Resources by Module

• DNA Analysis Considerations
• Organic Extraction
• Chelex 100 Extraction
• Other Extraction Techniques
• Quantitation

DNA Analysis Considerations

Works Cited

1. Wilson, I. G. 1997. Inhibition and facilitation of nucleic acid amplification. Appl Environ Microbiol 63 (10): 3741–51.
2. Harry, M., B. Gambier, Y. Bourezgui, and E. Garnier-Sillam. 1999. Evaluation of purification procedures for DNA extracted from organic rich samples: Interference with humic substances. Analusis 27 (5): 439–42.
3. Al-Soud, W. A., and P. Radstrom. 2001. Purification and characterization of PCR-inhibitory components in blood cells. J Clin Microbiol 39 (2): 485–93.
4. Shutler, G. G., Gagnon, P., Verret, G., Kalyn, H., Korkosh, S., Johnston, E., and Halverson, J. 1999. Removal of a PCR inhibitor and resolution of DNA STR types in mixed human-canine stains from a five year old case. J Forensic Sci 44 (3): 623–6.
5. Innis, Michael A., David H. Gelfand, John J. Sninsky, and Thomas J. White, eds. 1990. PCR protocols: A guide to methods and applications. San Diego, CA: Academic Press.
6. Bourke, M. T., C. A. Scherczinger, C. Ladd, and H. C. Lee. 1999. NaOH treatment to neutralize inhibitors of Taq polymerase. J Forensic Sci 44 (5): 1046–50.
7. Chung, D. T., J. Drabek, K. L. Opel, J. M. Butler, B. R. McCord. 2004. A study on the effects of degradation and template concentration on the amplification efficiency of the STR Miniplex primer sets. J Forensic Sci 49 (4): 733–40.

Organic Extraction

Works Cited

1. Lorente, M., C. Entrala, J. A. Lorente, J. C. Alvarez, E. Villanueva, B. Budowle. 1998. Dandruff as a potential source of DNA in forensic casework. J Forensic Sci 43 (4): 901–2.
2. Drobnic, K. 2003. Analysis of DNA evidence recovered from epithelial cells in penile swabs. Croatian Medical Journal 44 (3): 350–54.
3. Schmerer, W. M., S. Hummel, and B. Herrmann. 1999. Optimized DNA extraction to improve reproducibility of short tandem repeat genotyping with highly degraded DNA as target. Electrophoresis 20 (8): 1712–16.
4. Primorac, D., S. Andelinovic, M. Definis-Gojanovic, I. Drmic, B. Rezic, M. M. Baden, M. A. Kennedy, M. S. Schanfield, S. B. Skakel, and H. C. Lee. 1996. Identification of war victims from mass graves in Croatia, Bosnia, and Herzegovina by use of standard forensic methods and DNA testing. J Forensic Sci 41(5): 891–94.
5. Zehner, R., J. Amendt, and R. Krettek. 2004. STR typing of human DNA from fly larvae fed on decomposing bodies. J Forensic Sci 49(2): 337–40.
6. Baechtel, F. S. 1989. The extraction, purification and quantification of DNA. In Proceedings of the International Symposium on the Forensic Aspects of DNA Analysis, 25–28. Washington, D.C.: U.S. Government Printing Office.
7. Comey, C. T. 1994. DNA extraction strategies for amplified fragment length polymorphism analysis. J Forensic Sci 39 (5): 1254–69.
8. Yoshida, K., K. Sekiguchi, N. Mizuno, K. Kasai, I. Sakai, H. Sato, and S. Seta. 1995. The modified method of two-step differential extraction of sperm and vaginal epithelial cell DNA from vaginal fluid mixed with semen. Forensic Sci Int 72(1): 25–33.

Online Links

• Differex™ System web page
  http://www.promega.com/catalog/catalogproducts.asp?catalog_name= Promega_Products&category_name=Differex+System&cookie_test=1
• Millipore Corporation Website
  UltraClean™ page on MO BIO's website
  http://www.mobio.com/products/categorylist.php?cat_id=5

Chelex 100 Extraction

Works Cited

1. Walsh, P. S., D. A. Metzger, and R. Higuchi. 1991. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 10 (4): 506–13.     
2. Suenaga, E., and H. Nakamura. 2005. Evaluation of three methods for effective extraction of DNA from human hair. J Chromatography Biology Analyt Technol Biomed Life Sci 820 (1): 137–41.
3. Vandenberg N., R. A. van Oorschot, and R. J. Mitchell. 1997. An evaluation of selected DNA extraction strategies for short tandem repeat typing. Electrophoresis 18 (9): 1624–6.
4. Tsuchimochi, T., M. Iwasa, Y. Maeno, H. Koyama, H. Inoue, I. Isobe, R. Matoba, M. Yokoi, and M. Nagao. 2002. Chelating resin-based extraction of DNA from dental pulp and sex determination from incinerated teeth with Y-chromosomal alphoid repeat and short tandem repeats. Am J Forensic Med Pathol 23 (3): 268–71.
5. Sweet, D., M. Lorente, A. Valenzuela, J. A. Lorente, and J. C. Alvarez. 1996. Increasing DNA extraction yield from saliva stains with a modified Chelex method. Forensic Sci Int 83 (3): 167–77.
6. Greenspoon, S. A., M. A. Scarpetta, M. L. Drayton, and S. A. Turek. 1998. QIAamp spin columns as a method of DNA isolation for forensic casework. J Forensic Sci 43 (5): 1024–30.
7. Hoff-Olsen, P., B. Mevag, E. Staalstrom, B. Hovde, T. Egeland, and B. Olaisen B. 1999. Extraction of DNA from decomposed human tissue: An evaluation of five extraction methods for short tandem repeat typing. Forensic Sci Int 105 (3): 171–83.
8. Comey, C. T. 1994. DNA extraction strategies for amplified fragment length polymorphism analysis. J Forensic Sci 39 (5): 1254–69.
9. Yoshida, K., K. Sekiguchi, N. Mizuno, K. Kasai, I. Sakai, H. Sato, and S. Seta. 1995. The modified method of two-step differential extraction of sperm and vaginal epithelial cell DNA from vaginal fluid mixed with semen. Forensic Sci Int 72 (1): 25–33.

Online Links

• Bio-Rad
  http://www.bio-rad.com

Other Extraction Techniques

Works Cited

1. Corning Life Sciences. 2006. Product catalog entry, Costar® Spin-X® centrifuge tube insert without membrane, nonsterile, 1000/case (item #9301).
2. Millipore Corporation. 2006. Product catalog entry, Microcon® centrifugal filter units. http://www.millipore.com/catalogue.nsf/docs/C3034
3. Horsman, K. M., S. L. Barker, J. P. Ferrance, K. A. Forrest, K. A. Koen, and J. P. Landers. 2005. Separation of sperm and epithelial cells in a microfabricated device: Potential application to forensic analysis of sexual assault evidence. Analytical Chemistry 77 (3): 742–49.
4. Greenspoon, S. A., M. A. Scarpetta, M. L. Drayton, and S. A. Turek. 1998 . QIAamp spin columns as a method of DNA isolation for forensic casework. J Forensic Sci 43 (5): 1024–30.
5. Sinclair, K., and V. M. McKechnie. 2000. DNA extraction from stamps and envelope flaps using QIAamp and QIAshredder. J Forensic Sci 45 (1): 229–30.
6. Vandenberg, N., and R. A. van Oorschot. 2002. Extraction of human nuclear DNA from feces samples using the QIAamp DNA Stool Mini Kit. J Forensic Sci 47 (5): 993–95.
7. Greenspoon, S. A., J. D. Ban, K. Sykes, E. J. Ballard, S. S. Edler, M. Baisden, and B. L. Covington. 2004. Application of the BioMek 2000 Laboratory Automation Workstation and the DNA IQ System to the extraction of forensic casework samples. J Forensic Sci 49 (1): 29–39.
8. Nagy, M., P. Otremba, C. Kruger, S. Bergner-Greiner, P. Anders, B. Henske, M. Prinz, and L. Roewer. 2005. Optimization and validation of a fully automated silica-coated magnetic beads purification technology in forensics. Forensic Sci Int 152 (1): 13–22.
9. Salvadore, J. M., and M. C. De Ungria. 2003. Isolation of DNA from saliva of betel quid chewers using treated cards. J Forensic Sci 48 (4): 794–97.
10. Thacker C., C. P. Phillips, and D. Syndercombe-Court. 2000. Use of FTA cards in small volume PCR reactions. Progress in Forensic Genetics 8 (1999): 473–75.

Online Links

• Filter Paper Cards on Whatman's website
  http://www.whatman.com/products/?pageID=7.31
• UltraClean™ page on MO BIO's website
  http://www.mobio.com/products/categorylist.php?cat_id=5

Quantitation

Works Cited

1. Baechtel, F. S. 1989. The extraction, purification and quantification of DNA. In Proceedings of the International Symposium on the Forensic Aspects of DNA Analysis, 25–28. Washington, D.C.: U.S. Government Printing Office.
2. Turner BioSystems. YEAR? Fluorescence theory. In An introduction to fluorescence measurements. (accessed August 31, 2006).
3. Turner BioSystems. A TD-700 Laboratory Fluorometer Method for PicoGreenR" Turner Designs. Luminometers and Fluorometers
4. "QuantiBlotTM. A DNA Quantitation Method" Perkin Elmer, April 1996. 7-15
5. Walsh, P. S., J. Varlaro, and R. Reynolds. 1992. A rapid chemiluminescent method for quantitation of human DNA. Nucleic Acids Res 20 (19): 5061-65.
6. Promega Corporation. 2006. Technical Bulletin, AluQuant® Human DNA Quantitation System, instructions for use of products DC1010 and DC1011, part #TB291. (accessed August 31, 2006)
7. Edwards, Kirstin, Julie Logan, and Nick Saunders, eds. 2004. Real-time PCR: An essential guide, 4–5. Wymondham, Norfolk, U.K.: Horizon Bioscience.
8. Edwards, Kirstin, Julie Logan, and Nick Saunders, eds. 2004. Real-time PCR: An essential guide, 18–22. Wymondham, Norfolk, U.K.: Horizon Bioscience.
9. Edwards, Kirstin, Julie Logan, and Nick Saunders, eds. 2004. Real-time PCR: An essential guide, 45–46. Wymondham, Norfolk, U.K.: Horizon Bioscience.
10. Timken, Mark D., Katie L. Swango, Cristián Orrego, Mavis Date Chong, and Martin R. Buoncristiani. 2005. Quantitation of DNA for forensic DNA typing by qPCR (quantitative PCR): Singleplex and multiplex modes for nuclear and mitochondrial genomes, and the Y chromosome. Final report for U.S. Department of Justice grant no. 2002-IJ-CX-K008.
11. Department of Biology, Davidson College. 2001. Real-time PCR method. Genomics course materials http://www.bio.davidson.edu/courses/ genomics/method/realtimepcr.html (accessed August 31, 2006).
12. Edwards, Kirstin, Julie Logan, and Nick Saunders, eds. 2004. Real-time PCR: An essential guide, 51–52. Wymondham, Norfolk, U.K.: Horizon Bioscience.
13. Applied Biosystems. 2003. QuantifilerTM Human DNA Quantification Kit and QuantifilerTM Y Human DNA Quantification Kit User's Manual, rev. B.
14. Butler, John M. 2005. Forensic DNA typing: Biology, technology, and genetics of STR markers. 2nd ed, 77–78. Burlington, MA: Elsevier Academic Press.

Online Links

• Abstract for AluQuant^® Human DNA Quantitation System
  http://www.promega.com/applications/hmnid/productprofiles/aluquant/Default.htm
• FRET at Wikipedia
  http://en.wikipedia.org/wiki/Fluorescence_resonance_energy_transfer