PCR - Polymerase Chain Reaction. PCR is an in vitro technique for the amplification of a region of DNA which lies between two regions of known sequence. PCR amplification is achieved by using oligonucleotide primers.
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Starting DNA sequence:
Liu et al. (1997) Appl Environ Microbiol 63:4516-4522
Run DGGE animation here – from http://www.charite.de/bioinf/tgge/
Very sensitive to variations in DNA sequence
Can excise and sequence DNA in bands
”One band-one species” isn’t always true
Cannot compare bands between gels
Only works well with short fragments (<500 bp), thus limiting phylogenetic characterization
Relatively easy to do
Results can be banked for future comparisons
Less sensitive phylogenetic resolution than sequencing
Each fragment length can potentially represent a diversity of microorganisms
Cannot directly sequence restriction fragments,making identification indirectRFLP vs. DGGE