Deletions of bases in one strand of duplex DNA, in contrast to single-base mismatches, produce highly kinked molecules: possible relevance to the folding of single-stranded nucleic acids

Abstract

A 32-base-pair (bp) DNA duplex with deletions in one strand, and thus extra bases in the opposing strand, was ligated head-to-tail to produce linear and circular multimers. The electrophoretic mobility of the linear multimers was analyzed in polyacrylamide gels and the size of the circular DNA was determined by electron microscopy. A 1-base deletion produced a marked retardation in the mobility of the linear multimers coincident with the formation of a population of multimeric circles of a smaller average size than the deletionless 32-mer; 2-, 3-, or 4-base deletions at the same site produced proportionately greater effects. Two 1-base deletions separated by 10 bp on the same strand produced a greater reduction in mobility than a 1-base deletion, whereas two 1-base deletions spaced by 5 bp on the same strand yielded a molecule that behaved more like the deletionless DNA. We conclude that deletions of 1-4 bases at a single site on duplex DNA produce molecules that behave as if they contain sharp bends or kinks. In contrast, single mismatches in the 32-bp duplex produced no abnormality in behavior relative to normally base-paired DNA in the gel mobility and electron microscopic assays. The possible role of such structures in organizing the three-dimensional folding of single-stranded nucleic acids is considered.