Affinity of a highly repetitive bent DNA for nuclear scaffold proteins from rat liver

A highly repetitive component in rat nuclear DNA was isolated by HindIII digestion and cloned. A self-ligated tandem dimer of the 370-bp cloned component was digested with each of DraI, HindIII and XmnI. The resulting 370-bp restriction fragments exhibited anomalously slow gel electrophoretic mobilities. Of them, the XmnI fragment had the slowest mobility. This suggested that sequence-directed bending of the helix axis is the strongest in this fragment. Moreover, the 370-bp restriction fragments had selective affinities for the nuclear scaffold proteins, P123 and P130. The affinity levels of XmnI fragment were higher than those of DraI or HindIII fragment. These results implied that the affinity of a highly repetitive component for the nuclear scaffold proteins depends on the degree of sequence-directed bending of the helix axis.