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Probe labelling by PCR

Douglas Rhoads drhoads at MERCURY.UARK.EDU
Wed Oct 23 08:34:11 EST 1996

> To:            yeast at net.bio.net
> Subject:       Probe labelling by PCR
> From:          David Humair <David.humair at bota.unine.ch>
> Date:          23 Oct 96 09:44:17 MET

> Hi netters,
> I'm looking for a protocol to label a probe by PCR with alpha P32dATP.
> Does somebody have such a protocol?
> Thanks for your help.
> 																						David Humair

PCR Labeling
	ref: D. Heiny and D. Rhoads  modification of  Schowalter and Sommer 
1989, Analytical Biochemistry:177:90-94.

For the production of very hot probes.  Probably only efficient for
amplicons  of app. 1100 bp.  Efficient PCR labeling requires low
concentrations of unlabeled deoxynucleoside triphosphates (dNTPs)
relative to standard PCR.  For longer amplicons (>500 bp) the
limiting amount of 32P- dATP causes accumulation of short products. 
For longer inserts up to around 1100 bp, doubling the dATP
concentration usu ally allows production of full length amplification
products.  Amplification is from =F31 ng of a target PCR fragment or
insert-containing-plasmid.  The size and source of the DNA insert to
amplify (am plicon), as well as the buffer formulation can affect the
final percent incorporation.  Since incomplete extension of the
primers results in undesirable small products (30-100 bp), total TCA
precipit able counts are poor indicators of the quality of the probe
synthesized.  Therefore, for new amplicons or those of larger size
you should determine an approximate size for the products by
resolving a small aliquot (1/500th of final product) on a small TEB
denaturing polyacrylamide gel.  Incorporations generally range from
50- 90% and produce up to 20 ng of probe at 4-6 x 10^9 cpm/ug.  The
major advantage of this method over nick-translation or random
priming is that final probe is not contaminated with cold template
(i.e., specific activity 6-10x higher).  One disadvantage of this
method is the size limit of the amplified region (amplicon).

The following protocol represents optimal conditions for samples
sealed in glass capillary tubes and cycled in a Idaho Technology
1605 Air Thermo-Cycler.

PCR Parameters:     90oC 30 sec
               90oC 15 sec   \
               45oC 15 sec    >    25x
               72oC 90 sec   /     Ramp set to S1
               72oC 3 min

Anneal temperature should be adjusted for the particular primers in
use according to what normally works for the primers being used.
Times for anneal and extension may also be adjusted to fit
particular PCR methods and machines other than the Idaho Aircycler. At
end of cycling, add 180 ul TE and 5 ug carrier yeast RNA.  Purify
over G-50 spin column (see General Techniques).  Quantitate by TCA
precipitation and possibly test on denaturing mini gel (see
Acrylamide DNA Gels).  Should be used within one day as a
hybridization probe. 
    "They named it GOLF because all the other four letter 
        words were taken."  Lee Trevino

||                  Douglas Rhoads                        ||              =
||drhoads at mercury.uark.edu || Dept. of Biological Sciences||
||drhoads at comp.uark.edu    || 601 Science Engineering     ||
||501-575-3251             || University of Arkansas      ||
||FAX 501-575-4010         || Fayetteville, AR 72701      ||
||      http://comp.uark.edu/~bioinfo/bisc.html           ||
||     My Dogma Just Got Run Over by Someone's Karma      ||

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