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

Random amplified polymorphic DNA (RAPD) fragments were prepared from samples of Calonectris diomedea (Cory's shearwater, Aves) and Haemonchus contortus (Nematoda) DNA by polymerase chain reaction (PCR) using decamers containing two restriction enzyme sites as primers. Six of 19 studied RAPD fra...

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Bibliographic Details
Published in:Molecular ecology 1999-03, Vol.8 (3), p.493-503
Main Authors: RABOUAM, CORINNE, COMES, ANA MARIA, BRETAGNOLLE, VINCENT, HUMBERT, JEAN-FRANÇOIS, PERIQUET, GEORGES, BIGOT, YVES
Format: Article
Language:English
Subjects:
Calonectris diomedea
commensal organism contamination
Cory's shearwater
Haemonchus contortus
Marine
nematode
PCR artefacts
population biology
RAPD
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Summary:Random amplified polymorphic DNA (RAPD) fragments were prepared from samples of Calonectris diomedea (Cory's shearwater, Aves) and Haemonchus contortus (Nematoda) DNA by polymerase chain reaction (PCR) using decamers containing two restriction enzyme sites as primers. Six of 19 studied RAPD fragments probably originated from traces of commensal microorganisms. Many rearranged fragments, absent in the original genomic DNA, were synthesized and amplified during the processing of all the DNA samples, indicating that interactions occur within and between strands during the annealing step of PCR. The model of interactions between molecular species during DNA amplification with a single arbitrary oligonucleotide primer was modified to include nested primer annealing and interactions within and between strands. The presence of these artefacts in the final RAPD have a major effect on the interpretation of polymorphism studies.
ISSN:0962-1083
1365-294X
DOI:10.1046/j.1365-294X.1999.00605.x