Pulsed-field and two-dimensional gel electrophoresis of long arrays of tandemly repeated DNA : analysis of human centromeric alpha satellite.

Complex genomes are characterized by large amounts of tandemly repeated DNA that can comprise up to several percent of the genome in some organisms (1,2). The analysis of the organization of this type of DNA presents certain challenges owing to its repetitive nature, genomic distribution, and large array size. The availability of the large-scale resolution of pulsed-field gel electrophoresis (PFGE) (3,4) has allowed an increased understanding of the genomic organization of long arrays of tandemly repeated DNA, including their overall size and internal polymorphic variation. Such analyses are useful for long-range physical mapping of the large blocks of repetitive DNA characteristic of complex genomes and allow genetic information to be obtained for these loci. Although described here for human centromerit alpha satellite DNA, these techniques are also applicable to other repetitive and multicopy DNA families.