Rapid fabrication of a microfluidic device with integrated optical waveguides for DNA fragment analysis

Abstract

The fabrication and performance of a microfluidic device with integrated liquid-core optical waveguides for laser induced fluorescence DNA fragment analysis is presented. The device was fabricated through poly(dimethylsiloxane) (PDMS) soft lithography and waveguides are formed in dedicated channels through the addition of a liquid PDMS pre-polymer of higher refractive index. Once a master has been fabricated, microfluidic chips can be produced in less than 3 h without the requirement for a cleanroom, yet this method provides an optical system that has higher performance than a conventional confocal optical assembly. Optical coupling was achieved through the insertion of optical fibers into fiber-to-waveguide couplers at the edge of the chip and the liquid-fiber interface results in low reflection and scattering losses. Waveguide propagation losses are measured to be 1.8 dB cm(-1) (532 nm) and 1.0 dB cm(-1) (633 nm). The chip displays an average total coupling loss of 7.6 dB due to losses at the optical fiber interfaces. In the electrophoretic separation and detection of a BK virus PCR product, the waveguide system achieves an average signal-to-noise ratio of 570 +/- 30 whereas a commercial confocal benchtop electrophoresis system achieves an average SNR of 330 +/- 30. To our knowledge, this is the first time that a waveguide-based system has been demonstrated to have a SNR comparable to a commercially available confocal-based system for microchip capillary electrophoresis.

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

“…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 …”

“…Depending on the substrate of choice, different methods can be used. Approaches reported in the literature include waveguide fabrication by silica on silicon [14][15][16][17], ion exchange in soda-lime glasses [18,19], photolithography in polymers [20,21] and liquid-core waveguides [22][23][24][25]. All these methods suffer, when applied to LOCs, from several limitations: (i) they are inherently planar techniques, i. e. they are able to define optical guiding structures only in two dimensions, close to the sample surface; (ii) they are multistep methods, involving multiple masking with critical alignments; (iii) they require cleanroom environment, and (iv) they typically create uneven surfaces which make sealing of the microfluidic channels problematic.…”

Review Article: Recent advancements in optofluidic flow cytometer

“…Review Article: Recent advancements in optofluidic flow cytometer integrated waveguides is to fill a "channel" in the device with a higher index material, such as polydimethylsiloxane ͑PDMS͒ 35,46,47 or any of various high-index liquids, 48 creating a lightguiding core relative to the lower-index device body material. In each case, the waveguide structure is generally created monolithically alongside the microfluidic flow channel, requiring few additional steps ͑generally just a filling step͒ and no alignment.…”

“…Offthe-shelf fiber optics are readily integrated into microfabricated devices. [35][36][37][38][39] Frequently this is accomplished by the use of a fiber sleeve, 35,[37][38][39][40][41][42][43] which guides fiber insertion to correctly position the fiber ͑see Fig. 6͒.…”

Theory, fabrication and applications of microfluidic and nanofluidic biosensors

“…Scaling down of length scales has already spawned extensive research activities in molecular diagnostic and analysis tools based on microfluidic and nanofluidic systems, described as LoC or m-TAS above. Systems have already been developed for cell sorting [70], rapid PCR and DNA microarrays [71][72][73][74] and diagnostic methods based on RNA detection for applications towards early cancer detection [75], point-of-care devices in unconventional or hazardous environments, and for management of diseases during pandemics and natural disasters [76][77][78][79][80].…”