BME100 s2014:T Group16 L5

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Lab Write-Up 1 | Lab Write-Up 2 | Lab Write-Up 3
Lab Write-Up 4 | Lab Write-Up 5 | Lab Write-Up 6
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OUR TEAM

Name: Angie Chan
Name: Jossel Nkunzi
Name: Ryan Hess
Name: Alireza Momeni
File:JosephSidman.jpg
Name: Jospeh Sidman


LAB 5 WRITE-UP

Background Information

SYBR Green Dye
SYBR Green Dye is a small molecular dye that fluoresces very well in the presnce of dsDNA but fluoresces very weakly in water or with single strands of DNA.


Single-Drop Fluorimeter
It's a light mounted on top of a box cantaining a battery. The light contraption has a slot for a slide. The slide holds the drop and can be adjusted to have the beam of fluorescent light shone through it. Group16a.jpg


How the Fluorescence Technique Works
The SYBR Green 1 compound glows green in the presence of fluorescent light when mixed with DNA. A picture can be taken of the drop with the DNA and SYBR Green 1 compound in the fluorescent light and analyzed in Image J to find the relative concentration of DNA.



Procedure

Smart Phone Camera Settings
[Instructions: The type of smart phone you used and how you adjusted the camera settings, if applicable (see worksheet page 4).]

  • Type of Smartphone:Samsung Galaxy S4
    • Flash: OFF
    • ISO setting: 800
    • White Balance: AUTO
    • Exposure: 2.0+
    • Saturation: N/A
    • Contrast: N/A


Calibration

The provided rack and an eraser was used to keep the phone in place. It is placed about 14cm from the fluorimeter which was raised by the height of two calculators to align the drop with the camera on the phone.

  • Distance between the smart phone cradle and drop = 14 cm


Solutions Used for Calibration

Initial Concentration of 2x Calf Thymus DNA solution Volume of the 2x DNA solution Volume of the SYBR GREEN 1 Dye solution Final DNA concentration in SYBR Green 1 solution
5 80 80 2.5
2 80 80 1
1 80 80 0.5


Placing Samples onto the Fluorimeter

STEP 1: Set your micropipette to 80 microliters STEP 2: Add 80 microliters of SYBR Green 1 (with the concentration of 5 micrograms per microliters) with the micropipette onto the first middle two circles on the slide on the fluorimeter device. STEP 3: The drop should align to the smartphone camera and the led light. After setting the smartphone to the correct settings, use the timer and capture the picture. As the timer starts, place the box down and wait for it to capture the picture. STEP 4: Remove the box and the drop on the fluorimeter device. STEP 5: Save the picture into the computer (via email, Dropbox, etc.) and use Image J to find the RAWINTENDEN value. STEP 6: With Image J, draw an ellipse around the green version of the image. Measure the RAWINTDEN value. STEP 7: Repeat 1-7



Data Analysis

Representative Images of Samples

WITH DNA

Group16glow.jpg


WITHOUT DNA

Group16noglow.jpg


Image J Values for All Samples

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.]



Fitting a Straight Line

GRAPHgroup16.jpg