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2012 BFY Abstract Detail Page

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Abstract Title: W26 - A simple, inexpensive single molecule DNA microscope
Abstract: Techniques for trapping, manipulating and measuring single macromolecules include optical trapping, magnetic tweezers, and flow stretching. These techniques have been used to study DNA replication, RNA folding, protein folding, and gene translation.1,2 These single molecule methods are out of reach for most undergraduates, mainly because of the difficulty of isolating single molecules. Participants in this workshop will learn about how we are making single molecule techniques both simpler and less expensive. Participants will get hands on experience with a microscope that has been used in several senior thesis projects by our students.

Our single molecule DNA microscope uses an upright microscope coupled to a webcam for imaging single DNAs. The DNA molecules are tethered on one end to a glass surface within a microfluidic cell. The DNAs are visualized by tethering paramagnetic microbeads to their free ends. The beads, which can be seen under visual light microscopy, also serve as "handles" for applying forces to the DNA using fluid drag and/or magnets.

We will cover basic webcam video microscopy and microfluidic flow cell construction. We will cover how these two elements can be used to study Brownian motion. Next, we will cover the basics of DNA tethering, including surface functionalization and DNA labeling. These techniques may be new to physicists, and we will discuss the challenges and requirements for successful tethering---the key to a successful single molecule experiment! Our DNA tethering technique takes several hours to complete, so we will not have time to demonstrate the complete method in each workshop. However, we will cover the important steps. We will end with discussion of ideas for different experiments that can be done with the microscope, including measuring the DNA-force extension curve, DNA replication, and DNA cleavage.

1. For an excellent review of the field, see the single molecule theme issue of Annual Reviews of Biochemistry 77 (2008).
2. W. J. Greenleaf, M. T. Woodside, and S. M. Block, "High-resolution single-molecule measurements of biomolecular motion," Annu. Rev. Biophys. Biomol. Struct. 36, 171-190 (2007).
Abstract Type: Workshop

Workshop Documents

Workshop Document: Download the Workshop Document
Workshop Document (2): Download the Workshop Document (2)
Workshop Document (3): Download the Workshop Document (3)
Workshop Document (4): Download the Workshop Document (4)
Workshop Document (5): Download the Workshop Document (5)
Workshop Document (6): Download the Workshop Document (6)

Author/Organizer Information

Primary Contact: Allen Price
Emmanuel College