DNA curvature modulates the nuclear matrix binding of mouse satellite DNA: A potential role in centromeric heterochromatin condensation

Localized to the centromeric heterochromatin of higher eukaryotic chromosomes is a class of AT rich, tandemly repetitive DNA known as satellite DNA (sDNA). To examine the potential role of DNA secondary structure in centromeric sDNA packaging, we have characterized the curvature of the mouse sDNA unit repeat, and examined the effects of DNA curvature on the nuclear matrix binding of mouse sDNA. Our results indicate that the mouse sDNA unit repeat is a curved molecule with multiple loci of curvature throughout its sequence. Tandem arrays of the unit repeat display an increase in curvature, indicating that the tandem repeat arrangement of sDNA found in vivo may serve to further facilitate the condensation which may be effected by DNA curvature. Our studies also reveal that mouse sDNA binds to the nuclear matrix with high efficiency and specificity, and that the DNA tandem arrays display an increase in nuclear matrix binding which parallels their increased curvature. Distamycin A which mitigates DNA curvature serves to decrease the matrix binding of mouse sDNA, and this effect is observed to be greater in sDNA molecules displaying increased curvature. These studies suggest that DNA curvature modulates the interaction of mouse centromeric sDNA with the nuclear matrix, providing a basis for the proposed role of DNA curvature in centromeric sDNA packaging. Further evidence for the importance of DNA curvature in matrix binding is provided by DNA competition studies which reveal two classes of nuclear matrix binding sites, one of which may be modulated by DNA curvature. In addition, under certain conditions an intermolecular complex, most likely a triplex, which binds to the matrix with high efficiences is observed. Based on these and other observations, we propose a model for cell-cycle regulated changes in condensation of mouse centromeric sDNA mediated by DNA binding proteins and their effects on DNA curvature