Protein-directed DNA structure. I. Raman spectroscopy of a high-mobility-group box with application to human sex reversal

Protein-directed reorganization of DNA underlies mechanisms of transcriptio n, replication, and recombination. A molecular model for DNA reorganization in the regulation of gene expression is provided by the sequence-specific high-mobility-group (HMG) box. Structures of HMG-box complexes with DNA are characterized by expansion of the minor groove, sharp bending toward the m ajor groove, and local unwinding of the double helix. The Raman vibrational signature of such DNA reorganization has been identified in a study of the SRY HMG box, encoded by the human male-determining region of the Y chromos ome. We observe in the human SRY-HMG:DNA complex extraordinarily large pert urbations to Raman bands associated with vibrational modes of the DNA backb one and accompanying large increases in intensities of Raman bands attribut able to base unstacking. In contrast, DNA major-groove binding, as occurs f or the bZIP protein GCN4 [Benevides, J. M., Li, T., Lu, X.-J., Srinivasan, A. R., Olson, W. K., Weiss, M. A., and Thomas, G. J., Jr. (2000) Biochemist ry 39, 548-556], perturbs the Raman signature of DNA only marginally. Raman markers of minor-groove recognition in the human SRY-HMG:DNA complex are d ue primarily to perturbation of specific vibrational modes of deoxyribose m oieties and presumably reflect desolvation at the nonpolar interface of pro tein and DNA. These Raman markers may be diagnostic of protein-induced DNA bending and:are proposed as a baseline for comparative analysis of mutation s in SRY that cause human sex reversal.