Fast and sensitive DNA analysis using changes in the FRET signals of molecular beacons in a PDMS microfluidic channel

Jaehyun Jung, Lingxin Chen, Sangyup Lee, Sungyong Kim, Gi Hun Seong, Jaebum Choo, Eun Kyu Lee, Chil Hwan Oh, Sanghoon Lee

Research output: Contribution to journalArticlepeer-review

62 Citations (Scopus)


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 not available: see fulltext.].

Original languageEnglish
Pages (from-to)2609-2615
Number of pages7
JournalAnalytical and Bioanalytical Chemistry
Issue number8
Publication statusPublished - 2007 Apr


  • DNA hybridization
  • Fluorescence resonance energy transfer
  • Lab-on-a-chip
  • Molecular beacon
  • Surface-enhanced Raman

ASJC Scopus subject areas

  • Analytical Chemistry
  • Biochemistry


Dive into the research topics of 'Fast and sensitive DNA analysis using changes in the FRET signals of molecular beacons in a PDMS microfluidic channel'. Together they form a unique fingerprint.

Cite this