Biology Reference
In-Depth Information
Biomolecules can undergo further degradative activity through environmental elements
and microbial activity. Water and oxygen are highly reactive compounds, meaning they
will readily interact with other molecules. In the case of DNA, these compounds will break
bonds apart through hydrolysis and oxidation, respectively. Several sources of radiation
(cosmic, ultraviolet (from the sun), and geological) affect DNA integrity. Finally, microorgan-
isms feed on the decaying organic material of organisms and utilize their own biomolecules
to break it down for consumption (your own saliva performs the same function).
The ultimate effect of all the above factors on DNA preservation depends heavily on the
environmental conditions in which the deceased organism ultimately winds up. Warm and
humid conditions favor autolytic, hydrolytic, oxidative, and microbial activity. Whether the
organism is exposed on the surface or buried also impacts biomolecular degradation,
though even a buried organism can suffer DNA damage, depending on how deeply buried
it is, or whether ground water is running through the soil, for example. Generally speaking,
the longer an organism has been dead, the more DNA damage and decay is expected.
However, environmental conditions play a very large role in whether DNA ultimately
preserves or not.
Research Involving Degraded DNA
Two categories of research exist to deal with degraded biomolecules:
ancient DNA
, or the
DNA analysis of long-deceased organisms (generally 100 or more years), and
forensic DNA
,
or the DNA analysis of recently deceased organisms for medicolegal purposes. The only
important difference between them is the expectation for the degree of DNA decay.
Generally, the relative decay rate of DNA from the nucleus (nDNA) is faster than of the
mitochondrion. This is true for two reasons. The first is because nDNA, relative to mtDNA,
is more vulnerable to autolysis, given that only a single membrane bounds the cell nucleus
while a double membrane bounds the entire mitochondrion and its genomic material. The
second reason is because mtDNA exists in a higher copy number per cell relative to
nDNA. Every mitochondrion has on average two and half copies of its genome, and cells
can contain up to 1000 to 2000 mitochondria! It is because of this overall difference in decay
rates that most ancient DNA research rests on mtDNA data, which, though more abundant,
contains less potential information due to the fact that it has only ca. 16,000 bases relative to
the 3 billion bases found in the nuclear genome. In contrast, forensic DNA research focuses
almost exclusively on data derived from nDNA for the purposes of individual identification.
Because the degree of expected decay should be less than that of ancient DNA, the successful
extraction of nDNA in forensic contexts is more of a possibility.
Controlling for Contamination
Because degraded DNA is by definition DNA that is subpar in quality, contamination from
sources containing higher quality DNA is a persistent problem. All the existing chemical
reactions designed to isolate DNA from other cell components (DNA extraction) and to
make copies of targeted sections of DNA (DNA amplification) will work better when the
DNA is of high quality (i.e., not decayed or damaged) because it is abundant and intact,
so chemicals can easily bind where they need to.
