Electrophoretic evidence that single-stranded regions of one or more nucleotides dramatically increase the...

The influence of single-stranded nicks and gaps on the flexibility of DNA has been investigated by subjecting to gel electrophoresis sets of molecules containing single-stranded regions of defined position and length. The DNA molecules were produced by ligating together synthetic oligomers that contained either nicks or single-stranded gaps of 1-4 nucleotides; the oligomer repeat lengths were 20, 21, 22, 23, or 26 bp, in order to produce nicks or gaps that were either in- or out-of-phase with the helix repeat of DNA. Nick-containing DNA molecules displayed nearly normal electrophoretic behavior, with maximum reductions in gel mobility (41 degrees C; 12% polyacrylamide gels) of approximately 10% for 230-bp molecules containing 10 nicks. In contrast, molecules containing gaps of 2-4 nucleotides demonstrated dramatic reductions in mobility, approaching one-half of the values of their full-duplex counterparts; molecules containing 1-nucleotide gaps displayed intermediate behavior. The observed (relative) mobilities of molecules containing gaps of more than 1 nucleotide were remarkably insensitive to temperature and to the presence of magnesium ions in the electrophoresis buffer. The central conclusion of the current study is that single-stranded gaps represent points of swivel-like character, whereas nicks retain much of the rigid character of double-helical DNA.