High‐resolution electrophoretic separation and integrated‐waveguide excitation of fluorescent DNA molecules in a lab on a chip

Dongre, C.; Weerd, Jasper van; Besselink, G.A.J.; Weeghel, R. van; Vázquez, Rebeca Martínez; Osellame, Roberto; Cerullo, Giulio; Cretich, Marina; Chiari, Marcella; Hoekstra, H.J.W.M.; Pollnau, Markus

doi:10.1002/elps.201000126

Cited by 17 publications

(22 citation statements)

References 23 publications

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“…As a result, a remarkably low limit of detection for DNA fragments analysis of 2:1 pM was achieved [87], which surpasses previously reported values in setups using on-chip-integrated fluorescence monitoring [84,90]. Optimization of the coating and sieving gel matrix led to excellent MCE separation of the DNA molecules under integrated …”

Section: Figurementioning

confidence: 63%

“…To perform this measurement the analytes are first labeled with a fluorescent molecule, then the CE separation is performed and finally fluorescence is excited and collected at the detection point. Femtosecond laser waveguide writing can be used as a post-processing tool to integrate inside MCE chips optical waveguides intersecting the microfluidic channels at various locations, in order to excite their content with high spatial selectivity [84][85][86][87]. Figure 9 shows a scheme of an MCE chip with integrated optical waveguides.…”

Section: Dna Fragments Separation By Microchip Capillary Electrophoresismentioning

confidence: 99%

“…This optofluidic chip was used for MCE separation and detection of a commercial DNA ladder consisting of 17 double-stranded fragments with sizes in the range of 50-3000 base-pairs (bp) [87]. Prior to this experiment, the inner walls of the microchannel network were coated with a polymer [88] in order to suppress the EOF and to minimize adsorption of DNA molecules on the channel wall.…”

Section: Figurementioning

confidence: 99%

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Femtosecond laser microstructuring: an enabling tool for optofluidic lab‐on‐chips

Osellame

Hoekstra

Cerullo

et al. 2011

Laser & Photonics Reviews

286

226

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This paper provides an overview of the rather new field concerning the applications of femtosecond laser microstructuring of glass to optofluidics. Femtosecond lasers have recently emerged as a powerful microfabrication tool due to their unique characteristics. On the one hand, they enable to induce a permanent refractive index increase, in a micrometer-sized volume of the material, allowing single-step, three-dimensional fabrication of optical waveguides. On the other hand, femtosecond-laser irradiation of fused silica followed by chemical etching enables the manufacturing of directly buried microfluidic channels. This opens the intriguing possibility of using a single laser system for the fabrication and three-dimensional integration of optofluidic devices. This paper will review the state of the art of femtosecond laser fabrication of optical waveguides and microfluidic channels, as well as their integration for high sensitivity detection of biomolecules and for cell manipulation.

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Section: Figurementioning

confidence: 63%

Section: Dna Fragments Separation By Microchip Capillary Electrophoresismentioning

confidence: 99%

Section: Figurementioning

confidence: 99%

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Femtosecond laser microstructuring: an enabling tool for optofluidic lab‐on‐chips

Osellame

Hoekstra

Cerullo

et al. 2011

Laser & Photonics Reviews

286

226

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“…Application of CE-based DNA sequencing in a lab-on-a-chip to identify genomic deletions or insertions associated with genetic illnesses critically depends on the detection of single basepair insertions or deletions from DNA fragments in the diagnostically relevant range of 150−1000 base-pairs, i.e., it requires a variance of σ 2 < 10 −3 , while only σ 2 < 10 −2 were reported [6, 32,33]. Here we test different calibration strategies and demonstrate CE-based DNA analysis in an optofluidic chip with sub-base-pair resolution (σ 2 ≈4 × 10 −4 ) of low concentrations of DNA molecules, thereby paving the way for the envisaged application.…”

Section: Introductionmentioning

confidence: 99%

Combined microfluidic-optical DNA analysis with single-base-pair sizing capability

Pollnau

Hammer

Dongre

et al. 2016

Biomed. Opt. Express

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DNA sequencing by microchip capillary electrophoresis (CE) enables cheap, highspeed analysis of low reagent volumes. One of its potential applications is the identification of genomic deletions or insertions associated with genetic illnesses. Detecting single base-pair insertions or deletions from DNA fragments in the diagnostically relevant size range of 150−1000 base-pairs requires a variance of σ 2 < 10 −3 . In a microfluidic chip post-processed by femtosecond-laser writing of an optical waveguide we CE-separated 12 blue-labeled and 23 red-labeled DNA fragments in size. Each set was excited by either of two lasers powermodulated at different frequencies, their fluorescence detected by a photomultiplier, and blue and red signals distinguished by Fourier analysis. We tested different calibration strategies. Choice of the fluorescent label as well as the applied fit function strongly influence the obtained variance, whereas fluctuations between two consecutive experiments are less detrimental in a laboratory environment. We demonstrate a variance of σ 2 ≈4 × 10 −4 , lower than required for the detection of single base-pair insertion or deletion in an optofluidic chip. 895-897 (1993). 5. G. J. M. Bruin, "Recent developments in electrokinetically driven analysis on microfabricated devices,"

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“…We achieve a spatial separation resolution of 12 μm, which can enable a 20-fold enhancement in electropherogram peak resolution, leading to plate numbers exceeding one million. We demonstrate a high sizing/calibration accuracy of 99% [3], and ultrasensitive fluorescence detection (limit of detection = 65 femtomolar, corresponding to merely 2-3 molecules in the excitation/detection volume) of diagnostically relevant double-stranded DNA molecules by integrated-waveguide laser excitation. Subsequently, we introduce a principle of parallel optical processing to this optofluidic lab-on-a-chip.…”

mentioning

confidence: 99%

Multi-color fluorescent DNA analysis in an integrated optofluidic lab on a chip

Dongre

Weerd²,

Weeghel³

et al.

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Sorting and sizing of DNA molecules within the human genome project has enabled the genetic mapping of various illnesses. By employing tiny lab-on-a-chip devices for such DNA analysis, integrated DNA sequencing and genetic diagnostics have become feasible. However, such diagnostic chips typically lack integrated sensing capability. We address this issue by combining microfluidic capillary electrophoresis with laser-induced fluorescence detection resulting in optofluidic integration towards an on-chip bio-analysis tool [1,2]. We achieve a spatial separation resolution of 12 μm, which can enable a 20-fold enhancement in electropherogram peak resolution, leading to plate numbers exceeding one million. We demonstrate a high sizing/calibration accuracy of 99% [3], and ultrasensitive fluorescence detection (limit of detection = 65 femtomolar, corresponding to merely 2-3 molecules in the excitation/detection volume) of diagnostically relevant double-stranded DNA molecules by integrated-waveguide laser excitation. Subsequently, we introduce a principle of parallel optical processing to this optofluidic lab-on-a-chip. Different sets of exclusively color-labeled DNA fragmentsotherwise rendered indistinguishable by their spatio-temporal coincidence -are traced back to their origin by modulation-frequency-encoded multi-wavelength laser excitation, fluorescence detection with a color-blind photomultiplier, and Fourier-analysis decoding. As a proof of principle, fragments from independent human genomic segments, associated with genetic predispositions to breast cancer and anemia, are extracted by multiplex ligation-dependent probe amplification, and simultaneously analyzed. Such multiple yet unambiguous optical identification of biomolecules opens new horizons for "enlightened" lab-on-a-chip devices. References:[1] C.

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High‐resolution electrophoretic separation and integrated‐waveguide excitation of fluorescent DNA molecules in a lab on a chip

Abstract: High-resolution electrophoretic separation and integrated-waveguide excitation of fluorescent DNA molecules in a lab on a chip. ELECTROPHORESIS, Wiley-VCH Verlag, 2010, 31 (15)

Cited by 17 publications

References 23 publications

Femtosecond laser microstructuring: an enabling tool for optofluidic lab‐on‐chips

Femtosecond laser microstructuring: an enabling tool for optofluidic lab‐on‐chips

Combined microfluidic-optical DNA analysis with single-base-pair sizing capability

Multi-color fluorescent DNA analysis in an integrated optofluidic lab on a chip

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