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Determining the Physical Properties of DNA in DNA Microarrays Using Optical Tweezers
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Megan McDonald , A. Malcolm Campbell , Dan Boye
# 05-A-3139-BPS
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Davidson College Biology Department, Davidson College Physics Department
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Introduction
Tweezer Setup
DNA microarrays measure genome activity
in cells. DNA is attached to aminomodified 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.
DNA-Bead Coupling
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Four quadrant
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Force Exerted on Bead
Stretching
ssDNA
Sample 1: 20.18 mW
Sample 2: 18.852 mW
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Voltage (volts)
Force (pN)
Voltage (volts)
Voltage (volts)
Time (seconds)
Voltage (volts)
Free Floating Bead
Empty Trap
Time (seconds)
Power (Watts)
Differing lengths of
DNA cause changes in
the force required to
stretch the DNA strand.
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Time (seconds)
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Bead 2 was attached to
a longer DNA strand
than Bead 1.
Conclusions
Proof of concept:
Power (Watts)
Time (seconds)
Time (seconds)
Future Work
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Sample 2: 80.137 mW
Use PCR fragments of Fragile X Mental Retardation Gene
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Successfully attached DNA to slide, and bead to DNA
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Known length and sequence with CCG trinucleotide repeat.
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Successfully measured elongation of ssDNA.
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Test for breaking vulnerability.
Measured force constant (k) of ssDNA
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Time (seconds)
Sample 1 80.137 mW
Linear section of DNA
elasticity, with maximum
extension of approximately
4µm, at a constant velocity of
18 µm/s.
Time (seconds)
Elasticity of ssDNA
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
Voltage (volts)
Control Data
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Voltage (volts)
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Using constant velocity, k = 88.9 µN/m
Experimental design and equipment successfully implemented.
Pull covalently bound DNA from slide.
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Predict topology of DNA bound to glass slide.
Measure hydrogen bonds between probe and target DNA.