University homepage | Suomeksi | På svenska | In English

Single Molecule Methods (Fall 2011)

(530190) Methods in Single Molecule Biophysics, (3op) , Fall 2011

 

This course will give students an overview of current experimental state of the art single molecule techniques used in biophysics and elsewhere. Emphasis will be on two areas: (1) novel single molecule instrumentation and measurement methods, and (2) nano-scale molecular physics, thermodynamics, and statistical methods required to interpret measurement data.

Homepage: http://h116.it.helsinki.fi/?page_id=345
Our lab homepage is at h116.it.helsinki.fi, and our optical tweezers research is here. The course was lectured previously in 2007 (old web page)

Lecturer : PhD Anders Wallin (anders.wallin “at” helsinki.fi)

Assistant : MSc Kalle Hanhijärvi (kalle.hanhijarvi “at” helsinki.fi)

Schedule : Fall 2011, period II. Lectures: Tue 14-16, in D116. Exercises: Wed 12-14, in D116.

First lecture: Tue 1.11.2011 14-16, D116, Physicum

Lectures:

Lecture 1, 1.11. PDF

– Introduction
– Length scales in single molecule biophysics (http://fi.wikipedia.org/wiki/Solu)
– Single molecule vs. ensemble measurements (A.E. Knight: Introduction: The “Single Molecule” Paradigm)
– Protein folding (Protein Folding Problem)

Lecture 2, 2.11. (NB!) PDF

Howard’s Book, chapter 2
– Forces on the micro-scale
– Mass, stiffness, damping, time-constants
– Langevin equation, diffusion simulations (simple diffusion simulation: simple diffusion simulation)

Lecture 3, 8.11. PDF

– Optical trapping (idea, experiment-geometry, example experiments)
– Force-range, position-detection range
– Basics of ray-optics and rayleigh regime theory
– Brownian dynamics (power-spectrum relation to Fourier transform). Derive power-spectrum
for free diffusion, trapped massless particle.

PSD examples: PDF

Reading for Lecture 3: Greenleaf et al. (2007)

Lecture 4, 15.11. PDF

Chain models for polymers(DNA)
– Freely Jointed Chain (FJC). 1D, 2D
– Worm-Like Chain (WLC)

FJC simulations: fjc.zip

Lecture 5, 22.11.

– Kramers-Bell “energy-landscape” model for RNA-hairpins.

Material:  Bustamante et al.  “Mechanical Processes in Biochemistry”
See/understand especially Fig 1 and Fig 2.

Slides/Talk by Felix Ritort ca. pages 13 – 34 (this talk has much advanced material which was not covered on the lecture!)

Lecture 6, 29.11.

– Fluorescence and super-resolution microscopy
Material: L. Schermelleh et al. “A guide to super-resolution fluorescence microscopy”
Video: “Nature Methods: Method of the Year 2008”

Lecture 7, 13.12.

– We will go through the papers you have selected for the home-exam.

More lecture material

Exercises:

  • Exercise 1,  9.11., PDF, Solutions
  • Exercise 2, 16.11., PDF (NB, corrected version!) trapdata.zip, Solutions
  • Exercise 3, 23.11., PDF, Solutions
  • Exercise 4, 30.11., PDF, Solutions, data files: ex4_data.zip

Home-Exam:

Everyone writes a brief review of a recent scientific publication relevant to the course. Length 2-5 pages. In finnish, swedish, or english. Submit by 31.12.2011. Take each figure and equation from the paper and explain it in sufficient detail so that a fellow student who has not taken this course can understand what is going on.

Possible papers:

– Rief et al. “The Complex Folding Network of Single Calmodulin Molecules”
– Smith et al. “The bacteriophage phi29 portal motor can package DNA against a large internal force”, Supplement
-Bouchiat et al. “Estimating the Persistence Length of a Worm-Like Chain Molecule from Force-Extension Measurements”
– Greenleaf, et al. “Direct Observation of Hierarchical Folding in Single Riboswitch Aptamers”
– Eva Rittweger, Kyu Young Han, Scott E. Irvine, Christian Eggeling, Stefan W. Hell (2009). “STED microscopy reveals crystal colour centres with nanometric Resolution.”. Nature Photonics 3 (3): 144–147.  10.1038/nphoton.2009.2.
– Michael J Rust, Mark Bates & Xiaowei Zhuang, Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM), Nature Methods3, 793 – 796 (2006) ,  doi:10.1038/nmeth929
– Keir C. Neuman and Steven M. Block, “Optical trapping”, Rev. Sci. Instrum. 75, 2787 (2004); doi:10.1063/1.1785844


 

Updated: 29.11.2011