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Molecular-Sized DNA or RNA Sequencing Machine

Keywords: Device, sequencing, DNA/RNA, Forster Resonance Energy Transfer (FRET), fluorophore

Summary: 
The National Cancer Institute's Gene Regulation and Chromosome Biology Laboratory  is seeking statements of capability or interest from parties interested in collaborative research to co-develop a molecular-sized DNA or RNA sSequencing machine.

Technology:
 Current high-throughput DNA sequencing methods suffer from several limitations. Many methods require multiple fluid handling steps, fixing of molecules on beads or a 2D surface, and provide very short read-lengths. The NIH inventors offer a potential DNA or RNA sequencing device that drastically simplifies the process by combining all elements for sequence detection in a single molecule.

 The Medusa Sequencer utilizes Forster Resonance Energy Transfer (FRET) to read a polynucleotide sequence while synthesizing a complementary strand. The device consists of a DNA (or RNA) polymerase labeled with a FRET donor fluorophore and attached to a set of four flexible arms. The tip of each arm carries a distinct set including one nonhydrolyzable nucleotide and one FRET acceptor fluorophore. While a Medusa Sequencer synthesizes a complementary polynucleotide strand, the four different arms continuously "test" the polymerase pocket creating a characteristic FRET signal for the correct nucleotide. The series of FRET signals reveals the unknown polynucleotide sequence.

Potential Commercial Applications:

• High-throughput DNA or RNA sequencing alternative to microarrays for expression analysis

Competitive Advantages:

• Single reagent for synthesis and sequencing
• Eliminates repetitive fluid handling steps
• Able to count single mRNA or DNA molecules
• Could be injected in living cells to read/count mRNA sequences directly
• High speed; one microscope obtains many sequences in parallel
• Can be 3D-arrayed in a gel for ultra-high density
• Use with Sequence Walkers for diagnostics

Development Stage: Discovery

Related Technologies:  US Patent Applications 60/749,858 ( 12/12/2005),  11/638,160 (12/12/2006), US, Patents 6,982,146 (06/ 0302006), PCT Application No. PCT/US00/23736 (08/ 29 / 2000), US Application No. 12/886,686 (08/29 / 2000).

Patent Status:  US Patent No. 7,871,777  (01/18 /2011)

Contact: Please submit an information request form at  http://techtransfer.cancer.gov or contact
John D. Hewes, Ph.D., (301) 435-3121, hewesj@mail.nih.gov.

Last updated: 05/01/2012

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