Tip-enhanced Raman spectroscopy of single RNA strands
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Tip-enhanced Raman Tip-enhanced Raman spectroscopy of single RNA spectroscopy of single RNA
strandsstrands
Elena Bailo and Volker DeckertElena Bailo and Volker DeckertISAS – Institute for Analytical SciencesISAS – Institute for Analytical Sciences
Dortmund, GermanyDortmund, Germany
Poltersdorf, 03-05.10.2007
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MotivationMotivation
Direct and label-free sequencing of Direct and label-free sequencing of single DNA strandsingle DNA strand
Characterization of the structure and Characterization of the structure and dynamic of cell wallsdynamic of cell walls
U. Neugebauer U. Neugebauer et al.et al. ChemPhysChem ChemPhysChem 20072007, , 88, 124., 124.
C. Budich C. Budich et alet al. J. Microsc. . J. Microsc. 20072007, (accepted), (accepted)
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TERS setupTERS setup
Coarse xy AFM-positioning
Piezo z-focusing
Piezo xy sample stage
Coarse xy sample stage
AFM
IFNF Laser
Spectrometer & CDD
A. Rasmussen, V. Deckert, J. Raman Spectrosc. 2006, 37, 311.
Bottom illumination configuration
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TERS tips preparationTERS tips preparation
AgThermal source
Si AFM tip
Low Rate ~ 0.05 nm/s
Diameter ~20 nm
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Tip and laser alignmentTip and laser alignment
Direct reflected image
X
PD
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Sample: Sample: Synthetic RNA homopolymer Synthetic RNA homopolymer
on micaon mica
Topographical Image
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Single RNA strandSingle RNA strand
AFM image Profile
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TERS experimentTERS experiment
15s,1mW, @ 530 nm
E. Bailo and V. Deckert, E. Bailo and V. Deckert, Angew. Chem. Int. Ed., Angew. Chem. Int. Ed., 20072007, , accepted.accepted.
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Band assignmentBand assignment
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CCC
CC
CCCCCCCC
Enhancement factorEnhancement factor
~ 60 bases
Laser spot
~ 1 µm
Ag Tip
Radius ~ 20 nm
~ 3000 bases
50 Fold
Signal-to-noise ratio
200:1x
104
Enhancement factor at least
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Spectral fluctuationsSpectral fluctuationsAg
Particle
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Band fluctuations:Band fluctuations:adenine-silver complexesadenine-silver complexes
H. Watanabe et al., Phys. Rev. B 2004, 69, 155418.
Predicted Raman spectra:
Vibrational frequencies
and
Raman intensities
change for each isomer
Ad-N1
Ad-N3
Ad-N7
Ad-N10
SERS
TERS
Adenine
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Band identificationBand identification
J. Florian et al. J. Phys. Chem. 1996, 100, 5578.
TERS on TERS on poly(cytosine)poly(cytosine)
RamanRaman
on cytosineon cytosineVibrational modesVibrational modes
801801 803803
10451045 10451045
10971097 11061106
11661166 11461146
12481248 12451245
12791279 12731273
13801380 13791379
14531453 14581458
14881488 14901490
15491549 15311531
16021602 16061606
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Ag particle
TERS and DNA sequencing TERS and DNA sequencing
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Summary and OutlookSummary and Outlook
Single RNA strands detectionSingle RNA strands detection Approx. 60 nucleobasesApprox. 60 nucleobases SNR ~ 200SNR ~ 200
Next step Next step Natural DNA or RNA sequencingNatural DNA or RNA sequencing
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AcknowledgementAcknowledgement
Volker DeckertVolker Deckert
Christian Budich, Marc RichterChristian Budich, Marc Richter
H. Herzog, E. Pulvermacher, B. GosciniakH. Herzog, E. Pulvermacher, B. Gosciniak
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Tip shapeTip shape
TIP
Sample