MedusaTM Sequencing Thomas D. Schneider, Ilya Lyakhov, and Danielle Needle Filed with the US Patent Office on 2005 December 12 2010 March 03: Claims allowed. European Patent 1960550 US Patent No. 7,871,777, Issued 18 Jan 2011 Imagine a sequencing machine the size of a molecule that could sequence RNA in a living cell!

Benefits of the Medusa^TM Sequencer

Medusa^TM Sequencing:
• is simple because there is only one reagent
• is accurate for counting individual mRNAs or DNAs
• has low error rate per base, and this can be improved by modifying the polymerase
• is fast because a single microscope can be used to obtain many sequences in parallel
• has exceptionally low cost per sequencing device
• has many options for technical improvements
• could be used in the clinic along with sequence walkers to analyze patient's genetic diseases
  (e.g. Medical Applications of Sequence Walkers: ABCR Mutation G863A)

Informal description of the Invention:
The Medusa^TM Sequencer is a single-molecule sequencing device that consists of a DNA (or RNA) polymerase attached to a set of four flexible arms. The tip of each arm carries a nonhydrolyzable nucleotide triphosphate analog and a spectrally distinct Forster Resonance Energy Transfer (FRET) acceptor fluorophore. A donor fluorophore attached to the polymerase excites an acceptor fluorophore by FRET if the fluorophores are close to each other. A Medusa^TM Sequencer binds to a DNA primer hybridized to the DNA or RNA to be sequenced. The four arms with nucleotide tips "test" the polymerase pocket by diffusing in and out. The arm tip that has the nucleotide complementary to the unknown base of the template will dwell longer in the pocket than the other three that are not complementary. However, the polymerase will not incorporate the nucleotide on the tip of the arm into the nascent strand because the nucleotide triphosphate α-β bond is nonhydrolyzable. FRET between the donor on the polymerase and the acceptor at the arm tip produces a characteristic spectrum that identifies the bound base. Free hydrolyzable dNTPs (or NTPs) allow the Medusa^TM Sequencer to step forward. The series of FRET signals reveals the unknown nucleotide sequence. A Medusa^TM Sequencer could also be injected into a cell to read mRNA sequences inside a living organism. Coded versions of the Medusa^TM Sequencer can signal when the device has been damaged.

PDF is available from www.freepatentsonline.com and here US7871777B2.pdf

See also High Speed Parallel Molecular Nucleic Acid Sequencing.

See also Rod-Tether Nanoprobes!

• Federal Register: April 5, 2006 (Volume 71, Number 65) [Page 17119-17121]
• WO/2007/070572 PROBE FOR NUCLEIC ACID SEQUENCING AND METHODS OF USE
  at the World Intellectual Property Organization.
  To see the application, click on 'Documents' and then get the "21.06.2007 Initial Publication without ISR (A2 25/2007)" zip file. This contains the entire application with drawings at the end.
• Published Application 20080299565 at the US Patent and Trademark Office 2009 Jan 09
• patentlens - complete application with figures. 2010 Jul 07
• United States Patent 7,871,777 Schneider, et al. January 18, 2011 issued at the United States Patent and Trademark Office. (If the link above fails, search for patent 7,871,777 at the USPTO.)