Presentation on theme: "Gel electrophoresis The gel electrophoresis method was developed in the late 1960's. It is a fundamental tool for DNA sequencing."— Presentation transcript:
1Gel electrophoresisThe gel electrophoresis method was developed in the late 1960's. It is a fundamental tool for DNA sequencing.
2+ - How fast will the DNA migrate? strength of the electrical field, buffer, density of agarose gel…Size of the DNA!*Small DNA move faster than large DNA…gel electrophoresis separates DNA according to sizeDNA+-PowersmalllargeWithin an agarose gel, linear DNA migrate inversely proportional to the log10 of their molecular weight.
3Vertical Gel Electrophoresis for Fish Remove combwellsGelFill chamber with bufferBreak off
4I.A. Calculate the Rf OF PROTEINS 1. Calculate the Rf value for each proteinband in the protein standard.Rf = migration distance of protein (origin to band)migration distance of dye front (origin to dye front)Figure 2. Formula for calculating the retardation factor (Rf) of a protein in SDS-PAGE.
6I.A. Rf OF PROTEINS2. Plot the molecular weights of your standard proteins (vertical axis) versus the Rf values (horizontal axis) on semi-log graph paper.
73. Draw a best-fit straight line through all your points. I.A. Rf OF PROTEINS3. Draw a best-fit straight line through allyour points.Molecular wts.Rf value
8I.A. Rf OF PROTEINS4. For each lane of fish protein extract, pick a single protein band and circle it on the graphic image that you will download from the class Laulima site. For each of these bands, determine its molecular weight using this standard curve.
9I.B. PROTEIN FINGERPRINTING Hypothesize Evolution Relationships Among the Fish Species AnalyzedI.B. PROTEIN FINGERPRINTINGAttempt to construct an evolutionary tree illustrating these relationships.
10Loading the Gel1. Lay out a small piece of Parafilm on a flat countertop.2. Place a 1 μL drop of SYBR Gold dye (labeled "SG"; stains the DNA with a fluorescent dye) on the Parafilm.3. Next to this drop, place a 1.7 μL drop of sample buffer (labeled "SB").4. Next to these drops, place a 2.3 μL drop of sterile water.5. Next to these drops place a 5 μL drop of your DNA sample and mix, using your pipetter all four drops together.6. Take up the entire mixture (10 μL) into a pipetter and carefully transfer to one of the wells in the agarose gel. Be sure tonote which well your sample was applied to in your laboratory notebook.Ladder:
11Loading the Gel7. Repeat these steps (1-6) with your PCR product, loading a different lane in the agarose gel.8. The instructor will load a DNA ladder (allows molecular weight estimation of your DNA sample).9. Once all of the wells are loaded, we will run the gel at 100 volts for about one hour.10. After one hour has elapsed, we will visualize the gel under UV light.11. Examine the gel image and identify which lanes contains your original DNA extract and your PCR product. Comparing the migration of your product to the DNA ladder, estimate the molecular weight of this product.
12Cathode(negative)Anode(positive)DNAbuffer Add enough electrophoresis buffer to cover the gel to a depth of at least 1 mm. Make sure each well is filled with buffer.
13Sample PreparationMix the samples of DNA with the 6X sample loading buffer (w/ tracking dye). This allows the samples to be seen when loading onto the gel, and increases the density of the samples, causing them to sink into the gel wells.6X Loading Buffer: SYBR Gold Dye (for color)Sample Buffer (SB)
14Loading the GelCarefully place the pipette tip over a well and gently expel the sample. The sample should sink into the well. Be careful not to puncture the gel with the pipette tip.
15Running the Gel (red +) (black -) Place the cover on the electrophoresis chamber, connecting the electrical leads. Connect the electrical leads to the power supply. Be sure the leads are attached correctly - DNA migrates toward the anode (red). When the power is turned on, bubbles should form on the electrodes in the electrophoresis chamber.
17Cathode(-) wellsDNA(-) Bromophenol BlueGelAnode(+)After the current is applied, make sure the Gel is running in the correct direction. Bromophenol blue will run in the same direction as the DNA.
18II.B. DNA QuantitationNanodrop spectrometer used to measure DNA concentrations
19Nanodrop spectrometer Clean with 1 μl nanopure waterClose, openWipe with kimwipe.Blank1 μl mastermixPress blank buttonClean with kimwipeMEASURE click leftBlank should read 0Sample1 μl DNA sampleREADINGSConcentrationAbsorbance260 nm280 nmPurityGood purity if below 2 and above 1.8