Plant Genome II Conference
Town & Country Conference Center, San Diego, CA, January, 1994.
PG-II: GENOMIC AND SUBGENOMIC DNA AMPLIFICATION FINGERPRINTING USING
ARBITRARY MINI-HAIRPIN PRIMERS
GENOMIC AND SUBGENOMIC DNA AMPLIFICATION FINGERPRINTING USING
ARBITRARY MINI-HAIRPIN PRIMERS
Gustavo Caetano-Anolles and Peter M. Gresshoff, Plant Molecular
Genetics, Institute of Agriculture and Center for Legume
Research, The University of Tennessee, Knoxville, TN 37901-1071
DNA amplification fingerprinting (DAF), the enzymatic
amplification of DNA directed by short oligonucleotides of
arbitrary sequence, produces complex and characteristic DNA
fingerprints. We have used extraordinarily stable mini-hairpin
oligonucleotide primers harboring a "core" arbitrary sequence at
the 3' terminus to prime the amplification of a wide range of
templates ranging from plasmid DNA to plant and animal genomes.
Both arbitrary core and hairpin sequence influenced the
amplification reaction. Oligonucleotide substitution with
degenerate bases tailored the complexity of fingerprint patterns.
Simulation studies of the amplification of plasmids pUC18 and
pBR322 using mini-hairpin primers with short arbitrary cores
permitted assignment of DAF amplification products to expected
amplicons and revealed existence of physical interaction between
annealing sites during amplification of first-round products.
Results show that mini-hairpin primers can be used to fingerprint
complex genomes and study subgenomic fragments like yeast
artificial chromosomes (YACs), cloned DNA and PCR amplified
fragments.
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