Professor Verdine's research interests lie in the emerging area of chemical genetics. He and his co-workers aim to gain a fundamental understanding of processes that control the expression and preserve the integrity of genetic information. Verdine's studies have served to illuminate the structural strategies employed by proteins to recognize specific sequences or architectural features of DNA and the mechanistic strategies by which proteins catalyze covalent modifications of DNA.

A major effort in Verdine's lab has involved the study of catalytic DNA binding proteins. Verdine has developed an approach toward the study of such proteins in which mechanistic information is used to design decoy substrates that will be faithfully recognized by the protein but fail to undergo normal processing, thereby leading to the formation of a frozen protein-DNA complex. A potentially illuminating example to illustrate the power of this approach is in the area of DNA methyltransferases. The Verdine laboratory developed the chemistry for obtaining stable complexes conatining a DNA methyltransferase covalently bound to a fluoronucleoside suicide inhibitor in duplex DNA (designed in Daniel Santi's lab). This chemistry has now been used by Verdine's lab in collaboration with William Lipscomb, and by a group at Cold Spring Harbor to obtain co-crystal structures of frozen methyltransferase-protein structures. These structures reveal that the enzyme extrudes its substrate base entirely from the DNA helix during the methyl transfer reaction. Although the base extrusion had been predicted by Verdine on the basis of mechanistic arguments, no one could have pridicted the remarkable frameshifting of base-pairs observed in the Verdine/Lipscomb structure, a hitherto unknown mode of induced fit in protein-DNA interactions. More recently, Verdine has reported the development of exceedingly tight-binding inhibitors of DNA glycosylases, an advance that paves the way for co-crystallography studies on this important class of DNA repair proteins. A parallel methylation damage in E. coli, by stripping aberrant methyl groups off DNA through irreversible transfer to one of the protein's own Cys residues. Working with Verdine and collaborator Gerhard Wagner, graduate student Larry Myers discovered that the protein contains a tightly bound zinc ion to which is coordinated the active site Cys residue. This example represented the first in which zinc was found to activate the nucleophilicity of one of its own cysteine residues. Further studies on Ada have led to a model for the mechanism of methylation-dependent switching of Ada from a DNA repair protein to a transcriptional activator.

Verdine's studies on fundamental aspects of protein-DNA interactions have relied heavily upon the ability to modify the structure of DNA through chemical synthesis. These efforts have led to the development of synthetic methods having broad utility, including invention of the post-synthetic approach for attaching functionalized tethers to DNA, the disulfide-cross-linking approach for controlling nucleic acid structure and dynamics, and template-directed interference (TDI) footprinting of protein-DNA interactions.

Verdine and his collaborators have also made important contributions toward understanding proteins of the Rel transcription factor family, which serve as critical regulators of the cellular response to a variety of external threats. One member of this family, NF-kappaB, is of particular interest because of its role as a mediator of immunity and inflammation, and because of its subversion by the human immunodeficiency virus to activate viral proliferation. Verdine and his colleague Steven Harrison led a team that solved the high-resolution structure of NF-kappaB; this and a related structure solved simultaneously by Paul Sigler's lab provide a basis for undertaking molecular approaches toward development of NF-kappaB antagonists. Verdine has also carried out groundbreaking studies on the nuclear factor of activated T cells (NF-AT), a Rel protein that controls the production of interleukin-2 in T cells exposed to peptide antigens. In the course of these studies, Verdine and his graudate student Lin Chen discovered the property of "orientational isomerism" in protein-DNA interactions, whereby some proteins bind DNA in multiple orientations. Remarkably, Chen and Verdine found that an orientationally isomeric protein can be forced to adopt only one DNA-bound configuration through cooperative interactions with another protein bound to an adjacent site in DNA. These findings add a new element of stereochemical diversity to the regulation of transcription by proteins.