Orientatie op natuurkunde onderzoek (BN group study)

Topics

Among the five topics, each student choose one topic to write their final report.

(A) Nanopore
(B) Fluorescence (FRET)
(C) Optical tweezers
(D) Magnetic tweezers
(E) Atomic force microscopy

Lab Tour

When: February 21, 2012
15:45 to 16:30 and 16:45 to 17:30 (45 minute tour)
Where: F082, (not F205), Building 22
Sign-up: http://doodle.com/cuvfq9z55mexgy4v
* You choose one session to attend. (If you'd like to, you may choose two.)
* The attendance is optional.
* There will be no lab tour for magnetic tweezers.

Office Hours

When: 6 March and 13 March 2012
15:45 to 17:30
Where: F082, (not F205), Building 22
* The attendance is optional.

Papers to Read

1. Review on single-molecule studies (Groups A, B, C, D & E)

The smaller the better (full text)

* This paper is mandatory for all the students.

2. Nanopore (Group A)

Solid-state nanopores. (pdf)
Dekker C.
Nat Nanotechnol. 2007 Apr;2(4):209-15. Epub 2007 Mar 4.
* This paper is mandatory.

Introduction to molecular biology and nanopore (Chapter 1) (Full text)
* Read Chapter 1. This paper is optional.

Translocation of double-strand DNA through a silicon oxide nanopore. (pdf)
Storm AJ, Chen JH, Zandbergen HW, Dekker C.
Phys Rev E Stat Nonlin Soft Matter Phys. 2005 May;71(5 Pt 1):051903. Epub 2005 May 6.
* A technical review. This paper is optional.

3. Fluorescence (Group B)

Advances in single-molecule fluorescence methods for molecular biology. (pdf)
Joo C, Balci H, Ishitsuka Y, Buranachai C, Ha T.
Annu Rev Biochem. 2008;77:51-76.

* This paper is mandatory.
* Skip pages from 59 to 66 (That is, read only from Page 51 to 58 and from 67 to 71)

A practical guide to single-molecule FRET. (pdf)
Roy R, Hohng S, Ha T.
Nat Methods. 2008 Jun;5(6):507-16.
* A technical review. This paper is optional.

3. Optical tweezers (Group C)

Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy. (pdf)
Neuman KC, Nagy A.
Nat Methods. 2008 Jun;5(6):491-505.
* This paper is mandatory.
* Skip reading the sections about magnetic tweezers and AFM.

lock, S.M. Constructing optical tweezers. In Cell Biology: A Laboratory Manual, D.L. Spector, R. Goldman, L. Leinwand (eds.) Cold Spring Harbor Press (1998). (Full Text)
* A technical review. This paper is optional.

4. Magnetic tweezers (Group D)

Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy. (pdf)
Neuman KC, Nagy A.
Nat Methods. 2008 Jun;5(6):491-505.
* This paper is mandatory.
* Skip reading the sections about optical tweezers and AFM .

Cellular strategies for regulating DNA supercoiling: a single-molecule perspective. (pdf)
Koster DA, Crut A, Shuman S, Bjornsti MA, Dekker NH.
Cell. 2010 Aug 20;142(4):519-30. Review.
* An extensive review. This paper is optional.

5. Atomic force microscopy (Group E)

Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy. (pdf)
Neuman KC, Nagy A.
Nat Methods. 2008 Jun;5(6):491-505.
* This paper is mandatory.
* Skip reading the sections about optical tweezers and magnetic tweezers.

High-speed AFM reveals the dynamics of single biomolecules at the nanometer scale. (pdf)
Katan AJ, Dekker C.
Cell. 2011 Nov 23;147(5):979-82.
* Advanced topic. This paper is optional.

Final Report