Molecular characterization of a DNA probe, U6.2, located close to the fragile X locus

A new DNA probe, U6.2, defining locus DXS304, was recently shown to be closely linked to the fragile X locus (FRAXA). It is polymorphic with a number of different enzymes, all of which are in complete linkage disequilibrium, which suggests an insertion/deletion type of polymorphism. Using the method of Sanger, we have sequenced 1,102 bp of the cloned U6.2 fragment. Analysis of the sequence showed there was a long direct repeat of 121 bp and two long inverted repeats. The first was 19 bp long, and the second was a palindromic invert of 20 bp. Such repeats could promote recombination in this region and could have been involved in the suggested insertion/deletion event that created the polymorphism detected at locus DXS304. Long fragments were observed using pulsed field gel electrophoresis (PFGE), but no length variations were seen. The sequence of U6.2 will be useful in developing a polymerase chain reaction (PCR) based assay for the restriction fragment length polymorphism (RFLP) detected at locus DXS304 which should assist with carrier detection and prenatal diagnosis of the fragile X syndrome.