The Optical Waveguide

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The Optical Waveguide
Picture by David Wulfman
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Fabricating the Optical WaveguideCombining Gel
Electrophoresis and a Planar Waveguide

• Matt Trusheim
• Breck School
• 2005

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Goal

• To design an Optical Waveguide (OWG) that
  combines gel electrophoresis and a planar
  waveguide.

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Introduction

• Genetic Testing
• Many medical applications
• Expensive
• Requires expertise
• Telemedicine
• Most laboratories send samples to a diagnostic
  laboratory for analysis
• Telemedicine allows for on-site testing
• Digital results can be sent through the Internet

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Introduction

• Gel Electrophoresis
• Common genetic testing methodology
• Expensive for multiple tests
• Steps in gel electrophoresis
• Fragmentation through PCR
• Loading the DNA sample
• Separation by size
• Marking of DNA with fluorescent markers
• Imaging the fluorescent markers

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Introduction

• Planar Waveguide (PWG)
• Initial design by Wulfman
• Efficient fluorescence detector
• Total internal reflection
• Designed for DNA microarrays
• Unproven genetic testing method
• Slide configuration
• Digital output

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Results

• Gel Configuration
• Tube vs. Slide
• Tube easier to cast
• Slide requires no adaptation
• Type of gel
• Agarose vs. Polyacrylamide
• Agarose is natural, inexpensive, nontoxic
• Polyacrylamide is less viscous, offers better
  resolution

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Results

• Dye Type
• Intercalating Dye vs. Fluorescent Primer
• Intercalating dyes are bright, but toxic and
  retard migration of the DNA fragment
• Primers cause no mobility problems and are
  simpler to use
• Added in PCR stage

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Results

• Staining Technique
• Premixing of DNA and dye
• Easiest to do
• Causes mobility problems
• Post-staining
• No mobility problems
• Impractical in tubes
• Premixing of gel and dye
• Causes slight mobility problems
• Loading Technique
• Flat vs. Shark Tooth

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Results

• Voltage
• Trials conducted at 280,240,200 v
• TBE buffer boiled at all voltages
• Run Time
• Dependent on voltage
• DNADye ratio
• 11000 ratio produced some results

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Modifications
PhotoMultiplier Tube (PMT)
Light Shutter Modified
Sample Bearing Glass Slide Changed to tube
Light Tight Chamber
Connector
Slide Mount
Light Source Shuttle Attached to Linear Variable
Displacement Transducer (LVDT)
Light Source Lens
Image used with permission from D. Wulfman
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Sample Gel Run
Tube gels imaged with a Polaroid camera
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OWG Output of Gel Run
OWG output of the gel indicated by the arrow
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Conclusion

• The Optical Waveguide was a successful prototype
  platform for genetic testing

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Discussion

• Unresolved issues
• Voltage
• Run Time
• DNADye Ratio

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Significance

• Telemedicine
• Inexpensive
• Easy to use
• Digital Output

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Acknowledgements

• David Wulfman
• Ron McGlennen
• Lois Fruen
• Team Research

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The Optical Waveguide
Picture by David Wulfman