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 configuration Coarse xy sample stage Coarse xy AFM-positioning IF Laser NF Piezo xy sample stage 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 High NA objective enable to 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 50 Fold 104 C Laser spot  ~ 1 µm Signal-to-noise ratio 200:1 ~ 3000 bases x Ag Tip Radius ~ 20 nm C 50 Fold 104 ~ 60 bases Enhancement factor at least

Spectral fluctuations Ag Particle

Band fluctuations: adenine-silver complexes SERS TERS Adenine Predicted Raman spectra: Vibrational frequencies and Raman intensities change for each isomer Ad-N1 Ad-N3 Ad-N7 Ad-N10 H. Watanabe et al., Phys. Rev. B 2004, 69, 155418.

Band identification TERS on poly(cytosine) Raman on cytosine Vibrational modes 801 803 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.

TERS and DNA sequencing Ag particle

Summary and Outlook Single RNA strands detection Next step 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