WET LAB DNA Barcoding: From Samples to Sequences - Northwest ...

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WET LAB Sometimes the amount of DNA in each band of the molecular weight standard is also known, so that scientists can estimate the amount of DNA in their samples. This is covered in more detail in Slide #19. c. The DNA samples are in Lanes 2–10. d. DNA gels are stained, in this case with a chemical called ethidium bromide, to visualize the DNA. e. Examples of the sizes of four molecular weight standard bands are shown: 5000 base pairs (bp), 2000 bp, 1000 bp, and 750 bp. 23. Ask students to estimate the sizes of the bands in Lane 2 (yellow arrow). The bottom band is approximately 900 bp, while the band above it is approximately 4500 bp. [Note: Lanes 2, 3, and 4 contain bands of approximately 900 and 4500 bp.] 24. Show Slide #14, which reviews the steps involved in agarose gel electrophoresis: making the gel, preparing your samples, loading your samples onto the gel, running the gel, and visualizing the gel. If your students have experience making and running agarose gels, you may wish to skip to Step #33. If your students do not have experience making and running agarose gels, you may wish to show one or more of the tutorial videos listed above under Lab 3: Teacher Preparation. Wet Lab: Slide #14 Using Bioinformatics: Genetic Research Wells: Holes in a gel into which samples are placed or “loaded.” 25. Show Slide #15, which reviews the first step: making the agarose gel. Tell students that agarose is made from a chemical called agar that is isolated from seaweed. Agar is also used as a thickening agent, and is what gives many consumer products their characteristic texture, including many sauces, puddings, and custards. The final product is similar in consistency to Jell-O ® and, as with Jell-O ® , the agarose is melted and poured into a mold. A small comb is placed in the liquid to form the holes or wells into which the DNA will be loaded. 336 ©Northwest Association for Biomedical Research—Updated October 2012
WET LAB Wet Lab: Slide #15 26. Tell students that the size of the pores in the DNA gel (determined by the amount of agarose used) influences how quickly (or slowly) the DNA will move through the gel. Scientists usually make agarose gels with 0.8% to 2.5% agarose. Today, students will be making and running a 1% agarose gel. 27. Show Slide #16, which reviews the second step in the process of agarose gel electrophoresis: sample preparation. A small volume of the PCR product is mixed with a loading buffer – a concentrated solution containing a dye and glycerol which makes the DNA both visible (which helps you load it on the gel) and heavy enough to sink into the well of the gel. The final volume is achieved by adding a small amount of water, if needed. PCR product: The DNA copied or “amplified” during PCR. Wet Lab: Slide #16 Wet Lab – DNA Barcoding: From Samples to Sequences 337 ©Northwest Association for Biomedical Research—Updated October 2012
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Page 5 and 6: WET LAB Lab 4: Preparation of PCR S
Page 7 and 8: WET LAB • Teachers may wish to ha
Page 9 and 10: WET LAB Wet Lab: Slide #3 Lysis or
Page 11 and 12: WET LAB • If students are not fam
Page 13 and 14: WET LAB Wet Lab: Slide #9 14. Show
Page 15 and 16: WET LAB Lab 3: Analyzing PCR Result
Page 17: WET LAB 20. Show Slide #12, and rem
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Page 23 and 24: WET LAB 34. Optional Graphing Exten
Page 25 and 26: WET LAB e. Deoxynucleotides (dNTPs)
Page 27 and 28: WET LAB Glossary Agarose gel electr
Page 29 and 30: WET LAB PCR beads: Lyophilized or
Page 31 and 32: WET LAB CLASS SET Lab 1: DNA Purifi
Page 33 and 34: WET LAB CLASS SET Day 2 Procedure:
Page 35 and 36: WET LAB CLASS SET 14. Place the spi
Page 37 and 38: WET LAB CLASS SET Lab 2: Copying th
Page 39 and 40: WET LAB CLASS SET 9. Add each of th
Page 41 and 42: WET LAB CLASS SET Lab 3: Analyzing
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Page 49 and 50: WET LAB KEY Lab 1: DNA Purification
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Page 55 and 56: WET LAB RESOURCE Aliquoting DNA Bar

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