Activation-induced cytidine deaminase (AID) catalyzes cytosine deamination (converting cytosine to uracil) at immunoglobulin (Ig) variable (V) and switch (S) regions in antigen- stimulated B cells to initiate somatic hypermutation (SHM) and class switch recombination (CSR). Recently, highly active monomeric recombinant AID has been generated and its crystal structure solved. Strikingly, the AID structure shows a bifurcated substrate-binding site; whereas recombinant AID avidly binds branched DNA structures, it only weakly binds ssDNA, which, until now, has been considered as the cognate substrate for AID in vivo. This groundbreaking discovery provides exceptional new insight into a collapsed R-loop model that we proposed several years ago. This untested model better explains many aspects of CSR. With new tools that we have developed in recent years, we propose to comprehensively test the hypothesis that the collapsed R-loop structure is the cognate substrate for AID during CSR.
B cells can make different types of antibodies via a gene recombination process called isotype switching. This application will test a novel model that helps explain how this gene recombination process works. We propose that a unique DNA structure containing branched DNA is recognized by the enzyme that initiates isotype switching.
