On the tertiary structure of satellite DNA

The primary structure of the Citrus ichangensis satellite DNA repeating unit has been estimated. The repeat is 181 bp long and contains four pentanucleotides of adenine residues. Oligomer forms of the stDNA repeating unit were detected by a partial hydrolysis of the C ichangensis stDNA by BspI restriction endonuclease. Experiments on comparative mobility of oligomers in agarose and polyacrylamide gels evidenced a certain retardation of those in polyacrylamide gel indicating to a slight bend in the repeating unit. The BEN computer program [9] was employed to calculate the spatial positions of monomer and oligomer axes of the satellite DNA repeating unit of Citrus ichangensis, mouse and African green monkey, and to plot their two-dimensional projections. The bends in the monomer for higher oligomer form proved to result in a hypothetical solenoid-like structure, termed coiled double helix (CDH).