp 3′ to editing site). These findings concur with predicted RNA-binding contacts from a previous structural model of the ADAR1 catalytic domain. Finally, we establish that neither 8-azaN as a free nucleoside nor a ssRNA bearing 8-azaN inhibits ADAR1 and demonstrate that the 8-azaN-modified RNA duplexes selectively inhibit ADAR1 and not the closely related ADAR2 enzyme.

We developed a highly stereoselective C–N and C–C bond‐forming reaction by carrying out a crystallization‐induced dynamic resolution (CIDR) of α‐bromo arylacetates followed by a stereoselective substitution reaction with an amine or azlactone nucleophile. Applications of this synthetic method to the preparation of highly enantioenriched nitrogen‐containing six‐membered heterocycles and α,β‐disubstituted aspartates are also presented.