Atomic force and electron microscopy of high molecular weight circular DNAcomplexes with synthetic oligopeptide trivaline

Intramolecular compact structures formed by high molecular weight circular superhelical DNA molecules due to interaction with synthetic oligopeptide t rivaline (1) were studied by atomic force and electron microscopy. Three DN A preparations were used: plasmids pTbo1, pRX10 and cosmid 27877, with size s 6120 bp, 10500 bp and 44890 bp respectively. Plasmid pTbo1 and pRX10 prep arations along with monomers contained significant amount of dimers and tri mers. Main structures in all preparations observed were compact particles, which coincide in their appearance and compaction coefficient (3,5-3,7) wit h triple rings described earlier. The size and structure characteristics of triple rings and other compact particles on atomic force images in general coincide with those obtained by EM (2). AFM (3) images allow to get additi onal information about the ultrastructural organization and arrangement of DNA fibers within the compact structures. Along with triple rings in pTbo1 and pRX10-TVP complexes significant amount of compact structures were obser ved having the shape of two or three compact rings attached to each other b y a region of compact fibre. Basing on the data of contour length measureme nts and the shape of the particles it was concluded that these structures w ere formed due to compaction of dimeric and trimeric circular DNA molecules . Structures consisting of several attached to each other triple rings were n ot found for pTbo1, pRX10 monomers or cosmid preparations - TVP complexes w here only single triple rings were observed. The conclusion is made that in itiation of compact fibre formation within the circular molecules depends o n the primary structure and for dimeric or trimeric circular molecules two or three compaction initiation points are present, located in each monomer unit within one circular DNA molecule. The nucleotide sequence dependent co mpaction mechanism providing independent compaction of portions of one circ ular molecule can be of interest for understanding of DNA compaction proces ses in vivo.