An altered DNA conformation in origin region I is a determinant for the binding of SV40 large T antigen

Abstract Seventeen base pairs of DNA from SV40 origin region I encode a tripartite binding site for a dimeric mass of SV40 large T antigen. Two binding components are the directly repeated pentanucleotide sequences 5′-GAGGC-3′/5′-GCCTC-3′. The third component is the asymmetric sequence 5′-TTTTTTG-3′/5′-CAAAAAA-3′ that separates the pentanucleotides. Nucleotide-specific features of this spacer element stabilize binding to the adjacent pentanucleotides. We report here that the spacer sequence determines a DNA conformation that correlates with high affinity binding of T antigen. The nature of the spacer sequence suggests that the DNA is bent. We propose that binding of T antigen to region I proceeds through monomer-pentanucleotide interactions and either protein-protein or protein-spacer interactions directed by the spacer-encoded structure.