@inproceedings{2299b362b0364c65bd8309d532eeb334,
title = "DNA separation and fluorescent detection in an optofluidic chip with sub-base-pair resolution",
abstract = "DNA sequencing in a lab-on-a-chip aims at providing cheap, high-speed analysis of low reagent volumes to, e.g., identify genomic deletions or insertions associated with genetic illnesses. Detecting single base-pair insertions/deletions from DNA fragments in the diagnostically relevant range of 150-1000 base-pairs requires a sizing accuracy of S < 10^-3. Here we demonstrate S = 4x10^-4. A microfluidic chip was post-processed by femtosecond-laser writing of an optical waveguide. 12 blue-labeled and 23 red-labeled DNA fragments were separated in size by capillary electrophoresis, each set excited by either of two lasers power-modulated at different frequencies, their fluorescence detected by a photomultiplier, and blue/red signals distinguished by Fourier analysis. Different calibration strategies were tested: a) use either set of DNA molecules as reference to calibrate the set-up and identify the base-pair sizes of the other set in the same flow experiment, thereby eliminating variations in temperature, wall-coating and sieving-gel conditions, and actuation voltages; b) use the same molecular set as reference and sample with the same fluorescence label, flown in consecutive experiments; c) perform cross-experiments based on different molecular sets with different labels, flown in consecutive experiments. From the results we conclude: Applying quadratic instead of linear fit functions improves the calibration accuracy. Blue-labeled molecules are separated with higher accuracy. The influence of dye label is higher than fluctuations between two experiments. Choosing a single, suitable dye label combined with reference calibration and sample investigation in consecutive experiments results in S = 4x10^-4, enabling detection of single base-pair insertion/deletion in a lab-on-a-chip.",
keywords = "single base-pair insertion/deletion, EWI-25962, IOMS-SNS: SENSORS, Capillary electrophoresis, IR-95788, Fluorescent detection, optofluidic chip, sub-base-pair sizing accuracy, METIS-312571, DNA separation",
author = "Markus Pollnau and Manfred Hammer and C. Dongre and Hugo Hoekstra",
note = "10.1117/12.2077515 ; Solid State Lasers XXIV, San Francisco, USA ; Conference date: 01-04-2015",
year = "2015",
month = apr,
doi = "10.1117/12.2077515",
language = "Undefined",
isbn = "978-1-62841-410-3",
series = "Proceedings of the SPIE",
publisher = "SPIE",
pages = "Paper 93200J",
booktitle = "Solid State Lasers XXIV",
address = "United States",
}