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Features of DNA fragments obtained by random amplified polymorphic DNA (RAPD) assays
Author(s) -
RABOUAM CORINNE,
COMES ANA MARIA,
BRETAGNOLLE VINCENT,
HUMBERT JEANFRANÇOIS,
PERIQUET GEORGES,
BIGOT YVES
Publication year - 1999
Publication title -
molecular ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.619
H-Index - 225
eISSN - 1365-294X
pISSN - 0962-1083
DOI - 10.1046/j.1365-294x.1999.00605.x
Subject(s) - rapd , biology , primer (cosmetics) , dna , genetics , genomic dna , dna profiling , multiple displacement amplification , polymerase chain reaction , microbiology and biotechnology , oligonucleotide , restriction enzyme , gene , dna extraction , genetic diversity , population , chemistry , demography , organic chemistry , sociology
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.