Tom Tullius and researchers in his laboratory at Boston University have been pioneers in using experimental methods to characterize DNA shape. They developed a technique called hydroxyl radical footprinting, which is widely used to study the structures of DNA, DNA-protein complexes, and RNA. His laboratory also works to explain connections between genomic sequence and structural properties of DNA, and has demonstrated that DNA shape is conserved during evolution.

As a member of the Center for Multiscale Analysis of Genomic and Cellular Networks, Tullius is collaborating with Barry Honig, Richard Mann, and Harmen Bussemaker to identify Hox protein-specific DNA-binding sites and probe their shapes. Using high-throughput and whole-genome methods, the team is working to identify sites that are Hox protein-specific and to characterize the structures of these sites using hydroxyl-radical cleavage measurements and computational tools. The Tullius and Honig groups are working together to develop new predictive algorithms for DNA shape. Their efforts will be combined with information extracted from Selex data by the Mann and Bussemaker groups about the binding sites recognized by individual Hox proteins. The ultimate goals of the project are to characterize the factors that determine specificity for the entire Hox family, both in terms of sequence and structure, and to identify the complete repertoire of DNA-binding sites for Hox-cofactor protein complexes.