BME100 s2014:T Group15 L5: Difference between revisions
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'''SYBR Green Dye'''<br> | '''SYBR Green Dye'''<br> | ||
SYBR Green Dye is a molecular dye that fluoresces very well with dsDNA and weakly with water or single stranded DNA. When it binds to the DNA (preferably double-stranded though single stranded will still work) this dye absorbs blue light and emits green light. It is used to quantify and visualize double stranded DNA. | SYBR Green Dye is a molecular dye that fluoresces very well with dsDNA and weakly with water or single stranded DNA. When it binds to the DNA (preferably double-stranded though single stranded will still work) this dye absorbs blue light and emits green light. It is used to quantify and visualize double stranded DNA. When SYBR Green Dye is used with water there is no fluorescence. The more dsDNA the more the SYBR Green Dye emits the light. | ||
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'''How the Fluorescence Technique Works'''<br> | '''How the Fluorescence Technique Works'''<br> | ||
The fluorescence technique works by having the dsDNA give a visual color signal for when it is present and having the fluorimeter capture a picture of the fluorescence that was produced. | The fluorescence technique works by having the dsDNA give a visual color signal for when it is present and having the fluorimeter capture a picture of the fluorescence that was produced. The concentration of DNA can be measured through this technique. | ||
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'''Smart Phone Camera Settings'''<br> | '''Smart Phone Camera Settings'''<br> | ||
* Type of Smartphone: Galaxy S3 | * Type of Smartphone: Galaxy S3 | ||
** Flash:Inactivated | ** Flash: Inactivated | ||
** ISO setting:800 | ** ISO setting: 800 | ||
** White Balance: Auto | ** White Balance: Auto | ||
** Exposure:Highest Setting | ** Exposure: Highest Setting | ||
** Saturation:Highest Setting | ** Saturation: Highest Setting | ||
** Contrast:Lowest Setting | ** Contrast: Lowest Setting | ||
'''Calibration'''<br> | '''Calibration'''<br> | ||
We Placed our smart phone on the cradle at a right angle from the slide. We then adjusted the height of the fluorimeter using the plastic trays so that our camera was able to take a picture of the sample drop sideways. | We Placed our smart phone on the cradle at a right angle from the slide. We then adjusted the height of the fluorimeter using the plastic trays so that our camera was able to take a picture of the sample drop sideways. | ||
* Distance between the smart phone cradle and drop =7.0cm | * Distance between the smart phone cradle and drop =7.0cm | ||
'''Solutions Used for Calibration' | |||
'''Solutions Used for Calibration''' | |||
{| {{table}} width=700 | {| {{table}} width=700 | ||
|- | |||
|- | |- | ||
| | |Initial Concentration of 2X Calf Thymus DNA solution (micrograms/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 | |||
|- | |- | ||
| | |} | ||
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# Turn on fluorimeter. | # Turn on fluorimeter. | ||
# Place a slide in the fluorimeter with the smooth side facing down. | # Place a slide in the fluorimeter with the smooth side facing down. | ||
# Set camera timer for | # Set camera timer for 5 seconds. Calibrate the photo options and lay the smartphone on cradle with camera app on. | ||
# Adjust height of fluorimeter | # Adjust height of fluorimeter to get a camera view of the slide nearly edge-on by placing on top of a stable, supporting lid. | ||
# Place 80 uL drop of SYBR Green I solution on first 2 clear circles in middle of slide. | # Place 80 uL drop of SYBR Green I solution on first 2 clear circles in middle of slide. | ||
# | # Changing tips, place 80 uL drop of sample/calibration solution on top of the SYBR GREEN I drop. | ||
# | # Adjust the slide so that the light illuminates the center of the drop and the drop focuses the light on the other side. | ||
# | # Adjust distance between smartphone and fluorimeter to 7cm away (>4cm). | ||
# | # Cover with light box but keep one flap up. | ||
# | # Make sure drop is focused one more time. | ||
# | # Depress the timer button on the camera to take the picture and lower the flap before picture is taken. | ||
# | # Remove the 160 uL drop using same tip from slide and discard liquid, as well as micropipetter tip, in waste liquid container. | ||
# | # Move the slide in the next position (center of next two circles). Once you have used all 5 possible measurement positions on the slide, switch slides. | ||
# Repeat steps 1-14 until all 8 samples have been photographed accordingly. | |||
<br> | <br> | ||
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'''Representative Images of Samples''' | '''Representative Images of Samples''' | ||
The following images show two samples in he fluorometer. The first pictures shows the negative control, the one with no DNA. The second pictures shows the positive control, the one with DNA. | |||
[[Image:dna pictures.jpg|550px]] | |||
Latest revision as of 08:36, 17 April 2014
BME 100 Spring 2014 | 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
LAB 5 WRITE-UPBackground InformationSYBR Green Dye
ProcedureSmart Phone Camera Settings
Calibration We Placed our smart phone on the cradle at a right angle from the slide. We then adjusted the height of the fluorimeter using the plastic trays so that our camera was able to take a picture of the sample drop sideways.
Solutions Used for Calibration
'Placing Samples onto the Fluorimeter.
Data AnalysisRepresentative Images of Samples The following images show two samples in he fluorometer. The first pictures shows the negative control, the one with no DNA. The second pictures shows the positive control, the one with DNA.
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 concentrations of calf thymus DNA) to convert INTDEN values into DNA concentration. Your positive control and negative control samples should be used as threshold values for determining whether an unknown (patient) sample is truly positive or negative.
Your negative control PCR result was 3.18 μg/mL
Patient 90616 : The average corrected concentration of this patients DNA is 5.06 μg/mL. The following image shows an example of the patient's PCR sample in fluorometer. Patient 91514 : The average corrected concentration of this patients DNA is 3.97 μg/mL. The following image shows an example of the patient's PCR sample in fluorometer.
Patient 90616 : This patient's results are less than the positive control, 16.15 μg/mL less, but they are higher than the negative control by 1.88 μg/mL. This patient is much closer to the negative control results therefore this patient has a negative test result. Patient 91514 : This patient's results are less than the positive control by 17.24 μg/mL but higher than the negative control by 0.79 μg/mL. This patient is drastically closer to the negative control therefore this patient has a negative test result.
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