Determining the Physical Properties of DNA in Microarrays Using Optical Tweezers

Megan McDonald1,2, A. Malcolm Campbell1, Dan Boye2

1Biology & 2Physics Depts., Davidson College, Davidson, NC

Introduction

The colors depict the ratios of expression for each gene.

Future Work

Currently

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.

Predictions

Principles of Optical Tweezers

Isolated a 977kb fragment of the FMR1 gene, to attach to beads

Integrated new photodetector system into optical tweezers setup

Optimized solution for suspending beads, to prevent sticking to slide.

Created aldehyde-functionalized beads from amines using glutaraldehyde.

LabVIEW code for calibration, data acquisition, & movement in x-y plane

Calibration of system with photodetector, new solution, and 1μm beads

UV-link DNA to glass slide and attach bead to DNA

Measure strength of DNA bound to glass

Combine force data with known sequence of DNA

Attempt to determine the structure of the bound single-stranded DNA.

memcdonald@davidson.edu

Research funded by the National Science Foundation and the Bank of America

Optical Tweezers Design

Coupling Beads to DNA

The chemistry of DNA covalently bound to glass

Predicted DNA force pattern from optical tweezers.