SYBR Green I is a fluorescent dye used for binding double-stranded DNA so that quantification and visualization is possible. SYBR Green is a synthetic, asymmetrical cyanine dye that was designed to work throughout a wide range of temperatures, bind in a way that does not interfere with enzymes such as DNA polymerases and nucleases, and accurately quantify DNA in varying concentrations. Real time PCR is the most common use for the dye, where the fluorescence increases as each PCR cycle amplifies the DNA so you can visually observe amplification.
Single-Drop Fluorimeter
The Single-Drop Fluorimeter is a device designed to help detect any presence of double stranded DNA in a liquid sample by measuring its fluorescence. It is essentially a small plastic device with a space on top for a multi-welled slide. The slide is illuminated by a single blue LED light which is turned on by a switch located on the right hand side of the Fluorimeter. The slide of the fluorometer is positioned so that the blue LED can iluminate any drop placed over a designated well.
The front top portion of the fluorimeter is shown. Illuminated droplet can be seen.
How the Fluorescence Technique Works
The fluorescence technique works by adding a fluorescent die to a liquid with an unknown percentage of double stranded DNA. The slides used in this analysis have a hydrophobic Teflon film on one side of the slide, designed to hold each sample in place. The film contains breaks which act as wells where liquids can be held in precise quantities. These breaks also keep each of the drops apart from one another so that the samples do not mix. All these traits make it easier to observe and analyze our samples when using the LED. When the samples are placed in the LED's range, any DNA stands at the top of the drop sized sample can be seen because the light causes them to fluoresce.
Procedure
Smart Phone Camera Settings
Type of Smartphone: Nokia Lumia 928
Flash: Off
ISO setting: 3200
White Balance: Auto
Exposure: 2
Saturation: N/A
Contrast: N/A
Calibration
The camera was placed in a cradle that kept it upright and facing the fluorimeter from a side angle nearly edge-on. It was kept at a distance of 13 centimeters from cradle to the drop, which was chosen to keep the drop in focus for the camera and remained constant throughout the experiment. An eraser was placed in the cradle with the phone in order to keep it snug against the side and in a consistent position. It was also necessary for the fluorimeter to be raised to a height that was suitable for the height of the camera so it was placed on top of a calculator.
Distance between the smart phone cradle and drop = 13 centimeters
Solutions Used for Calibration
Initial Concentration of 2X Calf Thymus DNA Solution (μg/mL
Volume of the 2X DNA solution (μL)
Volume of the SYBR Green I Dye solution (μL)
Final DNA concentration in SYBR Green I solution (μg/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
0
Placing Samples onto the Fluorimeter
Place the slide, smooth side down, in the fluorimeter (make sure it's on).
Check the height of the flourimeter and camera position.
Pipet 80μL drop of the SYBR Green I solution between the first two clear circles in the middle of the slide.
Pipet 80μL drop of the sample solution on top of the SYBR Green I drop.
Move the slide so that the fluorimeter's light illuminates the center of the drop and focuses light on the other side.
Place the lightbox over the setup with the flap still open and check the camera focus again.
Take picture with the camera using a set timer with the lightbox flap down.
Check the picture.
Pipet the drop off of the slide and into the liquid waste container.
Move the slide to the next set of clear circles in preparation for the next drop.
Repeat steps until all slide positions have been used and then replace the slide with a new one.
Data Analysis
Representative Images of Samples
Sample with DNA (Positive Control)
Sample with no DNA (Negative Control)
Image J Values for All Samples
Set
Area
Mean
IntDen drop
Intden/area
'
'
'
'
'
'
'
'
'
'
'
5
40443
8708426
215.3259155
1
26700
3603137
134.9489513
0.25
31888
3904086
122.4311967
Area 1
2
3
Intden 1
2
3
avg intden
intden/area 1
2
3
avg
PCR Product concentration
Corrected Concentration
control "+"
24164
33340
32796
5935034
5733849
6214941
5961274.667
245.6147161
171.9810738
189.5030187
202.3662695
4.353497315
52.24196778
control "-"
27960
28148
26952
2634292
4594063
2243889
3157414.667
94.21645207
163.2109919
83.2550089
113.5608176
-0.146398904
-1.75678685
A1
43012
30232
20364
8556840
5916286
4822294
6431806.667
198.9407607
195.6961498
236.8048517
210.4805874
4.76466113
57.17593356
A2
31908
44900
30804
6063436
7480390
5670458
6404761.333
190.0287075
166.6011136
184.0818725
180.2372312
3.232188052
38.78625662
A3
33908
38724
31868
5571646
7873538
6476711
6640631.667
164.3165625
203.3245016
203.2355655
190.2922098
3.741687856
44.90025427
B1
22064
20108
31680
1701487
1883730
3583667
2389628
77.11598078
93.68062463
113.1208018
94.63913573
-1.105186941
-13.26224329
B2
30332
22200
19016
2329264
2527096
1937352
2264570.667
76.79229856
113.8331532
101.880101
97.50185089
-0.960129167
-11.52155
B3
27608
20360
23712
3234192
2178949
4335590
3249577
117.1469139
107.0210707
182.8437078
135.6705642
0.973932818
11.68719382
Patient A
3.912845679
46.95414815
Patient B
-0.36379443
-4.365533157
Fitting a Straight Line
PCR Results Summary
Instructor's summary: You completed 8 PCR reactions in a previous lab. You used the SYBR Green I staining and imaging technique to measure the amount of amplified DNA in each PCR reaction. You used a standard curve (based on known concentration of calf thymus DNA) to convert INTDEN values into DNA concentration. Your positive control and negative control samples are used to determine the threshold values for determining whether an unknown (patient) sample is truly positive or negative.
Your positive control PCR result was 4.35 μg/mL
Your negative control PCR result was -0.146 μg/mL
and a quantitative description (μg/mL) of what you observed
Patient 10072: When DNA from this patient was combined with the SYBR green dye and viewed in the fluorimeter, it produced an average Intdens reading of 3.91 μg/mL
Patient 83576 : When DNA from this patient was combined with the SYBR green dye and viewed in the fluorimeter, it produced an average Intdens reading of -0.364 μg/mL
Compare each patient's results to the positive control value and the negative control value. Draw a final conclusion for each patient (positive or negative) and explain why you made that conclusion.
Patient 10072 : Each of the samples from this patient very closely resembled the positive control. All drops glowed bright fluorescent green in the fluorimeter. This patient appears to have tested positively for the gene of interest because the SYBR green dye was able to attach to double-stranded DNA molecules and fluoresce. Since the dye was able to do this, the PCR reactions must have produced many copies of the target strand of DNA, meaning it was present in the samples from this patient.
Patient 83576 : Each of the samples from this patient very closely resembled the negative control. None of the drops glowed or fluoresced when viewed in the fluorimeter. This patient appears to have tested negatively for the gene of interest because the SYBR green dye did not bind to any double-stranded DNA molecules to fluoresce. Since no double-stranded DNA molecules were produced in the PCR reaction, the patient did not have the target sequence of DNA.