lecture 2 application of optical tweezers in single-molecule experiments with dna
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Lecture 2 Application of optical tweezers in single-molecule experiments with DNA. Entropic elasticity of a single DNA molecule. DNA and RNA stretching experiments. First experiment by Carlos Bustamante and co-workers Science (1992). Nucleotides Adenine, Guanine, Cytosine, Tymine. A ... T - PowerPoint PPT PresentationTRANSCRIPT
Lecture 2Application of optical tweezers in single-molecule experiments
with DNA
DNA and RNA stretching experiments
Entropic elasticity of a single DNA molecule
o
AP 34
A ... TG ... CC ... GT ... A . . .
Nucleotides Adenine, Guanine, Cytosine, Tymine
First experiment by Carlos Bustamante and co-workers Science (1992)
Optical Tweezers
Mazolli, Maia Neto, and Nussenzveig, Proc. R. Soc. London, Ser. A 459, 3021 (2003)Viana, Rocha, Mesquita, Mazolli, Maia Neto, Nussenzveig, Appl. Phys. Lett. (2006) and PRE (2007)Neves, Fontes, Pozzo, Thomaz, Chilce, Rodriguez, Barbosa, Lenz-Cesar, Optics Express (2006)
A. Ashkin, Phys. Rev. Lett. 24, 156 (1970)
Recent theoretical and experimental advances
Visible He-Ne back-scattering profile
4
1
14
12
LzL
z
A
kTF
Marko-Siggia equation
z= end-to-end distanceA= persistence lengthL= contour length
S. Harris et al. BJ 2005 (large scale MD, entropic effects, denaturing bubbles);
G. Weber et al. Nature Phys., 2009 (microscopic elasticity).
Force x extension curve
DNA/Ethidium BromideFit to the neighbor exclusion model
Ethidium bromide Daunomycin
M. S. Rocha et al. JPC 2007
Psoralen
Circles: intercalated
Squares: intercalated +UVA light
Psoralen
Márcio. S. Rocha,doctoral thesis UFMG (2008)
ni
n
bpPnK
nCC
1
1 1
14104.28.8
13.043.1
MK
n
i
77.01
64.0 max
n
0
0
L
LL
neighbor exclusion model
Psoralen intercalated fraction
Persistence length abrupt transition around r ~ 0.4
r = concentration of drug bound/concentration of DNA base-pairs
r=0.4 r=0.5
ab initio DFT calculation DNA/Psoralen
ab initio DFT calculation DNA/Psoralen
“DNA-psoralen: single-molecule experiments and first principles calculations”M. S. Rocha, A. D. Lúcio, S. S. Alexandre, R. W. Nunes, and O. N. Mesquita (APL, 2009)
0
20
40
60
80
100
120
140
160
-2 0 2 4 6 8
cyclodextrin
Cc/Cbp
Water transport in a single MDCK kidney cell
How to measure the volume of a cell?
MDCK Kidney Cell
Isoosmotic medium Hiperosmotic medium
Osmoregulation
Effect of vasopressin (AVP) on water transport
Lucio, Santos, and Mesquita, PRE (2003)
Stretching DNA
Stretching RNA
The 3 Main Classes of Motor Proteins
DNA condensation
Fluctuation theorem
PRL, 050601 (2002)
MORPHOLOGY-DEPENDENT RESONANCES (MDR) MODES
Blood 92, 2975 (1998)
PRL 93, 078102 (2004)
Acustooptical deflectors
•Optical Tweezers is a very convenient tool to manipulate, apply and measure forces on single molecules (pN range). It can be used to measure and change transition states during protein folding, with access to the time evolution of these processes.
•It can be used for manipulating single cells for measurements of membrane elasticity, water transport and for manipulation of organelles inside the cell.
•It has been used as an interesting tool to test new ideas on Statistical Physics of small systems.
•It has been used for manipulation of nanowires, carbon nanotubes and silver nanoparticles.
•Applications of optical tweezers have increased much during the last few years.