Characeteristics of DNA superstructures formed upon interaction with feast/famine regulatory proteins, FFRPs.

By analyzing the 3D structures of full length FFRPs, which were crystallized previously in the absence of DNA, characteristics of DNA superstructures formed upon interaction with these proteins have been predicted. A pair of α-helices 3 in an FFRP dimer are positioned, so that they will bind to two DNA sites separated by 9, or a slightly fewer, basepairs. The nucleotide sequences of the two DNA sites will be reverse complementary to each other, reflecting the symmetric positioning of the two recognition helices. With this DNA fragment embedded in the center of a unit of ∼20 basepairs, four such units, altogether of ∼80 basepairs, will circle around the disk-like assembly of FFRP. Around each helical turn of the cylindrical assembly of FFRP, six such units, i.e. ∼120 basepairs, would wrap.(Communicated by Masanori OTSUKA, M. J. A., April 14, 2003)