Biology Reference
In-Depth Information
The first way to control for contamination is to minimize a sample's exposure to the DNA
of any organisms, but especially the DNA of organisms in the species that is closely related to
the sample. Why is this? Recall that PCR works by targeting genomic regions of interest using
short sequences of about 20 bases called
primers
(so called because these short sequences
prime
the reaction, or set it up). Most individuals within a species are probably going to
have the exact same sequence within these 20 bases, or at most, a single base difference
only. This is especially true for
Homo sapiens
, members of which show 99.8% sequence simi-
larity. This means that a PCR will pick up all sequences of individuals within that species.
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In the case of a human sample, the number of archaeological excavators, curators, and any
others should be minimized. Samples expected to undergo DNA analysis should be carefully
retrieved. In archaeological contexts, this means wearing a protective suit, a hair cover, a face-
mask, and gloves. Samples should be transferred to a specialized laboratory in DNA-free
containers.
A specialized laboratory for the analysis of degraded DNA is a clean room laboratory
(
Figure 16.7
). Clean rooms have controlled airflow: the intake of air is controlled so that it
is filtered of particles that might bear bits of DNA copies. The room itself has positive pres-
sure, so that once air comes in, it can only move out through a single exit. Rooms are regularly
cleaned with chemicals that will immediately break up contaminating DNA. Everyone who
works in the clean room has a copy of their DNA markers and/or sequences on file to be
compared to the degraded DNA results, just in case. Finally, any researchers going into
the room wear protective suits, shoe covers, facemasks, and hair covers.
CASE
STUDY: SETTING UP A DEGRADED DNA ANA
LYSIS
This case study will take you through the trials and tribulations of setting up a DNA-based
analysis of skeletonized remains, which can include either bones or teeth. By definition, you
will be embarking on an analysis of degraded DNA.
What is Your Question?
Before embarking on your project, you will need to know what question you are address-
ing. To frame the question, you will need to decide what your theoretical approach is. For
example, are you addressing a long-debated issue within evolutionary studies, or one within
the medicolegal community? You will need to develop a hypothesis (or hypotheses), and
predictions for those hypotheses, that are based on whatever theoretical approach you will
use (see DiGangi and Moore [Chapter 2], this volume). Then, your theory, hypotheses, and
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To explain this in more detail, consider the following situation: Let's say that your dog chews a human
bone from which you want to extract DNA. Would PCR pick up the dog DNA and the human DNA, or
only the dog or only the human DNA? The long answer to that is that it depends on the genomic region
you target using PCR. It is possible to target a region that is evolutionarily conserved (meaning it is the
same) between dogs and humans, such that PCR cannot discriminate between the human and dog DNA.
Conversely, it is possible to target regions that we know to be different between dogs and humans, in which
case we can use PCR to amplify only dog or only human DNA.
