Journal of the European Optical Society - Rapid publications, Vol 9 (2014)

Waveguide structures for efficient evanescent field coupling to zero mode waveguides

M. Sarkar, A. J. H. Wachters, H. P. Urbach, J. J. H. Schleipen, P. J. van der Zaag, R. Wimberger-Friedl


The use of waveguide structures is examined to improve the efficiency of evanescent field coupling into zero-mode waveguides. Model calculations show that waveguide excitation using diffractive structures, increases the magnitude of the evanescent electric field by an order of magnitude compared to far field excitation of the evanescent field. A more efficient excitation of fluorescent markers used in e.g. sequencing instrumentation ultimately enables real-time single molecule detection using laser systems with moderate output power.

© The Authors. All rights reserved. [DOI: 10.2971/jeos.2014.14019]

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M. Margulies. M. Egholm, W. E. Altman, S. Attiya, J. S. Bader, L. A. Bemben, J. Berka, et al., ”Genome sequencing in microfabricated high-density picolitre reactors,” Nature 437, 376–380 (2005).

D. R. Bentley, S. Balasubramanian, H. P. Swerdlow, G. P. Smith, J. Milton, C. G. Brown, K. P. Hall, et al., ”Accurate whole human genome sequencing using reversible terminator chemistry,” Nature 456, 53–59 (2008).

K. J. McKernan, H. E. Peckham, G. L. Costa, S. F. McLaughlin, Y. Fu, E. F. Tsung, C. R. Clouser, et al., ”Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding,” Genome Res. 19, 1527–1541 (2009).

D. Lipson, T. Raz, A. Kieu, D. R. Jones, E. Giladi, E. Thayer, J. F. Thompson, et al., ”Quantification of the yeast transcriptome by single-molecule sequencing,” Nat. Biotechnol. 27, 652–658 (2009).

J. Eid, A. Fehr, J. Gray, K. Luong, J. Lyle, G. Otto, P. Peluso, D. Rank, et al., ”Real-time DNA sequencing from single polymerase molecules,” Science 323, 133–138 (2009).

M. J. Levene, J. Korlach, S. W. Turner, M. Foquet, H. G. Craigshead, and W. W. Webb, ”Zero-mode waveguides for single-molecule analysis at high concentrations,” Science 299, 682–686 (2003).

P. M. Lundquist, C. F. Zhong, P. Zhao, A. B. Tomaney, P. S. Peluso, J. Dixon, B. Bettman, et al., ”Parallel confocal detection of single molecules in real time,” Opt. Lett. 33, 1026–1028 (2008).

B. A. Flusberg, D. R. Webster, J. H. Lee, K. J. Travers, E. C. Olivares, T. A. Clark, J. Korlach, and S. W. Turner, ”Direct detection of DNA methylation during single-molecule, real-time sequencing,” Nat. Methods 7, 461–465 (2010).

R. G. Blazej, P. Kumaresan, and R. A. Mathies, ”Microfabricated bioprocessor for integrated nanoliter-scale Sanger DNA sequencing,” Proc. Nat. Acad. Sciences 103, 7240–7245 (2006).

E. Servoli, H. Feitsma, B. Kaptheijns, P. J. van der Zaag, and R. Wimberger-Friedl, ”Improving DNA capture on microarrays by integrated repeated denaturing,” Lab Chip. 12, 4992–4999 (2012).

M. Xu, H. P. Urbach, D. K. G. de Boer, and H. J. Cornelissen, ”Wire-grid diffraction gratings used as polarizing beam splitter for visible light and applied in liquid crystal on silicon,” Opt. Express 13, 2303–2320 (2005).

M. G. Moharam, E. B. Grann, D. A. Pommet, and T. K. Gaylord, ”Formulation for stable and efficient implementation of the rigorous coupled-wave analysis of binary gratings,” J. Opt. Soc. Am. A 12, 1068–1076 (1995).

X. Wei, A. J. H. Wachters, and H. P. Urbach, ”Finite-element model for three-dimensional optical scattering problems,” J. Opt. Soc. Am. A 24, 866–881 (2007).

A. Yariv, and P. Yeh, Optical Waves in Crystals (Wiley Interscience Publication, Hoboken, 1984).

I. P. Kaminow, W. L. Mammel, and H. P. Weber, ”Metal-clad optical waveguides: analytical and experimental study,” Appl. Optics 13, 396–405 (1974).

C. Pollock, and M. Lipson, Integrated Photonics (Kluwer Academic Publishers, Dordrecht, 2003).