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Progress toward ultrafast DNA sequencing using solid-state nanopores.

Gautam V Soni1, Amit Meller

  • 1Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.

Clinical Chemistry
|September 25, 2007
PubMed
Summary
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This study introduces a new optical nanopore sequencing method. It uses fluorescent molecular beacons to detect DNA sequences with improved single nucleotide differentiation for faster sequencing.

Area of Science:

  • Biotechnology
  • Nanotechnology
  • Genomics

Background:

  • Nanopore-based DNA and RNA molecule analysis aims for ultrafast DNA sequencing.
  • Purely electronic measurements lack signal contrast for single nucleotide differentiation.
  • A novel optical detection method for DNA sequence translocation through nanopores is proposed.

Purpose of the Study:

  • To develop a novel optical detection method for DNA sequencing using nanopores.
  • To overcome the limitations of purely electronic measurements in achieving single nucleotide differentiation.
  • To enable ultrafast DNA sequencing through enhanced signal contrast.

Main Methods:

  • DNA sequences are biochemically converted into 2-unit codes (2 10-bp nucleotide sequences).
  • Designed DNA Polymers hybridize to complementary, fluorescently labeled, self-quenching molecular beacons.

Related Experiment Videos

  • Molecular beacons are unzipped during translocation through a <2-nm nanopore, unquenching fluorescent tags detected by dual-color total internal reflection fluorescence (TIRF) microscopy.

    • Main Results:

    • A dual-color TIRFM microscope with single-molecule resolution was constructed.
    • Fabrication of 1D and 2D arrays of solid-state nanopores was achieved.
    • A nanofluidic cell assembly enabled TIRF-based optical detection of voltage-driven DNA translocation.

    Conclusions:

    • A novel nanopore DNA sequencing technique utilizing optical readout of unzipping DNA is presented.
    • The technique offers enhanced single nucleotide differentiation for sequence readout.
    • Potential for large-scale parallelism using nanopore arrays is demonstrated.