DNA nanotubes with
well defined length
Alex Turkin
TopMaster in Nanoscience
Supervisor: Prof. Andreas Herrmann
Polymer Chemistry and Bioengineering
Groningen, June 23, 2010
Outline

The beauty of DNA



Experiment




Hybridization
Imaging
Problem at hand


Diversity of possible structures
Magical DNA strand
Length ‘control’ via emulsion droplets
Results
Conclusions
What is DNA ?
First DNA structures
Bases
Nucleotides
N. C. Seeman, J.Chen, Nature 1991, 350, 631.
DNA origami
P. W. K. Rothemund, Nature 2006, 440, 297.
DNA origami
P. W. K. Rothemund, http://www.dna.caltech.edu/~pwkr/
Complexity


> 7000 base pair DNA
> 200 staples


Each synthesized and purified
Purchased
.............................
DNA 52mer

A new sequence!
C. Mao et al., Angew. Chem. Int. Ed. 2006, 45, 1942 –1945
DNA 52mer

Association process of the 52mer

Initial strand

Two stranded complex
Formation of a sheet
St

ep
2
Step 1
N Steps
C. Mao et al., Angew. Chem. Int. Ed. 2006, 45, 1942 –1945
DNA 52mer

The sheet rolls into a nanotube
1
÷
20
μm
C. Mao et al., Angew. Chem. Int. Ed. 2006, 45, 1942 –1945
Experiment

Hybridization
Hybridization
(cooling-down)
Denaturation
(heating-up)
AFM imaging

Broad length distribution
10 nm
10 nm
2 μm
2 μm
Length control

Confined volume imposes restrictions on
nanotube growth
10 μm
Emulsion

Dropwise addition of aqueous phase to
oil+surfactant phase while being stirred
H2O
Oil

The size of water droplets is 3.9 ± 1.7 μm
Results

Hybridized in solution
10 nm

Hybridized in emulsion
10 nm
2 μm
250 nm
Results
Length distribution
1.0
Solution, cDNA = 1 M
Emulsion, cDNA = 1 M
0.8
a.u.

0.6
0.4
0.2
0.0
0
1
2
3
4
5
6
7
Nanotube length, m
8
9
10
Results
Length distribution vs. DNA concentration
1.0
cDNA = 1 M
cDNA = 5 M
0.8
a.u.

0.6
0.4
0.2
0.0
200
400
600
800
Nanotube length, nm
1000
Possible applications


“ It might be possible that shortening the
DNA-NTs is necessary for its
internalization [into cancer cells] ”*
Template for nanofabrication

Metallic nanowires
* C. Mao et al., Biomacromolecules 2008, 9, 3039–3043
Conclusions



Well defined DNA nanostructures have been
created by hybridizing the 52mer in emulsion
droplets
The experiment has been performed for
several DNA concentrations
The proposed method can be used to control
the length distribution of DNA-nanotubes and
could possibly be employed to control the
size of other nanoobjects
Manuscript in preparation
Acknowledgements


TopMaster groupmates
Polymer Chemistry and Bioengineering
department






Andreas Herrmann
Jan Zimmermann
Minseok Kwak
Andrew Musser
Alberto Rodriguez Pulido
Tobias Schnitzler
Thank you