# US 2010/0167277 A1 · Fret sequencing by DNA scanning proteins > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 2010/0167277 A1 - Document ID: US20100167277A1 - Status: Published application - Kind: A1 - Application number: 12/317,680 - Filed: 2008-12-29 - Published: 2010-07-01 - Earliest claimed: 2008-12-29 - Inventors: Ryan Anthony Harper - Web page: https://patentgrep.com/patent/US20100167277A1 ## CPC - C12Q 1/6869: Methods for sequencing - C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES ## Abstract This patent describes a novel method for DNA sequencing. A DNA hybrid is created such that one strand contains nucleotides (A, G, C, T/U) bound to different FRET acceptor fluorophores that emits a distinct, differentiable wavelength. A DNA scanning protein carrying a FRET donor fluorophore is also added. A laser with a wavelength that excites the donor molecule irradiates the reaction. As the protein complex passes over a nucleotide on the DNA strand, a FRET reaction occurs between the donor and acceptor fluorophores. The acceptor fluorophore will emit a distinct wavelength which is detected and correlated to a specific nucleotide. As the DNA scanning protein moves along the DNA molecule the entire sequence of nucleotides can be determined by correlating the wavelengths emitted with the specific nucleotide associated with it. ## Claims ### Claim 1 A method to Sequence Nucleic Acids, comprising: A. A fluorescently labeled nucleic acid molecule. B. A protein, or protein complex, that has the ability to move along a nucleic acid molecule and is attached to at least one fluorescent molecule. Whereby a FRET reaction can occur between the said fluorescently labeled nucleic acid molecule and the said protein when a fluorescent molecule is excited. ### Claim 2 (depends on 1) The method of claim 1 wherein the said fluorescently labeled nucleic acid molecule is composed of A, T, G, and C and are each bound to a different and distinguishable fluorescent molecule. ### Claim 3 (depends on 1) The method of claim 1 wherein the said fluorescently labeled nucleic acid molecule are composed of A, U, G, and C and are each bound to a different and distinguishable fluorescent molecule. ### Claim 4 (depends on 1) The method of claim 1 wherein the said nucleic acid molecule is double stranded DNA and is fluorescently labeled only on one strand. ### Claim 5 (depends on 1) The method of claim 1 wherein the said nucleic acid molecule is single stranded DNA. ### Claim 6 (depends on 1) The method of claim 1 wherein the said nucleic acid molecule is RNA. ### Claim 7 (depends on 1) The method of claim 1 wherein unincorporated fluorescently labeled nucleotides are removed from the reaction before the addition of said protein. ### Claim 8 (depends on 1) The method of claim 1 wherein the said protein is a protein from the mismatch repair protein complex. ### Claim 9 (depends on 1) The method of claim 1 wherein the said protein is a DNA polymerase which moves along a single stranded of the said fluorescently labeled nucleic acid molecule and adds unlabled, normal, nucleotides. ### Claim 10 (depends on 1) The method of claim 1 wherein the fluorescent molecules on said fluorescently labeled nucleic acid molecule is FRET acceptors and the fluorescent molecule on the said protein is FRET donor molecules. ### Claim 11 (depends on 1) The method of claim 1 wherein the fluorescent molecules on said fluorescently labeled nucleic acid molecule is FRET donors and the fluorescent molecule on the said protein is FRET acceptor molecules. ### Claim 12 (depends on 1) The method of claim 1 wherein a laser specifically excites the fluorescent molecule on the said protein. ### Claim 13 (depends on 1) The method of claim 1 wherein a laser specifically excites the fluorescent molecule on the said fluorescently labeled nucleic acid molecule. ### Claim 14 (depends on 1) The method of claim 1 wherein the said FRET reaction is detected and correlated to a specific nucleotide allowing one to determine the sequence of the said fluorescently labeled nucleic acid molecule. ### Claim 15 (depends on 1) The method of claim 1 where many of the said fluorescently labeled nucleic acid molecules are attached to a solid surface and many of the said FRET reactions occur simultaneously. ### Claim 16 (depends on 1) The method of claim 1 where many of the said proteins are attached to a solid surface and many of the said FRET reactions occur simultaneously. ### Claim 17 (depends on 1) The method of claim 1 where a software program analyses the emission spectra from the said FRET reaction and correlates the said emission spectra to a the appropriate nucleotide. ### Claim 18 (depends on 1) The method of claim 1 wherein the fluorescent molecule on the said protein is a luminescent molecule. ### Claim 19 (depends on 1) The method of claim 1 where a zero-mode waveguide nanostructure arrays are used to detect the said FRET reaction. ### Claim 20 (depends on 1) The method of claim 1 where a microscope is used to detect the said FRET reaction.