BME100 f2013:W1200 Group1 L5

BME 100 Fall 2013	Home People Lab Write-Up 1 | Lab Write-Up 2 | Lab Write-Up 3 Lab Write-Up 4 | Lab Write-Up 5 | Lab Write-Up 6 Course Logistics For Instructors Photos Wiki Editing Help
OUR TEAM Name: Chloe Kwon Name: Jeff Miles Name: Casey Weinstein Name: Nima Afzalian Name: Mario Gonzalez LAB 5 WRITE UP Background Information SYBR Green Dye SYBR Green Dye is a small molecular dye that does not fluoresce well in water or with single strands of DNA, but fluoresces very well with dsDNA. It is combined with the DNA solution in order to detect fluorescence. Single-Drop Fluorimeter The single-drop fluorimeter detects fluorescence within the drop of DNA solution. It measures the wavelength distribution and intensity when light passes through the DNA solution. Add a PHOTO for bonus points How the Fluorescence Technique Works The fluorescence technique works by combining a fluorescent SYBR green dye with the DNA solution. When the blue light beam from the single-drop fluorimeter, the drop will turn a fluorescent green color indicating the presence of DNA. The droplet's color will be detected by the smartphone and the picture will then be analyzed using the ImageJ software. Procedure Smart Phone Camera Settings Type of Smartphone: HTC One Flash: on ISO setting: 800 White Balance: Auto Exposure: Neurtral Saturation: Neutral Contrast: Lowest Setting Calibration 1. Switch the blue light on on the fluorimeter. 2. Adjust camera settings on smart phone to match the above settings. 3. Place smart phone in cradle so that it is perpendicular to the table and the camera lens is level with the glass slide and the drop. 4. Place cradle and phone as close as possible to the drop so that the drop remains in sharp focus. 5. Use the provided ruler to measure the distance between the drop and the camera lens. In our case, this distance was 8.5 cm. Distance between the smart phone cradle and drop = 8.5 cm Solutions Used for Calibration Calf Thymus DNA solution concentration (microg/mL) Volume of the 2x DNA solution (µL) Volume of the SYBR Green I Dye solution (µL) Final DNA concentration in SYBR Green I Assay (ng/mL) 5 80 80 2.5 2 80 80 1 1 80 80 0.5 0.5 80 80 0.25 0.25 80 80 0.125 0 80 80 blank Placing Samples onto the Fluorimeter 1. Insert the slide into the fluorimeter, smooth side down. 2. Use the micropipette to place 80µL of the SYBR green dye in the second row of the middle column of the slide. 3. Micropipette 80µL of the specific calf thymus DNA on top of the SYBR green dye. 4. Ensure that the light is turned on. Then start self timer on phone and place light box over entire set up. Data Analysis Representative Images of Samples No DNA With DNA Image J Values for All Samples [Instructions: See worksheet page 8. To save time on typing a new Wiki table from scratch, use THIS TOOL to auto-generate a Wiki table: Excel-to-Wiki Converter. Copy the headers and values from the Excel spreadsheet you made, paste them into the form field, click submit, copy the Wiki code that the tool generated, and replace TABLE GOES HERE (below) with your auto-generated code.] info info info info! x x x x x x x x x x x x x x x x x x x x x x x x Fitting a Straight Line [Instructions: Place an IMAGE of your Excel plot with a line of best fit here. See worksheet page 9]