Analysis of major histocompatibility complex class II gene in water voles using capillary electrophoresis-single stranded conformation polymorphism

Authors

  • J. BRYJA,

    Corresponding author
    1. Centre de Biologie et Gestion des Populations (UMR 22), INRA, Campus International de Baillarguet, CS 30016, 34988 Montferrier sur Lez Cedex, France;
    2. Department of Population Biology, Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, 67502 Studenec 122, Czech Republic
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  • M. GALAN,

    1. Centre de Biologie et Gestion des Populations (UMR 22), INRA, Campus International de Baillarguet, CS 30016, 34988 Montferrier sur Lez Cedex, France;
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  • N. CHARBONNEL,

    1. Centre de Biologie et Gestion des Populations (UMR 22), INRA, Campus International de Baillarguet, CS 30016, 34988 Montferrier sur Lez Cedex, France;
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  • J.-F. COSSON

    1. Centre de Biologie et Gestion des Populations (UMR 22), INRA, Campus International de Baillarguet, CS 30016, 34988 Montferrier sur Lez Cedex, France;
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J. Bryja, E-mail: bryja@brno.cas.cz. Tel./Fax: ++420-568627950

Abstract

Analysis of a single strand conformation polymorphism (SSCP) using capillary electrophoresis (CE) is a novel method to study polymorphism of DNA sequences in large scale population studies. We optimized CE-SSCP analysis to study the major histocompatibility complex (MHC) class II alpha gene (DQA) polymorphism. Short-chain linear polyacrylamide (6%) as sieving matrix, TrisCl (pH 8.5) as buffer for sample dilution, and 27 °C, 9 kV as electrophoresis parameters were suitable for sufficient resolution of all alleles. We found that almost 25% of clones contained a PCR (polymerase chain reaction) artefact and strict criteria have to be applied when using cloning and sequencing to analyse the allelic diversity of MHC genes.

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