Interaction of nuclear proteins with intrinsically curved DNA in a matrix attachment region of a tobacco gene.

Two scaffold/matrix attachment regions (S/MARs), designated S/M I and S/M II, are located in the 5'-flanking region of the tobacco basic class I chitinase gene, CHN50. Structural analysis of these S/MARs showed that S/M II contained an intrinsically curved DNA sequence that is located between -1786 and -1722 relative to the initiation site of transcription. Electrophoretic mobility shift assays and southwestern blotting analysis were performed to identify the tobacco nuclear proteins that bind specifically to this curved DNA. These experiments revealed that nuclear proteins bound specifically to the curved DNA. Moreover, the nuclear proteins appeared to recognize the overall structure of the intrinsically curved DNA, as distinct from binding to the DNA with sequence specificity. Southwestern blotting analysis showed that proteins of 22, 24, 28 and 34 kDa bound specifically to the curved DNA. The possible functions of the binding proteins and their relationship to previously identified nuclear proteins, such as high-mobility-group proteins, are discussed.