Anti-DNA autoantibodies: the other DNA-binding proteins

Using the methods developed to study protein DNA complexes, a small number of workers has begun to characterize the interactions of lupus anti-DNA antibodies with their DNA antigens. These studies indicate that anti-ssDNA generally possess a high affinity for poly(dT) and use aromatic side-chains on complex formation, in common with many previously reported anti-ssDNA, and several DNA-binding proteins. We find that our anti-ssDNA differ from these latter two species in that they are not cross-reactive with non-nucleic acid antigens, unlike many other anti-ssDNA, and their complexation does not appear to be accompanied by significant cation release, as for some DNA-binding proteins. Moreover, in some cases our anti-ssDNA are apparently sequence-specific. Due to the small number of anti-dsDNA mAbs studied, our current understanding of these proteins is limited. However, we have recently obtained a high-resolution crystal structure of 4B2, that reacts with both ss- and dsDNA. This structure should enable us to facilitate mutagenesis experiments to identify the molecular features of dsDNA recognition.

One can envisage several practical benefits of applying a systematic biophysical approach to studying lupus anti-DNA·DNA. For example, once the molecular basis of anti-DNA·DNA interactions has been defined, it may be possible to use anti-DNA as biochemical reagents such as repressors of protein-DNA binding or as catalysts that manipulate DNA. Indeed, the enormous diversity of the immune repertoire and the case with which anti-DNA can be customized by site-directed and random mutagenesis provides the potential to generate anti-DNA with a wide range of properties. Alternatively, by understanding the molecular basis of anti-DNA·DNA interactions it may be possible to identify molecules that disrupt the specific interaction between anti-DNA and their DNA antigens. Such molecules could eventually form the basis of new agents to treat immune-complex mediated kidney damage and have fewer complications than the nonspecific agents currently used to treat lupus. In fact, by screening combinatorial small molecule libraries, we have already identified several promising anti-DNA antagonists.58 Thus, we believe that the next few years will be an exciting period in anti-DNA research. We review some common approaches that have been used to examine the specificity, affinity, and mode of binding of lupus anti-DNA for DNA antigens, We highlight the recent use of biophysical methods that have been used to study DNA-binding proteins, such as transcription factors, and demonstrate their utility when used in the study of lupus anti-DNA. ga]473|The application of set theory to combinatorial processes provides valuable tools for the planning, description, execution, and evaluation of combinatorial events.