OUR TEAM
LAB 5 WRITE-UP
Background Information
SYBR Green Dye
The SYBR green dye has the ability to fluorescence when there is a presence of double-stranded DNA (dsDNA). According to Life Technologies, SYBR dyes are one of the best high-sensitivity reagents for staining DNA and RNA. The green dye binds to the DNA, causing the DNA to absorb blue light and reflect green light.
Single-Drop Fluorimeter
[Instructions: A description of the single-drop fluorimeter device. Add a PHOTO for bonus points]
A single-drop fluorimeter device detects PCR-amplified DNA molecules based on the amount of flourescent material in the sample. A blue LED light is shined upon the sample; a camera can then capture green light flourescened by the DNA.
How the Fluorescence Technique Works
The fluorescence technique works by adding DNA and SYBR Green 1 dye to see how much fluorescence shines through with the picture. The higher the concentration the more fluorescence that should be visual when looking at the light shining through the drop. This happens because of the blue LED light, which shines onto the sample and excites the dye, causing it to fluorescence green light. The sample congregates at the glass spots on the slide because the rest of the slide is coated in a highly hydrophobic material.
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: iPhone 5
- Flash: off
- ISO setting: auto (could not find option on model used)
- White Balance: auto (could not find option on model used)
- Exposure: auto (could not find option on model used)
- Saturation: auto (could not find option on model used)
- Contrast: auto (could not find option on model used)
Calibration
[Instructions: Describe how to set up your camera in front of the fluorimeter. Add a PHOTO of this set-up for bonus points.]
The phone was placed in the cradle at an appropriate angle to view the slide from the side. The fluorimeter was raised in front of the phone to get the right angle. A light box was placed over the set up to provide darkness to take the picture of the light flowing through the DNA and SYBR Green 1. The fluorescence in the sample was easily seen with higher concentrations of SYBR Green 1.
- Distance between the smart phone cradle and drop = 7.5 cm
[Instructions: See worksheet page 6.]
Solutions Used for Calibration [Instructions: See worksheet page 6.]
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
- [Instructions: Step one, in your OWN words]
- [Instructions: Step two, in your own words]
- [Instructions: Step three, in your own words]
- [Instructions: Step etc., in your own words]
Data Analysis
Representative Images of Samples
[Instructions: Show an IMAGE where you drew a circle around the droplet with the freehand tool for a sample with no DNA]
2.5 DNA Concentration Image J Analysis
Image J Values for All Samples
Calf Thymus DNA Concentration (FINAL), μg/mL
|
'
|
AREA
|
Mean Pixel Value
|
RAWINTDEN OF THE DROP
|
RAWINTDEN OF THE BACKGROUND
|
2.5 |
image 1 |
17828 |
17.006 |
303179 |
39188
|
2.5 |
image 2 |
20135 |
41.771 |
841061 |
40835
|
2.5 |
image 3 |
19078 |
45.546 |
868928 |
43759
|
1 |
image 1 |
20575 |
20.664 |
425158 |
40548
|
1 |
image 2 |
22096 |
19.014 |
420125 |
49107
|
1 |
image 3 |
21896 |
18.092 |
396148 |
46448
|
0.5 |
image 1 |
20792 |
29.294 |
609079 |
42845
|
0.5 |
image 2 |
21090 |
29.49 |
621944 |
44877
|
0.5 |
image 3 |
22716 |
29.888 |
678927 |
46969
|
0.25 |
image 1 |
18271 |
26.316 |
480825 |
35867
|
0.25 |
image 2 |
17540 |
23.916 |
419479 |
33950
|
0.25 |
image 3 |
17392 |
23.244 |
404253 |
34440
|
0.125 |
image 1 |
21953 |
13.737 |
301576 |
44788
|
0.125 |
image 2 |
18710 |
9.657 |
180684 |
41616
|
0.125 |
image 3 |
21953 |
12.31 |
270236 |
47888
|
0 |
image 1 |
18376 |
12.349 |
226917 |
40649
|
0 |
image 2 |
20532 |
10.045 |
206243 |
37931
|
0 |
image 3 |
17009 |
11.212 |
190697 |
36581
|
Fitting a Straight Line
[Instructions: Place an IMAGE of your Excel plot with a line of best fit here. See worksheet page 9]
|