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Tip-enhanced Raman spectroscopy
of single RNA strands
Elena Bailo and Volker Deckert
ISAS – Institute for Analytical Sciences
Dortmund, Germany
Poltersdorf, 03-05.10.2007
Motivation


Direct and label-free sequencing of single
DNA strand
Characterization of the structure and
dynamic of cell walls
U. Neugebauer et al. ChemPhysChem 2007, 8, 124.
C. Budich et al. J. Microsc. 2007, (accepted)
TERS setup
AFM
Bottom illumination
Coarse xy AFM- configuration
Coarse xy
sample stage
IF
Piezo xy
sample stage
NF
positioning
Laser
Spectrometer
& CDD
Piezo z-focusing
A. Rasmussen, V. Deckert, J. Raman Spectrosc. 2006, 37, 311.
TERS tips preparation
Si AFM tip
Ag
Thermal
source
Diameter ~20 nm
Low Rate ~ 0.05 nm/s
Tip and laser alignment
Direct reflected image
X
PD
Sample:
Synthetic RNA homopolymer
on mica
Topographical Image
Single RNA strand
AFM image
Profile
TERS experiment
15s,1mW, @ 530 nm
E. Bailo and V. Deckert, Angew. Chem. Int. Ed.,
2007, accepted.
Band assignment
Enhancement factor
Laser spot
 ~ 1 µm
Signal-to-noise ratio
~ 3000 bases
Ag Tip
C
Radius ~ 20 nm CC
C
C
C
C
~ 60 bases
C
C
C
C
C
C
200:1
x
50 Fold
104
Enhancement factor
at least
Spectral fluctuations
Ag
Particle
Band fluctuations:
adenine-silver complexes
SERS
TERS
Predicted Raman spectra:
Adenine
Vibrational frequencies
Ad-N1
and
Ad-N3
Raman intensities
change for each isomer
Ad-N7
Ad-N10
H. Watanabe et al., Phys. Rev. B 2004, 69, 155418.
Band identification
TERS on
poly(cytosine)
801
Raman
on cytosine
803
1045
1045
1097
1106
1166
1146
1248
1245
1279
1273
1380
1379
1453
1458
1488
1490
1549
1531
1602
1606
J. Florian et al. J. Phys. Chem. 1996, 100, 5578.
Vibrational modes
TERS and DNA sequencing
Ag particle
Summary and Outlook

Single RNA strands detection
Approx. 60 nucleobases
 SNR ~ 200


Next step

Natural DNA or RNA sequencing
Acknowledgement

Volker Deckert

Christian Budich, Marc Richter

H. Herzog, E. Pulvermacher, B. Gosciniak
Tip shape
TIP
Sample