THE DIFFERENT MOBILITY OF COMPLEMENTARY STRANDS DEPENDS ON THE PROPORTION AC GT/

The electrophoretic mobility of DNA fragments on denaturing polyacryla mide gel depends on various factors. One of these is the base composit ion of a single-stranded DNA (ssDNA). We confirmed that one strand and its complementary strand of polymerase chain reaction (PCR) products migrated with different mobilities in all alleles detected at 12 out o f the 13 short tandem repeat (STR) loci studied. The mobility differen ces between complementary strands (MD) were also observed regardless o f end-polishing with Pfu DNA polymerase. MD was therefore not influenc ed by additional nucleotides to each strand of the PCR products. We th en analyzed the relation between MD and the base composition using one representative allele at each of the 13 loci. The results indicated t hat MD was affected by the adenine plus cytosine (AC) content in the s sDNA and was proportional to the values of the AC content divided by t he guanine plus thymine (GT) content in the AC-rich strand (the propor tion AC/GT). When the proportion AC/GT was well-balanced, MD decreased . The same tendency was observed even in the end-polished strands. In this study, the electrophoretic mobility of an ssDNA on denaturing pol yacrylamide gels was shown to depend on the proportion AC/GT. Unless t he same side of the PCR products is labelled in the context of a PCR-b ased STR typing, distinct alleles may be mistaken for identical ones b ecause of the different mobility of complementary strands. Accordingly , the labelled strand should be described if only one strand of the PC R products is detected. When using an allelic ladder marker as a size standard, the labelled side should be unified between STR alleles and the allelic ladder alleles. (C) 1998 Elsevier Science Ireland Ltd.