Fast and sensitive DNA analysis using changes in the FRET signals of molecular beacons in a PDMS microfluidic channel |
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Authors: | Jaehyun Jung Lingxin Chen Sangyup Lee Sungyong Kim Gi Hun Seong Jaebum Choo Eun Kyu Lee Chil-Hwan Oh Sanghoon Lee |
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Institution: | (1) Department of Applied Chemistry, Hanyang University, Ansan, 426-791, South Korea;(2) Department of Chemical Engineering, Hanyang University, Ansan, 426-791, South Korea;(3) Department of Dermatology, Korea University, Seoul, 136-174, South Korea;(4) Department of Biomedical Engineering, Korea University, Seoul, 136-701, South Korea |
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Abstract: | A new DNA hybridization analytical method using a microfluidic channel and a molecular beacon-based probe (MB-probe) is described.
A stem-loop DNA oligonucleotide labeled with two fluorophores at the 5′ and 3′ termini (a donor dye, TET, and an acceptor
dye, TAMRA, respectively) was used to carry out a fast and sensitive DNA analysis. The MB-probe utilized the specificity and
selectivity of the DNA hairpin-type probe DNA to detect a specific target DNA of interest. The quenching of the fluorescence
resonance energy transfer (FRET) signal between the two fluorophores, caused by the sequence-specific hybridization of the
MB-probe and the target DNA, was used to detect a DNA hybridization reaction in a poly(dimethylsiloxane) (PDMS) microfluidic
channel. The azoospermia gene, DYS 209, was used as the target DNA to demonstrate the applicability of the method. A simple
syringe pumping system was used for quick and accurate analysis. The laminar flow along the channel could be easily controlled
by the 3-D channel structure and flow speed. By injecting the MB-probe and target DNA solutions into a zigzag-shaped PDMS
microfluidic channel, it was possible to detect their sequence-specific hybridization. Surface-enhanced Raman spectroscopy
(SERS) was also used to provide complementary evidence of the DNA hybridization. Our data show that this technique is a promising
real-time detection method for label-free DNA targets in the solution phase.
Figure FRET-based DNA hybridization detection using a molecular beacon in a zigzag-shaped PDMS microfluidic channel |
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Keywords: | Fluorescence resonance energy transfer Molecular beacon Lab-on-a-chip Surface-enhanced Raman DNA hybridization |
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