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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.
– These are typically short, single stranded oligonucleotides which are
complementary to the outer regions of known sequence.

• The oligonucleotides serve as primers for DNA polymerase and the

denatured strands of the large DNA fragment serves as the template.
– This results in the synthesis of new DNA strands which are
complementary to the parent template strands.
– These new strands have defined 5' ends (the 5' ends of the
oligonucleotide primers), whereas the 3' ends are potentially
ambiguous in length.
• http://ocw.mit.edu/NR/rdonlyres/Civil-and-Environmental-Engineering/1-89Fall-2004/321BF8FF-75BE-4377-8D74-8EEE753A328C/0/11_02_04.pdf
Primer selection
• Primer is an oligonucleotide sequence – will target
a specific sequence of opposite base pairing (A-T,
G-C only) of single-stranded nucleic acids

• For example, there is a

– ¼ chance (4-1) of finding an A, G, C or T in any given DNA
sequence; there is a
– 1/16 chance (4-2) of finding any dinucleotide sequence (eg.
AG); a
– 1/256 chance of finding a given 4-base sequence.
• Thus, a sixteen base sequence will statistically be
present only once in every 416 bases (=4 294 967
296, or 4 billion): this is about the size of the human or
maize genome, and 1000x greater than the genome
size of E. coli.
Primer Specificity
• Universal – amplifies ALL bacterial DNA
for instance
• Group Specific – amplify all denitrifiers for
• Specific – amplify just a given sequence
Forward and reverse primers
• If you know the sequence targeted for
amplification, you know the size which the
primers should be anealing across
• If you don’t know the sequence… What
do you get?
DNA Polymerase
• DNA Polymerase is the enzyme responsible for
copying the sequence starting at the primer from
the single DNA strand
• Commonly use Taq, an enzyme from the
hyperthermophilic organisms Thermus aquaticus,
isolated first at a thermal spring in Yellowstone
National Park
• This enzyme is heat-tolerant  useful both because
it is thermally tolerant (survives the melting T of
DNA denaturation) which also means the process is
more specific, higher temps result in less mismatch
– more specific replication
• Restriction Fragment Length Polymorphism
• Cutting a DNA sequence using restriction
enzymes into pieces  specific enzymes cut
specific places
Starting DNA sequence:

Enzyme X Enzyme X
5’-TTC- 5’-TTC-
3”-AAG- 3”-AAG-


• DNA can be processed by RFLP either directly (if
you can get enough DNA from an environment) or
from PCR product
• T-RFLP (terminal-RFLP) is in most respects
identical except for a marker on the end of the
• Works as fingerprinting technique because
different organisms with different DNA sequences
will have different lengths of DNA between
identical units targeted by the restriction enzymes
– specificity can again be manipulated with PCR primers

Liu et al. (1997) Appl Environ Microbiol 63:4516-4522

• Fragmentation products of differing length
are separated – often on an agarose gel
bed by electrophoresis, or using a
capilarry electrophoretic separation
• Denaturing gradient gel electrophoresis
– The hydrogen bonds formed between complimentary base
pairs, GC rich regions ‘melt’ (melting=strand separation or
denaturation) at higher temperatures than regions that are AT
• When DNA separated by electrophoresis through a gradient of
increasing chemical denaturant (usually formamide and urea), the
mobility of the molecule is retarded at the concentration at which
the DNA strands of low melt domain dissociate.
– The branched structure of the single stranded moiety of the
molecule becomes entangled in the gel matrix and no further
movement occurs.
– Complete strand separation is prevented by the presence of a
high melting domain, which is usually artificially created at one
end of the molecule by incorporation of a GC clamp. This is
accomplished during PCR amplification using a PCR primer
with a 5' tail consisting of a sequence of 40 GC.

Run DGGE animation here – from http://www.charite.de/bioinf/tgge/

• Advantages • Advantages
– Relatively easy to do – Very sensitive to variations in
– Results can be banked for DNA sequence
future comparisons – Can excise and sequence
• Limitations DNA in bands
– Less sensitive phylogenetic • Limitations
resolution than sequencing – Somewhat difficult
– Each fragment length can – ”One band-one species” isn’t
potentially represent a diversity always true
of microorganisms – Cannot compare bands
– Cannot directly sequence between gels
restriction fragments,making – Only works well with short
identification indirect fragments (<500 bp), thus
limiting phylogenetic
• Fluorescent in-situ hybridization
– Design a probe consisting of an
oligonucleotide sequence and a tag
– Degree of specificity is variable!
– Hybridize that oligonucleotide sequence to the
rRNA of an organism – this is temperature
and salt content sensitive
– Image using epiflourescence, laser excitation
confocal microscopy
• Technique DIRECTLY images active
organisms in a sample
Fluorescent sitehybridisation
(FISH) using DNA probes
Probe Fluorescein
(- 20 bases) TA GC TG G C A G T
16S rRNA
16S gene
* * * *
* *


* *
16S gene * * Cell
B Drift Slime Streamer
10 µm

Oligunucleotide design
FISH variations
• FISH-CARD – instead of a fluorescent
probe on oligo sequence, but another
molecule that can then bond to many
fluorescent probes – better signal-to-noise
• FISH-RING – design of oligo sequence to
specific genes – image all organisms with
DSR gene or nifH for example
Clone Library

• http://ocw.mit.edu/NR/rdonlyres/Civil-and-Environmental-Engineering/1-89Fall-2004/321BF8FF-75BE-4377-8D74-8EEE753A328C/0/11_02_04.pdf