Modifying the helical structure of DNA by design: recruitment of an architecture-specific protein to an enforced DNA bend Original Research Article

Background: Proteins can force DNA to adopt distorted helical structures that are rarely if ever observed in naked DNA. The ability to synthesize DNA that contains defined helical aberrations would offer a new avenue for exploring the structural and energetic plasticity of DNA. Here we report a strategy for the enforcement of non-canonical helical structures through disulfide cross-linking; this approach is exemplified by the design and synthesis of an oligonucleotide containing a pronounced bend. Results: A localized bend was site-specifically introduced into DNA by the formation of a disulfide crosslink between the 5′ adenines of a 5′-AATT-3′ region in complementary strands of DNA. The DNA bend was characterized by high-resolution NMR structure determination of a cross-linked dodecamer and electrophoretic mobility assays on phased multimers, which together indicate that the cross-linked tetranucleotide induces a helical bend of ≈30° and a modest degree of unwinding. The enforced bend was found to stimulate dramatically the binding of an architecturespecific protein, HMG-D, to the DNA. DNase I footprinting analysis revealed that the protein is recruited to the section of DNA that is bent. Conclusions: The present study reports a novel approach for the investigation of non-canonical DNA structures and their recognition by architecture-specific proteins. The mode of DNA bending induced by disulfide cross-linking resembles that observed in structures of protein-DNA complexes. The results reveal common elements in the DNA-binding mode employed by sequence-specific and architecture-specific HMG proteins.