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Related Experiment Videos

Features of DNA fragments obtained by random amplified polymorphic DNA (RAPD) assays

Rabouam1, Comes, Bretagnolle

  • 1Centre d'Etudes Biologiques de Chize, UPR CNRS 4701, Villiers-en-Bois, Beauvoir-sur-Niort, France.

Molecular Ecology
|April 13, 1999
PubMed
Summary

Random amplified polymorphic DNA (RAPD) analysis revealed artefacts caused by DNA strand interactions during polymerase chain reaction (PCR). These artefacts significantly impact the interpretation of genetic polymorphism studies in species like Cory

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Area of Science:

  • Molecular Biology
  • Genetics
  • Parasitology

Background:

  • Random amplified polymorphic DNA (RAPD) is a PCR-based technique used for genetic analysis.
  • Understanding DNA amplification processes is crucial for accurate genetic polymorphism studies.

Purpose of the Study:

  • To investigate the origin and nature of artefacts observed in RAPD fragments.
  • To refine the model of DNA amplification interactions during PCR.

Main Methods:

  • DNA extraction from Calonectris diomedea and Haemonchus contortus.
  • Polymerase chain reaction (PCR) amplification using decamer primers.
  • Analysis of RAPD fragments for artefacts and their potential origins.

Main Results:

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  • Six of 19 RAPD fragments likely originated from commensal microorganisms.
  • Rearranged DNA fragments, not present in the original DNA, were synthesized during PCR.
  • Evidence of intra- and inter-strand interactions during the PCR annealing step.

    • Conclusions:

    • Artefacts generated during PCR significantly affect the interpretation of RAPD polymorphism studies.
    • A modified model accounting for nested primer annealing and strand interactions is proposed.
    • Careful consideration of PCR artefacts is necessary for reliable genetic analyses.