Fast and sensitive DNA analysis using changes in the FRET signals of molecular beacons in a PDMS microfluidic channel.
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.
Jung
Jaehyun
J
Department of Applied Chemistry, Hanyang University, Ansan 426-791, South Korea.
Chen
Lingxin
L
Lee
Sangyup
S
Kim
Sungyong
S
Seong
Gi Hun
GH
Choo
Jaebum
J
Lee
Eun Kyu
EK
Oh
Chil-Hwan
CH
Lee
Sanghoon
S
D001483:Base Sequence; D004247:DNA / Q000032:analysis*; D015342:DNA Probes; D031541:Fluorescence Resonance Energy Transfer; D044085:Microfluidics / Q000295:instrumentation*; D012680:Sensitivity and Specificity; D013050:Spectrometry, Fluorescence; D013059:Spectrum Analysis, Raman
D015342:DNA Probes; D004247:DNA