A
modern approach to the specific location of genes on chromosomes is a technique
for the hybridization of DNA and RNA "in situ." With this procedure,
specific radioactive RNA or DNA (known as probes) can be isolated (or synthesized
"in vitro") and then annealed to chromosomes which have been treated
in such a manner that their basic double stranded DNA has been
"melted" or dissociated.
In
theory, and fortunately in practice, when the DNA is allowed to re-anneal, the
probe competes for the binding, but only where it mirrors a complimentary
sequence. Thus, RNA will attach to the location on the chromosome where the
code for its production is to be found. DNA will anneal to either RNA which is
still attached to a chromosome, or to the complimentary sequence DNA strand
within the chromosome. Since the probe is radioactive, it can be localized via
autoradiographic techniques.
Finally,
it is possible to produce an RNA probe that is synthesized directly from
repetitive sequences of DNA, such as that found within the nucleolar organizer
region of the genome. This RNA is known as cRNA (for copied RNA) and is a
convenient source of a probe for localizing the nucleolar organizer gene within
the nucleus, or on a specific chromosome.
The
use of in situ hybridization begins with good cytological preparations of the
cells to be studied, and the preparation of pure radioactive probes for the
analysis. The details depend upon whether the hybridization is between DNA
(probe) and DNA (chromosome), DNA (probe) and RNA (chromosome), or between RNA
(probe) and DNA (chromosome).
Preparation
of the Probe:
Produce
radioactive RNA by incubating the cells to be measured in the presence of 
H-uracil, a specific precursor to
RNA. Subsequent to this incubation, extract rRNA from the sample and purify
through differential centrifugation, column chromatography or electrophoresis.
Dissolve the radioactive RNA probe in 4X Saline-Citrate containing 50%
formamide to yield a sample that has 50,000 to 100,000 counts per minute, per
30 microliter sample, as determined with a scintillation counter. Add the
formamide is added to prevent the aggregation of RNA.
H-uracil, a specific precursor to
RNA. Subsequent to this incubation, extract rRNA from the sample and purify
through differential centrifugation, column chromatography or electrophoresis.
Dissolve the radioactive RNA probe in 4X Saline-Citrate containing 50%
formamide to yield a sample that has 50,000 to 100,000 counts per minute, per
30 microliter sample, as determined with a scintillation counter. Add the
formamide is added to prevent the aggregation of RNA.
Preparation
of the Slides:
Fix
the materials to be studied in either 95% ethanol or in 3:1 methanol:water,
attach to pre-subbed slides (as squashes for chromosomes) and air dry.
Hybridization
Place
the air dried slides into a moist chamber, usually a disposable petri dish
containing filter paper and carefully place 30 microliters of RNA probe in 4X
SSC-50% formamide onto the sample.
Carefully
add a cover slip (as in the preparation of a wet mount), place the top on the
container and place in an incubator at 37° C for 6-12 hours.
Washing:
Pick
up the slides and dip into 2X SSC so that the coverglass falls off.
Place
the slides in a coplin jar containing 2X SSC for 15 minutes at room
temperature.
Transfer
the slides to a treatment with RNase (50 microgram/ml RNase A, 100 units/ml
RNase T1 in 2X SSC) at 37° C
for 1 hour.
Wash
twice in 2X SSC, 15 minutes each.
Wash
twice in 70% ethanol, twice in 95% ethanol and air dry.
Autoradiography:
Add
photographic emulsions to the slides and after a suitable exposure period,
develop the slides, counterstain and add cover slips.
Analyze
the slides by determining the location of the radioactive probe on the
chromosomes or within the nuclei.
(Dr.
William H. Heidcamp)
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