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Related Experiment Video

Updated: Jun 14, 2026

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA
12:05

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA

Published on: October 1, 2017

Single-molecule sequence detection via microfluidic planar extensional flow at a stagnation point.

Rebecca Dylla-Spears1, Jacqueline E Townsend, Linda Jen-Jacobson

  • 1Department of Chemical Engineering, University of California, Berkeley, CA, USA.

Lab on a Chip
|April 2, 2010
PubMed
Summary

This study uses microfluidic flow to stretch single DNA molecules, enabling precise detection of target sequences. This technique improves accessibility for sequence-specific markers, enhancing genomic DNA analysis.

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Last Updated: Jun 14, 2026

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA
12:05

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A Droplet-Based Microfluidic Approach and Microsphere-PCR Amplification for Single-Stranded DNA Amplicons
11:40

A Droplet-Based Microfluidic Approach and Microsphere-PCR Amplification for Single-Stranded DNA Amplicons

Published on: November 14, 2018

Area of Science:

  • Biophysics
  • Molecular Biology
  • Microfluidics

Background:

  • Accurate mapping of target sequences along genomic DNA is crucial for molecular diagnostics.
  • Traditional methods for DNA analysis can be limited by accessibility of internal binding sites.

Purpose of the Study:

  • To develop a microfluidic method for trapping and extending single double-stranded (ds) DNA molecules.
  • To enable sequence-specific detection of target sequences along the DNA backbone with high precision.

Main Methods:

  • Utilizing a microfluidic stagnation point flow in a cross-slot device to create planar extensional flow.
  • Employing mutant EcoRI-based fluorescent markers for sequence-specific binding to labeled ds DNA.
  • Direct observation and measurement of marker positions along stretched DNA using fluorescence microscopy.

Main Results:

  • Achieved precise detection of five target site positions within 1.5 kb with standard deviations <1.5 kb.
  • Demonstrated controlled DNA elongation via flow strength, impacting marker accessibility.
  • Showed improved binding to internal dsDNA sequences with increased sample mixing and DNA extension.

Conclusions:

  • Microfluidic stagnation point flow offers a robust method for single-molecule DNA analysis and mapping.
  • The technique enhances accessibility of internal DNA binding sites, improving marker binding efficiency.
  • This approach provides a valuable tool for high-resolution genomic DNA sequence detection.