STEP 3: MICROSATELLITES GIVE US INDIVIDUAL
BAR CODES
What Are Microsatellites?
The genetic code of DNA is made up of 4 different DNA bases (known in
shorthand by A, C, T, G). Microsatellite loci (singular: locus) are
sites within the genetic code where there are a variable number of repeats
of a short but specific DNA base sequence. The repeated sequences may
consist of 2-5 bases. These microsatellite sequences are inherited,
and chimpanzees (and humans) get two copies (alleles) for each microsatellite
locus – one from mom and one from dad:
EXAMPLE: At one site, the repeated sequence could be AACG. This sequence
might be repeated anywhere from
2 times (AACGAACG), 8 base pairs
3 times (AACGAACGAACG), 12 base pairs, or
4 times (AACGAACGAACGAACG), 16 base pairs
in different individuals.
Since each individual has two copies of the
repeat sequence, they could have two of the same copy (8:8, 12:12, 16:16)
or they could have two different copies (8:12, 8:16, 12:16).
While, in reality, the number of repeats is typically much larger (often
100-300 base pairs), you get the picture. You can see that by using
multiple microsatellite loci (we use 11), we can create a genotype,
like a genetic bar code, for each chimpanzee that uniquely identifies
it. And because each individual’s genotype contains information
shared with both mom and dad, we can use that to determine who the parents
are.
A Little Laboratory Magic
In order to figure out each chimpanzee’s genotype, we have to
know the repeat number (or length of the allele) for each of the two
copies at each microsatellite locus. Remember, we also only get a
little bit of DNA from those few cells that come with the poop. So
we do two things, one is we use a procedure called polymerase chain
reaction (PCR) to make many, many copies of the microsatellite DNA.
Second, while we copy the DNA, we also label the new copies of
DNA with fluorescence so that we can visualize it. We do this by running
the DNA through a special gel – DNA is negatively charged, and
it will move through the tiny pores of the gel towards the positive
end created when electricity is applied to the gel. Because the pores
of the gel are small, shorter pieces of DNA (which have less base
pairs) move more easily through the gel than big pieces. We run the
microsatellite DNA pieces of unknown size through the gel with fluorescently
labeled DNA of known size (called a ladder), and we use an automated
sequencing machine to track the fluorescence. A computer program then
helps us determine the size (number of base pairs) of the unknown microsatellite
DNA by comparing how quickly it runs through the gel to how quickly the known sizes of DNA do. Once this is done for each microsatellite locus, then
we will have our genetic bar code, or genotype for each chimp.
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