DNA Sequence Organization by Electron Microscopy

The size and arrangement of repetitive and inverted repeat (foldback) sequences in rat DNA were studied by visualization of hybrid and heteroduplex structures in the electron microscope. The self-reassociation of repetitive sequence-bearing DNA strands often results in the formation of four-ended "H" structures, whose duplex regions equal the repetitive sequence length and can be measured in the electron microscope. In this way, it was determined that the average size of the class of numerous short repetitive sequences is 400 ± 1.50 nucleotides. Heteroduplex structures were prepared between long total DHA single strands and short repetitive sequence-bearing strands. The analysis of these structures confirms that the size of the repetitive sequences is 400 nucleotides on average. length measurements between adjacent duplexes show that the average spacing between two interspersed repeats is at least 1500-1800 nucleotides. Short and long period interspersion patterns of repetitive and unique sequences can be discriminated. By examining 29.4 kb single strands after brief renaturation the size and distribution of foldback sequences were determined. There are 1.9 x 105 fold-back pairs per rat genome, spaced an average of 9.7 kb a part throughout at least 73% of the DNA. Repetitive, inverted repeat and unique sequences are interspersed with each other in at least half the genome.