Lo3 Group 3 Module 3 Final Report

DNA Degradation as a Function of Decom-
position Environment
Lindsey McNaughton & Elizabeth Bell
CHE 4350 Module 3 Report
10 May 2017
ABSTRACT
Phenol-chloroform extraction and ethanol precipitation were used to analyze DNA degra-
dation on a collection of decomposing tissue samples exposed to varying environmental factors.
Due to the 80% genetic similarity to the human genome, bovine liver and muscle samples were
used. These samples were decomposed in air, deionized water, creek water, and soil at tempera-
tures of 4, 25, and 37(°C) for a period of 4 weeks. DNA was extracted weekly to be visualized
using agarose gel electrophoresis. It was hypothesized the liver tissue would decompose at a
faster rate than the muscle and the overall degradation would increase with temperature. The
agarose gels produced the anticipated smearing indicative of degraded DNA and it was deter-
mined that the temperature and sample type correlated with the level of degradation observed.
INTRODUCTION
Genetic fingerprinting became accessible to the public in 1986 when Dr. Alec Jefferys
used DNA to link semen stain samples collected from two rape/murders in Leicester United
Kingdom (History of DNA Profiling). The application of this technique exonerated an innocent
man with the conviction of the actual perpetrator, Colin Pitchfork. Further development of this
technique has improved DNA profiling and its applications in criminal investigations. Despite
the ability to identify perpetrators in criminal investigations with genetic evidence, determination
of the time of death has remained a challenge. “Traditionally, the PMI is estimated based on var-
ious physical and biochemical changes occurring shortly after death, such as rigor, algor and
livor mortis” (Berge et.al., 2016). Modern methods for determining postmortem interval vary, but
fail to provide more than an 8 hour window time estimate (Johnson, 2002). Analysis of DNA
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degradation as a function of decomposition could lead to a new approach in the estimation of
postmortem intervals.
Extraction of DNA from crime scenes can be difficult due to relatively small sample sizes
and environmental stressors which cause DNA degradation. “The phenol–chloroform method is a
well-established forensic extraction procedure even though it is known to be laborious compared
with alternative approaches and involves toxic reagents, such as phenol, which requires special
safety precautions in the laboratory” ( Köchl et. al., 2005). This method allows DNA to be ex-
tracted in the presence of other proteinaceous material.
The rate of decomposition is known to be influenced by external variables such as type of
clothing, presence of a body bag and/or coffin, soil type, burial depth, water context, am-
bient temperature, weather conditions, air circulation, accessibility to insects, body mass
index (BMI) of the deceased, agonal state and microbiome composition. Moreover, it is
described that different tissue types may be affected differently by these degradation pro-
cesses, as tissues are differentially shielded from the external factors or microbial sources
and because enzymes tend to be more active in tissues such as the kidney and liver, re-
sulting in putrefaction, thus early DNA degradation in these tissue cells (Berge et. al.,
2016)
This study aims to apply the phenol-chloroform method to search for trends in DNA
degradation of bovine tissue samples with increased decomposition in varying environmental
conditions.
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MATERIALS & METHODS
Samples of bovine tissue were purchased from a local butchery, and samples of soil and
water were collected from Cherry Creek. The bovine samples were then portioned into 50 mL
falcon tubes; 24 designated for bovine liver and 24 for top round. Each tissue sample was divid-
ed into varying mediums (air, 30 mL deionized water, 30 mL creek water, and 25 mL soil) and
held at either 4, 25, or 37°C . 12 tubes from each sample set were duplicates set aside for use in
the event a sample became compromised.
An initial sample of 1g was collected from each tissue into a clean microcentrifuge tube
and phenol-chloroform extraction was performed using a 1:1 volume of phenol:chlorofor-
m:isoamyl alcohol. The samples were centrifuged an additional 5 minutes upon the removal of
the tissue sample from the microcentrifuge tube. Glycogen (20ug/uL), 7.5 M Ammonium Ac-
etate, and 100% ethanol were then added to each sample in preparation of ethanol precipitation.
The samples were placed in -20 °C until the precipitation could be completed.
Portions of each sample (Appendix A: Tables 1A-C) were collected weekly to perform
phenol-chloroform extraction and ethanol precipitation. The samples were centrifuged for 45
minutes at room temperature due to a lack of equipment that could centrifuge the size and quanti-
ty at 4°C. After the second set of samples were collected the 37°C samples were terminated due
to departmental complaints. Agarose gel electrophoresis of the initial sample was conducted to
determine the best fit ladder. The DNA isolated was quantified using the NanoDrop Spectropho-
tometer and concentrated for approximately 3 hours. Once the DNA was concentrated TEN buf-
fer was used to re-suspend the sample and agarose gel electrophoresis was executed.
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RESULTS
Initial gels failed to express DNA samples collected 5 April 2017 (Appendix A: Figures
2A-D). The two samples that had distinguishable bands on the gel had a NanoDrop reading be-
tween 190-230 ng/µL while all other samples had lower concentrations (Appendix A: Figure
3A). A SpeedVac was used to concentrate the samples and the gels were repeated (Appendix A:
Figures 4A-D). Degradation was observed as indicated by the streaking and shadowing of the
sample paths. All subsequent samples were analyzed with NanoDrop and concentrated prior to
agarose gel electrophoresis (Appendix A: Figures 3A-C). Week two samples, collected 12 April
2017, also expressed the expected smearing indicative of DNA degradation (Appendix A: Fig-
ures 5A-D). Extensive degradation was observed on week three gels, collected 19 April 2017.
Individual bands were difficult to observe due to the intensity of smearing on the gels (Appendix
A: Figure 6A-C).
Quantification of the DNA observed was conducted using GelAnalyzer 2010© (Ap-
pendix C). This program used the manufacturer standards provided (Appendix B) to analyze the
band intensity and calculate observed molecular weight.
DISCUSSION
The gels that were run initially were a problem that needed to be figured out. There were
two samples that showed up on the gels, but none of the rest did. The samples that did show up
had distinguishable bands, but they were in the early stages of shadowing and smearing. It was
suggested by Dr. Cook to concentrate the DNA and re-run the gels and see what happened. After
concentration and re-running the gels more samples showed up on the gels. There were a few
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samples that had excellent banding and smearing. There were a few that had no discernible bands
but had clear paths down the gel. It was assumed that these samples continued to decay from the
time of sampling initially to the running of the second set of gels for sample one and that resulted
in the extremely smeared results. Sample week two gels were much closer to what was expected.
There were the bands with complete smearing between them. The more complete the smearing
the more degraded the DNA. There are some bands still distinguishable for a couple samples,
and some are so degraded that they only have the shading at the end of the gels. For the final gels
there are samples that didn’t show up at all, and for those samples it was thought that the concen-
tration wasn’t high enough to show up on the gels. The gels for the final samples were the most
smeared and streaked of all. There were still a few samples that had one distinguishable band,
but the majority of the samples had no distinguishable bands and had extreme shadowing toward
the end of the gel. The shadowing on the end show that the DNA degraded to the point that it all
grouped at the bottom.
After analyzing the gels it was determined that the longer the DNA stayed in the envi-
ronments the more it was degraded. It was observed that for the majority of the 37°C samples
showed the most shadowing and least discernible bands. The room temperature samples had
bands that were not as bright and a moderate amount of shadowing. The 4°C samples had the
clearest bands and the least shadowing. In the last samples the 4°C samples were the only ones
that had a strong band still. Overall it was observed that week to week the DNA degraded more
and more. All of the results observed support the hypothesis. The 37°C samples decayed the
fastest, the room temperature samples had moderate decay speed, and the 4°C samples held up
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the best. Also it was observed that the decay got more and more extreme as the weeks went by
and overall the liver decayed faster than the top round samples.
Future adaptations of this experiment could provide useful insights applicable to forensic
studies. Collection of initial samples in time intervals over a 48 hour period would provide a
comparison more applicable to determining the postmortem interval. A longer duration of study
with more frequent sampling would allow for a statistical approach to quantifying the data; per-
haps with a standardized T-test to determine if decomposition is statistically significant in rela-
tion to degradation. To reduce procedure time the QIAAamp® DNA Mini kit extraction method
could be applied rather than phenol-chloroform. In a recent study it was determined to produce
less isolated DNA, but can be further amplified using PCR while reducing exposure to toxins
(Jakovski et. al. 2015). Analyzing the soil and water samples for fauna present using microbio-
logical techniques would provide more insight towards the fauna in decomposing environments
and their effects on the collected DNA samples. Sequencing of the collected DNA for compari-
son of that visible on the agarose gel would also be an interesting adaptation of this project. In
addition, genetic sequencing would give a more accurate picture of the way the DNA degrades,
whether it would degrade predictably at any given time point or if it would just be random.
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ACKNOWLEDGEMENTS
We would like to gratefully acknowledge Dr. Megan Filbin-Wong for her collaboration in
the development of this project and Dr. Carma Cook for her dedicated time and assistance in the
execution of the research. We would also like to thank the Western Daughter’s Butcher Shoppe in
Denver, CO for providing fresh, locally sourced samples for us to use.
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References 
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Bonham, A. J.; Ragan, E.; Drotar, A. M.; Elkins, K. M.; Filbin-Wong, M. E. Metropolitan State
University of Denver Biochemistry Laboratory Manual, 2016. Available at: https://metrostate-
bb.blackboard.com/bbcswebdav/pid-4846211-dt-content-rid-15790571_1/courses/201730.32536/
CHE4350_Lab_Manual_F16.pdf
Boyer, R. F. Biochemistry laboratory: modern theory and techniques, 2nd ed.; Prentice Hall: 
Boston, 2012.
Berge, M. V. D.; Wiskerke, D.; Gerretsen, R. R. R.; Tabak, J.; Sijen, T. DNA and RNA profiling
of excavated human remains with varying postmortem intervals. International Journal of Legal
Medicine.2016, 130 (6), 1471–1480 DOI: 10.1007/s00414-016-1438-9.
History of DNA profiling http://www2.le.ac.uk/departments/emfpu/to-be-deleted/explained/pro-

filing-history (accessed Apr 28, 2017).
How to Use Phenol / Chloroform for DNA Purification https://www.thermofisher.com/us/en/

home/references/protocols/nucleic-acid-purification-and-analysis/dna-extraction-protocols/phe-
nol-chloroform-extraction.html (accessed Mar 13, 2017).
Jakovski, Z.; Ajanovska, R. J.; Stankov, A.; Pavlovski, G.; Poposka, V.; Marjanovic, D. Compar-
ative study of two dna extraction methods in different tissues and conditions of degradation.
Forensic Science International: Genetics Supplement Series.2015, 5 DOI: 10.1016/j.fsigss.
2015.09.159.
Johnson, L. A.; Ferris, J. A. J. Analysis of postmortem DNA degradation by single-cell gel elec-
trophoresis. Forensic Science International 2002, 126 (1), 43–47.
Köchl, S.; Niederstätter, H.; Parson, W. DNA Extraction and Quantitation of Forensic Samples
Using the Phenol–Chloroform Method and Real-Time PCR. Methods in Molecular Biology
2005, 297, 013–030 DOI: 10.1385/1-59259-867-6:013.
Phillips, K.; Mccallum, N.; Welch, L. A comparison of methods for forensic DNA extraction:
Chelex-100® and the QIAGEN DNA Investigator Kit (manual and automated). Forensic Science
International: Genetics.2012, 6 (2), 282–285 DOI: 10.1016/j.fsigen.2011.04.018.
Your DNA may be degraded https://www.thermofisher.com/us/en/home/life-science/pcr/real-

time-pcr/qpcr-education/real-time-pcr-troubleshooting-tool/snp-genotyping-troubleshooting/trail-
ing-clusters/dna-may-be-degraded.html (accessed Mar 11, 2017). 
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Appendix A: Samples 
Appendix A Samples
TABLE 1A: Sample 1 Group collected on 5 April 2017 one week after initial decomposi-
tion environments were established.  
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Appendix A Samples
TABLE 1B: Sample 2 Group collected on 12 April 2017 two weeks after initial decompo-
sition environments were established. 
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Appendix A Samples
TABLE 1C: Sample 3 Group collected on 19 April 2017 three weeks after initial decom-
position environments were established.
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Appendix A Samples
FIGURES 2A-D: INITIAL AGAROSE GELS OF SAMPLE 1 GROUP AND INITIAL DNA SAMPLES
!
FIGURE 2A: Initial agarose gel of S1G
1 2 3 4 5 6 7 8
Low 37°C Top 4°C Top 4°C Top 4°C Liver 4°C 4°C Top 25°C Top
Mass Round Round Round DiH2O Liver Round Round
Ladder CCK Soil CCK CCK DiH2O CCK
H 2O H 2O H 2O H 2O
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Appendix A Samples
FIGURE 2B: Initial agarose gel of S1G
1 2 3 4 5 6 7 8
Log 2 4°C Top 37°C 25°C Top 37°C 25°C Top 25°C 4°C Liver
Ladder Round Liver Round Liver Air Round Liver Soil
Air DiH2O Air Soil DiH2O
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Appendix A Samples
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Appendix A Samples
FIGURE 2C: Initial agarose gel of S1G
1 2 3 4 5 6 7 8
Low 37°C 25°C 37°C Top 37°C Top 4°C Liver 37°C Top Log 2
Mass Liver Liver Round Round Air Round Ladder
Ladder CCK CCK DiH2O Soil
H 2O H 2O
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Appendix A Samples
FIGURE 2D: Initial agarose gel of S1G
1 2 3 4 5 6 7 8
Log 2 Initial Initial 25°C 25°C 37°C 25°C Top Low

Ladder Top Liver Liver Liver Air Liver Round Mass
Round Sample Soil Soil DiH2O Ladder
Sample Day 1
Day 1
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Appendix A Samples
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Appendix A Samples
FIGURES 3 A-C: NANODROP DATA OF SAMPLE GROUPS
FIGURE 3A: Sample 1 Group NanoDrop data. Red indicates samples that were observed
on gel. Threshold concentration is 190 ng/uL.
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Appendix A Samples
FIGURE 3B: Sample 2 Group NanoDrop data prior to DNA concentration.
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Appendix A Samples
FIGURE 3C: Sample 3 Group NanoDrop data prior to DNA concentration
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Appendix A Samples
FIGURES 4 A-D: AGAROSE GELS OF SAMPLE 1 GROUP (S1G) AND INITIAL DNA SAM-
PLES USING CONCENTRATED DNA
FIGURE 4A: Agarose gel of S1G using concentrated DNA
1 2 3 4 5 6 7 8
37°C 37°C 37°C 37°C Top 37°C Top 37°C Top 37°C Top Low
Liver Liver Liver Air Round Round Round Round Mass
CCK DiH2O Soil CCK DiH2O Air Ladder
H 2O H 2O
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Appendix A Samples
FIGURE 4B: Agarose gel of S1G and initial DNA samples using concentrated DNA.
1 2 3 4 5 6 7 8
25°C Top 25°C Top 25°C Top 25°C Top Initial Initial Log 2 37°C
Round Round Round Round Top Liver Ladder Liver Soil
Soil CCK DiH2O Air Round Sample
H 2O Sample Day 1
Day 1
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Appendix A Samples
FIGURE 4C: Agarose gel of S1G using concentrated DNA
1 2 3 4 5 6 7 8
Low 4°C Liver 4°C Liver 4°C Liver 4°C Liver 4°C Top 4°C Top Log 2
Mass Air DiH2O CCK Soil Round Round Ladder
Ladder H 2O Air DiH2O
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Appendix A Samples
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Appendix A Samples
FIGURE 4D: Agarose gel of S1G using concentrated DNA
1 2 3 4 5 6 7 8
Log 2 4°C Top 4°C Top 25°C 25°C 25°C 25°C Low
Ladder Round Round Liver Air Liver Liver Liver Soil Mass
CCK Soil DiH2O CCK Ladder
H 2O H 2O
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Appendix A Samples
FIGURES 5 A-D: AGAROSE GELS OF SAMPLE 2 GROUP (S2G) USING CONCENTRATED DNA
1 2 3 4 5 6 7 8
37°C 37°C 37°C 37°C Top 37°C Top 37°C Top 37°C Top Low
Liver Liver Liver Air Round Round Round Round Mass
CCK DiH2O Soil CCK DiH2O Air Ladder
H 2O H 2O
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Appendix A Samples
FIGURE 5B: Agarose gel of S2G using concentrated DNA
1 2 3 4 5 6 7 8
25°C Top 25°C Top 25°C Top 25°C Top None None Log 2 37°C
Round Round Round Round Ladder Liver Soil
Soil CCK DiH2O Air
H 2O
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Appendix A Samples
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Appendix A Samples
1 2 3 4 5 6 7 8
Low 4°C Liver 4°C Liver 4°C Liver 4°C Liver 4°C Top 4°C Top 4°C Top
Mass Air DiH2O CCK Soil Round Round Round
Ladder H 2O Air DiH2O CCK
H 2O
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Appendix A Samples
FIGURE 5D: Agarose gel of S2G using concentrated DNA
1 2 3 4 5 6 7 8
Log 2 4°C Top 25°C 25°C 25°C 25°C Log 2 Low

Ladder Round Liver Air Liver Liver Liver Soil Ladder Mass
Soil DiH2O CCK Ladder
H 2O
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Appendix A Samples
FIGURES6 A-D: AGAROSE GELS OF SAMPLE 3 GROUP (S3G) USING CONCENTRATED

DNA
1 2 3 4 5 6 7 8
Low 4°C Top 4°C Top 4°C Top 4°C Top 4°C Liver 4°C Liver 4°C Liver
Mass Round Round Round Round Air DiH2O CCK
Ladder Air DiH2O CCK Soil H 2O
H 2O
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Appendix A Samples
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Appendix A Samples
FIGURE 6B: Agarose gel of S3G using concentrated DNA
1 2 3 4 5 6 7 8
Log 2 4°C Liver 25°C 25°C None None None None

Ladder Soil Liver Air Liver
DiH2O
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Appendix A Samples
1 2 3 4 5 6 7 8
Low 25°C Top 25°C Top 25°C Top 25°C Top 25°C 25°C Log 2
Mass Round Round Round Round Liver Soil Liver Ladder
Ladder Soil CCK DiH2O Air CCK
H 2O H 2O
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Appendix A Samples
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Appendix B: Standards
Lindsey McNaughton
 
Appendix B Standards
FIGURE 1: Standards created using manufacturer ladder and graphing log molecular weight by
distance (cm) travelled from well to produce best fit line 
Log 2 Ladder
1
0.75
0.5
Log MW (kbp)
0.25
0
y = -0.1916x + 0.8575
-0.25
R² = 0.9815
-0.5
-0.75
-1
0 2.5 5 7.5 10
Distance (cm)
Low Mass Ladder

3.4
2.55
Log MW (kbp)
1.7
y = -0.2701x + 3.6926
R² = 0.9967
0.85
0
0 1.8 3.5 5.3 7
Distance (cm)
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FIGURE 2: Log 2 Ladder Standard using GelAnalyzer 2010
Molecular Weight by band of Log 2 Ladder
Best Fit Line of Log 2 Ladder 
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Log 2 Manufacturer Ladder Used to Establish Standards
Intensity of bands by pixel for Log 2 Ladder
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FIGURE 3: Low Mass Ladder Standard using GelAnalyzer 2010
Molecular Weight by band of Low Mass Ladder
Best Fit Line of Low Mass Ladder
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Low Mass Manufacturer Ladder Used to Establish Standards
Intensity of bands by pixel for Low MassLadder 
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Appendix C: GelAnalyzer 2010© Results
Lindsey McNaughton 
Sample 1 Group
 
COLLECTED 1 WEEK FROM INITIAL ENVIRONMENT
Appendix C GelAnalyzer 2010© Results
FIGURE 1A-H: APPENDIX A, FIGURE 4A GEL ANALYZED USING GELANALYZER 2010 SOFTWARE
Sample 1 Group Page 46

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!
FIGURE 1A: 37°C Liver: CCK H2O
FIGURE 1B: 37°C Liver: Di H2O 

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!
FIGURE 1C: 37°C Liver: Air
FIGURE 1D: 37°C Top Round: Soil 

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!
FIGURE 1E: 37°C Top Round: CCK H2O
FIGURE 1F: 37°C Top Round: Di H2O 

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!
FIGURE 1G: 37°C Top Round: Air
FIGURE 1H: Low Mass Ladder with standards created using GelAnalyzer 2010 applied

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!
FIGURE 2A-D: APPENDIX A, FIGURE 4B GEL ANALYZED USING GELANALYZER 2010 SOFTWARE
 

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!
FIGURE 2A: 25°C Top Round: Soil
FIGURE 2B: Liver Initial Sample 

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!
FIGURE 2C: Log 2 Ladder
FIGURE 2D: 37°C Liver: Soil 

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!
FIGURE 3A-F: APPENDIX A, FIGURE 4C GEL ANALYZED USING GELANALYZER 2010 SOFTWARE
 

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!
FIGURE 3A: Low Mass Ladder standards applied individually
FIGURE 3B: Log 2 Ladder standards applied individually

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!
FIGURE 3C: Low Mass Ladder
FIGURE 3D: 4°C Top Round:Air 

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FIGURE 3E: 4°C Top Round: Di H2O
FIGURE 3F: Log 2 Ladder 

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FIGURE 4A-F: APPENDIX A, FIGURE 4D GEL ANALYZED USING GELANALYZER 2010 SOFTWARE
 

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!
FIGURE 4A: Log 2 Ladder

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!
FIGURE 4B: 4°C Top Round: CCK H2O
FIGURE 4C: 4°C Top Round: Soil 

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!
FIGURE 4D: 4°C Liver: DiH2O
FIGURE 4E: 4°C Liver: CCKH2O 

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!
FIGURE 4F: Low Mass Ladder 

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!
Sample 2 Group
COLLECTED 2 WEEKS FROM INITIAL ENVIRONMENT 
FIGURE 5A-G: APPENDIX A, FIGURE 5A GEL ANALYZED USING GELANALYZER 2010 SOFTWARE 

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FIGURE 5A: 37°C Liver: CCK H2O
FIGURE 5B: 37°C Liver: Di H2O 

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FIGURE 5C: 37°C Top Round: Soil
FIGURE 5D: 37°C Top Round: CCK H2O

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FIGURE 5E: 37°C Top Round: Di H2O
FIGURE 5F: 37°C Top Round: Air 

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FIGURE 5G: Low Mass Ladder

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!
FIGURE 6A-F: APPENDIX A, FIGURE 5B GEL ANALYZED USING GELANALYZER 2010 SOFTWARE

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!
FIGURE 6A: 25°C Top Round: Soil
FIGURE 6B: 25°C Top Round: CCK H2O

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FIGURE 6C: 25°C Top Round: DiH2O
FIGURE 6D: 25°C Top Round: Air

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FIGURE 6E: LOG 2 LADDER
FIGURE 6F: 37°C Liver: Soil

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FIGURE 7A-G: APPENDIX A, FIGURE 5C GEL ANALYZED USING GELANALYZER 2010 SOFTWARE

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!
FIGURE 7A: LOW MASS LADDER
FIGURE 7B: 4°C Liver: Air 

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!
FIGURE 7C: 4°C Liver: DiH2O
FIGURE 7D: 4°C Liver: Soil 

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FIGURE 7E: 4°C Top Round: Air
FIGURE 7F: 4°C Top Round: DiH2O 

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FIGURE 7G: 4°C Top Round: CCK H2O

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FIGURE 8A-F: APPENDIX A, FIGURE 5D GEL ANALYZED USING GELANALYZER 2010 SOFTWARE 

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!
FIGURE 8A: LOG 2 LADDER
FIGURE 8B: 4°C Top Round: Soil 

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FIGURE 8D: 4°C Liver: DiH2O 

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FIGURE 8E: 25°C Liver: CCK H2O
FIGURE 8F: 25°C Liver: Soil 

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FIGURE 8G: LOG 2 LADDER

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FIGURE 8F: LOW MASS LADDER

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Sample 3 Group
COLLECTED 3 WEEKS FROM INITIAL ENVIRONMENT 
FIGURE 9A-G: APPENDIX A, FIGURE 6A GEL ANALYZED USING GELANALYZER 2010 SOFTWARE 

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!

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FIGURE 9B: 4°C Top Round: Air
FIGURE 9C: 4°C Top Round: DiH2O 

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FIGURE 9D: 4°C Top Round :Soil
FIGURE 9E: 4°C Liver: Air

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FIGURE 9F: 4°C Liver: DiH2O
FIGURE 9G: 4°C Liver: CCK H2O 

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FIGURE 10A-D: APPENDIX A, FIGURE 6B GEL ANALYZED USING GELANALYZER 2010 SOFT-
WARE 

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!
FIGURE 10A: LOG 2 LADDER
FIG-
URE 10B: 4°C Liver: Soil 

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!
FIGURE 10D: 25°C Liver: DiH2O

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!
FIGURE 11A-G: APPENDIX A, FIGURE 6C GEL ANALYZED USING GELANALYZER 2010 SOFT-
WARE 

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!
FIG- URE
11B: 25°C Top Round:Soil 

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FIGURE 11C: 25°C Top Round: CCK H2O
FIGURE 11D: 25°C Top Round: DiH2O 

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FIGURE 11E: 25°C Top Round: Air
FIGURE 11F: 25°C Liver: Soil 

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FIGURE 11G: 25°C Liver: CCK H2O
FIGURE 11H: LOG 2 LADDER 

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!
Weekly Sample Molecular Weight
1 Week 2 Weeks 3 Weeks
37°C Top Round Air 2281 15 N/A
11859
37°C Top Round 5301 N/A

2281
DiH2O
56
37°C Top Round CCK 2281 4115 N/A

H2O
1557
37°C Top Round Soil 2301 12026 N/A
1599 4136
37°C Liver Air 2281 0 N/A
37°C Liver DiH2O 2294 12026 N/A
74 4305
37°C Liver CCK H2O 2286 11859 N/A
3993
37°C Liver Soil 53666 7833 N/A
289
Molecular Weight Summary Page 99

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!
25°C Top Round Air 0 10391 10750
7484
25°C Top Round Di- 0 10440 5952

H2O
331
25°C Top Round CCK 0 10506 10574

H2O
509 0
109
25°C Top Round Soil 7277 10457 10674
7000 7343
25°C Liver Air 0 8069 34523
0 772
25°C Liver DiH2O 68474 8069 33374
1697 0 629
25°C Liver CCK H2O 1569 8028 10425
25°C Liver Soil 0 0 10574
3094

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!
4°C Top Round Air 0 305507 4608
13298 2720
141 0
4°C Top Round DiH2O 3129 319204 2670
632
4°C Top Round CCK 68474 8056 0

H2O
5503
4°C Top Round Soil 1123 7973 11684
4588
4°C Liver Air 0 338426 0
142
139
4°C Liver DiH2O 0 353599 0
4°C Liver CCK H2O 1880 353599 0
144
4°C Liver Soil 0 0 34523
932
737

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!

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Lo3 Group 3 Module 3 Final Report

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DNA Degradation as a Function of Decom-

Lindsey McNaughton & Elizabeth Bell

CHE 4350 Module 3 Report

dation on a collection of decomposing tissue samples exposed to varying environmental factors.

well-established forensic extraction procedure even though it is known to be laborious compared

tracted in the presence of other proteinaceous material.

The rate of decomposition is known to be influenced by external variables such as type of

degradation of bovine tissue samples with increased decomposition in varying environmental

the event a sample became compromised.

and phenol-chloroform extraction was performed using a 1:1 volume of phenol:chlorofor-

band intensity and calculate observed molecular weight.

grouped at the bottom.

haps with a standardized T-test to determine if decomposition is statistically significant in rela-

Denver, CO for providing fresh, locally sourced samples for us to use.

History of DNA profiling http://www2.le.ac.uk/departments/emfpu/to-be-deleted/explained/pro-

How to Use Phenol / Chloroform for DNA Purification https://www.thermofisher.com/us/en/

Your DNA may be degraded https://www.thermofisher.com/us/en/home/life-science/pcr/real-

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FIGURE 2B: Initial agarose gel of S1G

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FIGURE 2C: Initial agarose gel of S1G

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FIGURE 2D: Initial agarose gel of S1G

Log 2 Initial Initial 25°C 25°C 37°C 25°C Top Low

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FIGURES 3 A-C: NANODROP DATA OF SAMPLE GROUPS

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FIGURE 3B: Sample 2 Group NanoDrop data prior to DNA concentration.

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FIGURE 3C: Sample 3 Group NanoDrop data prior to DNA concentration

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FIGURE 4A: Agarose gel of S1G using concentrated DNA

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FIGURE 4C: Agarose gel of S1G using concentrated DNA

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FIGURE 4D: Agarose gel of S1G using concentrated DNA

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FIGURE 5A: Agarose gel of S2G using concentrated DNA

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FIGURE 5B: Agarose gel of S2G using concentrated DNA

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FIGURE 5C: Agarose gel of S2G using concentrated DNA

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FIGURE 5D: Agarose gel of S2G using concentrated DNA

Log 2 4°C Top 25°C 25°C 25°C 25°C Log 2 Low

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FIGURES6 A-D: AGAROSE GELS OF SAMPLE 3 GROUP (S3G) USING CONCENTRATED

FIGURE 6A: Agarose gel of S3G using concentrated DNA

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FIGURE 6B: Agarose gel of S3G using concentrated DNA

Log 2 4°C Liver 25°C 25°C None None None None

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FIGURE 6C: Agarose gel of S3G using concentrated DNA

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Best Fit Line of Log 2 Ladder 

Intensity of bands by pixel for Low MassLadder 

FIGURE 1B: 37°C Liver: Di H2O 

FIGURE 1D: 37°C Top Round: Soil 

FIGURE 1F: 37°C Top Round: Di H2O 

FIGURE 2B: Liver Initial Sample 

FIGURE 2D: 37°C Liver: Soil 

FIGURE 3D: 4°C Top Round:Air 

FIGURE 3F: Log 2 Ladder 

FIGURE 4C: 4°C Top Round: Soil 

FIGURE 4E: 4°C Liver: CCKH2O 

FIGURE 4F: Low Mass Ladder 

FIGURE 5B: 37°C Liver: Di H2O 

FIGURE 5F: 37°C Top Round: Air 