Circular superhelical DNA complexes with synthetic oligopeptide: unusual compact structures and influence of bent sequences on the results of compaction

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

Intramolecular compact structures formed by high molecular weight circular superhelical DNA molecules due to interaction with synthetic oligopeptide trivaline (1) were studied by atomic force and electron microscopy. Three DNA preparations were used: plasmids pTbol, pRX10 and cosmid 27,877, with sizes 6,120 bp, 10,500 bp and 44,890 bp respectively. Plasmid pTbo1 and pRX10 preparations along with monomers contained significant amount of dimers and trimers. Main structures in all preparations observed were compact particles, which coincide in their appearance and compaction coefficient (3,5-3,7) with 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 additional information about the ultrastructural organization and arrangement of DNA fibers within the compact structures. Along with triple rings in pTbol and pRX10-TVP complexes significant amount of compact structures were observed having the shape of two or three compact rings attached to each other by a region of compact fibre. Basing on the data of contour length measurements and the shape of the particles it was concluded that these structures were formed due to compaction of dimeric and trimeric circular DNA molecules. Structures consisting of several attached to each other triple rings were not found for pTbol, pRX10 monomers or cosmid preparations--TVP complexes where only single triple rings were observed. The conclusion is made that initiation of compact fibre formation within the circular molecules depends on 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 compaction mechanism providing independent compaction of portions of one circular molecule can be of interest for understanding of DNA compaction processes in vivo.

Concatemerization of tRNA molecules in the presence of trivaline derivative

The interaction of tRNA with trivaline dansyl hydrazide trifluoroacetate (DHTV) has been studied. The shape of curves of fluorimetric titration of tRNA with DHTV and vice versa can be explained only by formation of DHTV dimers on tRNA molecules, and subsequent association of DHTV-saturated tRNA molecules with each other. The ability of tRNA molecules to form concatemers in solution in the presence of DHTV has been demonstrated by electron microscopy. Electron microscopy of the tRNA-DHTV complexes stained with uranyl acetate revealed flexible rods 6-7 nm thick and up to several micrometers long.