Helping Students Discover Genomics, Proteomics

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Thanks to Davidson College, NSF-REU, and Bank of
America for their generous support.
Determining the Physical Properties of DNA in DNA
Microarrays Using Optical Tweezers
Megan McDonald1,2, A. Malcolm Campbell1, Dan Boye2
05-A-3139-BPS
1Davidson College Biology Department, 2Davidson
College Physics Department
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Introduction
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DNA-Bead Coupling
Tweezer Setup
DNA microarrays measure genome activity in cells.
DNA is attached to amino-modified glass slides
through UV-induced covalent bonds, and
fluorescent DNA is used to reveal mRNA
production. To date, no one understands the
physical properties of DNA attached to glass,
which would certainly affect the outcome of the
microarray. Optical tweezers can be used to
determine physical properties.

• Amino-modified slide and beads
• UV light binds DNA to glass
• DNA boiled to expose amino groups
• Beads treated with glutaraldehyde
• Beads bind to DNA

Four quadrant
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Stretching ssDNA
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Control Data
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Force Exerted on Bead
Sample 1 20.18 mW
Sample 2 18.852 mW
Empty Trap
Free Floating Bead
Voltage (volts)
Voltage (volts)
Force (pN)
Time (seconds)
Time (seconds)
Sample 2 80.137 mW
Sample 1 80.137 mW
Linear section of DNA elasticity, with maximum
extension of approximately 4µm, at a constant
velocity of 18 µm/s.
Voltage (volts)
Voltage (volts)
Voltage (volts)
Voltage (volts)
Time (seconds)
Time (seconds)
Power (Watts)
Time (seconds)
Time (seconds)
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Conclusions
Future Work
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Elasticity of ssDNA
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• Proof of concept
• Successfully attached DNA to slide, and bead to
  DNA
• Successfully measured elongation of ssDNA.
• Measured force constant (k) of ssDNA
• Using constant velocity, k 88.9 µN/m
• Experimental design and equipment successfully
  implemented.

• Use PCR fragments of Fragile X Mental
  Retardation Gene
• Known length and sequence with CCG trinucleotide
  repeat.
• Test for breaking vulnerability.
• Pull covalently bound DNA from slide.
• Predict topology of DNA bound to glass slide.
• Measure hydrogen bonds between probe and target
  DNA.

Differing lengths of DNA cause changes in the
force required to stretch the DNA strand. Bead 2
was attached to a longer DNA strand than Bead 1.
Time (seconds)
Power (Watts)
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