NAN 771E - Single-Molecule Biophysics
Th 1-3:30

DescriptionExperimental methodologies and theoretical underpinnings of single-molecule biophysics research, with a focus on the role of such studies in nanoscience. Topics include widely-used preparations, techniques, and models for interpreting results.

Class Syllabus: Link

Required Text:

Handbook of Single-Molecule Biophysics, Peter Hinterdorfer and Antoine van Oijen (Eds.); 1st Edition (2009), ISBN: 978-0-387-76496-2

The content of this book is available electronically (PDF format) through UNCG access HERE.

Additional required reading (references cited in the text above, recent additions to the subject matter, etc.) will be made available through links below.


Week 1, 2: Molecular imaging and tracking with fluorescence      

Week 3, 4: Forrester Energy Resonance Transfer and correlation microscopy

Week 5, 6: Molecular imaging in vivo and sub-diffraction imaging

Week 7, 8: Molecular detection and analysis with nanopores and nanochannels

Week 9, 10: Single-molecule manipulation with optical and magnetic tweezers

Week 11, 12: Single-molecule manipulation, imaging, and force spectroscopy with AFM

Week 13, 14: Student Presentations

Calendar (w/ Links)

1/17: Introduction, Discussion - Life at Low Reynold's Number (Purcell)

1/24: READ Ch. 1 - Single-Molecule Fluorescent Particle Tracking (Ahmet Yildiz)

          Other resources: FIONA, Motor motion models, Effects of anisotropy

1/31: READ review article "Single Molecule approach to molecular  biology in living bacterial cells" by Xie, et al.

2/7:   READ Ch. 5 - Single-Molecule FRET: Methods and Biological Applications (Hwang, et al.)

2/14: READ discussion papers:

          1) Detecting Force-Induced Molecular Transitions with Fluorescence Resonant Energy Transfer by Tarsa, et al (pdf)

          2) Single-Pair FRET Characterization of DNA Tweezers by Muller, et al (pdf)

          3) Protein folding studied by single-molecule FRET by Schuler and Eaton (pdf)

2/21: READ Ch. 8 - Fluorescence Correlation Spectroscopy in Living Cells (Weidemann and Schwille)

          DUE: Design a single molecule FRET experiment and write up a description that includes (i) why FRET is used, (ii) how it will be done in as much detail as

                    possible, and (iii) what the anticipated results should look like and reveal

2/28:  READ Ch. 11 - Nanopores: Generation, Engineering, and Single-Molecule Applications (Howorka and Siwy)

3/7:   READ discussion papers:

          1) Continuous base identification for single-molecule nanopore DNA sequencing by Clarke, et al (pdf)

          2) Single-molecule transport across an individual biomimetic nuclear pore complex by Kowalczyk, et al (pdf)

          3) Detection of local protein structure along DNA using solid-state nanopores by Kowalczyk, et al (pdf)

          4) Deciphering ionic current signatures of DNA transport through a nanopore by Aksimentiev (pdf) Link to example videos

3/21:  READ Ch. 12 - Single-Molecule Manipulation Using Optical Traps (Woodside and Valentine)

3/28:  READ Ch. 13 - Magnetic Tweezers for Single-Molecule Experiments (Vilfan, et al)

4/4: READ discussion papers:

          1) Magnetic Forces and DNA Mechanics in Multiplexed Magnetic Tweezers by De Vlaminck, et al (pdf)

          2) Magnetic Tweezers Measurement of Single Molecule Torque by Celedon, et al (pdf)

          3) Thin-foil magnetic force system for high-numerical-aperture microscopy by Fisher, et al (pdf)

4/11: DUE: Design an experiment that uses tweezer techniques (optical, magnetic, or a combination) and write up a description that includes (i) why tweezers are                 

                     specifically a good tool for the measurement, (ii) how it will be done in as much detail as possible, and (iii) what you would expect the results to look like 

                     and reveal (your hypothesis)

4/18: READ Ch. 14 - Folding of Proteins Under Mechanical Force (Schlierf and Rief)

4/25: READ Ch. 19 - Atomic Force Microscopy of Protein–Protein Interactions (Zhang, et al.)