Screening DNA Repeat Tracts of Phase Variable Genes by Fragment Analysis

  • Freda E. -C. Jen
  • Kate L. SeibEmail author
  • Aimee Tan
Part of the Methods in Molecular Biology book series (MIMB, volume 1969)


Fragment analysis (or fragment length analysis) is a PCR-based method which allows quantification of the size and proportion of a DNA repeat tract length of a phase-variable region. Primers are labeled with a fluorescent dye, the resulting amplicons are processed by capillary electrophoresis, and results are analyzed for amplicon size and proportion by associated software (such as Peakscanner). Here we describe the process of designing primers and controls to screen for the number of repeats in a polymeric tract of a phase-variable gene in Neisseria meningitidis (the DNA methyltransferase ModA is used as an example, but this method can be applied to other phase-variable genes).

Key words

Fragment analysis Polymeric DNA tract Phase-variable gene DNA repeat sequence 


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Institute for GlycomicsGriffith UniversityGold CoastAustralia

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