DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Based on the filing receipt, the effective filing date of this application is May 19,
2021 which is the filing date of Foreign Application Number (EPO) PCT/EP2021/063310 from which the benefit of priority is claimed.
Information Disclosure Statements
The information disclosure statements (IDS) dated 01/16/2026 and 02/07/2024 have been considered by the examiner.
Status of Claims
Claims 1-19 are pending and examined herein.
Claim Interpretation
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.
This application includes one or more claim limitations that do not use the word “means,” but are nonetheless being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, because the claim limitations use a generic placeholder that is coupled with functional language without reciting sufficient structure to perform the recited function and the generic placeholder is not preceded by a structural modifier. Such claim limitations are:
The phrase “an affinity reagent configured to attach to the predetermined structure” in claim 1.
The phrase “a complementary attachment site configured to attach to the attachment” in claim 2.
Because these claim limitations are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, they are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof.
The phrase “an affinity reagent configured to attach to the predetermined structure” in claim 1 is interpreted to be “an antibody, a single-domain antibody (also known as nanobody), a combination of at least two single-domain antibodies, an aptamer, an oligonucleotide, a morpholino, a PNA complementary to a predetermined RNA, DNA target sequence, a ligand (for example a drug or a drug-like molecule), or a toxin, for example a Phalloidin a toxin that binds to an actin filament”, as disclosed on p. 3, lines 1-5 of the applicant’s specification.
The phrase “a complementary attachment site configured to attach to the attachment” in claim 2 is interpreted as equivalent to “The attachment site 108a and the complementary attachment site 108b are unique to the marker 100 and may for example be formed by oligomers such as an oligonucleotide comprising a unique sequence of nucleotides”, as disclosed on p. 15, lines 9-11 of the applicant’s specification.
If applicant does not intend to have these limitations interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitations to avoid them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitations recite sufficient structure to perform the claimed function so as to avoid them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1 and 18-19 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 1 recites, “the linker structure comprises at least one cleavage site […] between one of the fluorescent dyes and the linker structure”. It is unclear how the cleavage site can be comprised in the linker structure and also between the linker structure and the fluorescent dye. Therefore, the metes and bounds of the claim cannot be ascertained.
The claim limitations “a fluorescence activated cell sorter configured to generate the first readout and the second readout” in claim 18 and “The device according to claim 17, configured to determine at least one of: a fluorescence emission intensity, a fluorescence lifetime, a value representing a fluorescence lifetime, an emission spectrum, an excitation fingerprint, or a fluorescence anisotropy of the fluorescent dyes” in claim 19 invoke 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. However, the written description fails to disclose the corresponding structure, material, or acts for performing the entire claimed function and to clearly link the structure, material, or acts to the function. The corresponding structures for performing the entire claimed functions are entirely absent from the applicant’s specification. The specification merely recites “In a preferred embodiment, the device comprises a microscope, a plate reader, a cytometer, an imaging cytometer, or a fluorescence activated cell sorter configured to generate the first and second readouts” (p. 13, para. 4) and “In another preferred embodiment, the device is configured to determine at least one of the following: a fluorescence emission intensity, a fluorescence lifetime, a value representing a fluorescence lifetime, an emission spectrum, an excitation fingerprint, and a fluorescence anisotropy of the fluorescent dyes” (p. 13, para. 5). Therefore, the claims are indefinite and are rejected under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph.
Applicant may:
(a) Amend the claims so that the claim limitations will no longer be interpreted as a limitation under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph;
(b) Amend the written description of the specification such that it expressly recites what structures, materials, or acts perform the entire claimed functions, without introducing any new matter (35 U.S.C. 132(a)); or
(c) Amend the written description of the specification such that it clearly links the structures, materials, or acts disclosed therein to the function recited in the claim, without introducing any new matter (35 U.S.C. 132(a)).
If applicant is of the opinion that the written description of the specification already implicitly or inherently discloses the corresponding structures, materials, or acts and clearly links them to the functions so that one of ordinary skill in the art would recognize what structures, materials, or acts perform the claimed functions, applicant should clarify the record by either:
(a) Amending the written description of the specification such that it expressly recites the corresponding structures, materials, or acts for performing the claimed functions and clearly links or associates the structures, materials, or acts to the claimed functions, without introducing any new matter (35 U.S.C. 132(a)); or
(b) Stating on the record what the corresponding structures, materials, or acts, which are implicitly or inherently set forth in the written description of the specification, perform the claimed functions. For more information, see 37 CFR 1.75(d) and MPEP §§ 608.01(o) and 2181.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1 and 3-4 are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Hoang (WO 2018094385 A1, published 2018-05-24, cited in IDS filed 02/07/2024).
With respect to claim 1, Hoang teaches a marker for marking a predetermined structure within a biological sample, the marker comprising: an affinity reagent configured to attach to the predetermined structure, a linker structure attached to the affinity reagent and extending from the affinity reagent, and at least two different fluorescent dyes arranged at the linker structure, wherein the linker structure comprises at least one cleavage site between one of the fluorescent dyes and the linker structure, and wherein the linker structure can be is capable of being cut at the cleavage site by a cleaving agent in order to remove at least one of the fluorescent dyes from the marker (see, e.g., affinity reagent – sheet 1 of 54, under “FIG. 1”, under “Target binding domain”; linker structure attached to the affinity reagent – sheet 3 of 54, under “FIG. 3”, under “Barcode Domain”; two different fluorescent dye on the linker structure – sheet 3 of 54, under “FIG. 3”, under “Reporter probe”, para. [0024]: “The first and at least second detectable labels […] can have different emission spectra”; cleavage site – para. [0023]: “The primary nucleic acid molecule can comprise at least two domains, a first domain capable of binding to at least one attachment region within at least one attachment position of the barcode domain and a second domain comprising comprises a first detectable label and an at least second detectable label”, and para. [0025]: “the cleavable linker is located between the first domain and the second domain”).
With respect to claim 3, Hoang teaches wherein the linker structure is formed by oligonucleotides (see, e.g., sheet 3 of 54, under “FIG. 3”, under “Barcode Domain”).
With respect to claim 4, Hoang teaches wherein the cleavage site is an enzymatic cleavage site and the linker structure is capable of being cut at the cleavage site by an enzymatic cleaving agent (see, e.g., para. [0158]: “An example of an enzymatically cleavable linker is the insertion of uracil for cleavage by the USER™ enzyme”).
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 1-4, 8-15, and 17-19 is/are rejected under 35 U.S.C. 103 as being unpatentable over Wu (US 20170176338 A1, published 2017-06-22) in view of Mao (WO 2005051967 A2, published 2005-06-09).
Wu teaches a marker for marking a predetermined structure within a biological sample, the marker comprising: an affinity reagent configured to attach to the predetermined structure, a linker structure attached to the affinity reagent and extending from the affinity reagent, and at least two different fluorescent dyes arranged at the linker structure, as in claim 1 (see, e.g., affinity reagent – para. [0087]: “a binding agent could include a protein, an antibody, a receptor, a recognition protein, a DNA segment, an aptamer, an RNA segment, a small molecule, or some other element configured to selectively interact with and/or to be interacted with by an analyte of interest”; linker structure attached to the affinity reagent – sheet 1 of 39, under “FIG. 1”, under “120b”, and para. [0085]: “backbones could be composed of single- or double-stranded DNA […] a DNA origami structure”; two different fluorescent dye on the linker structure – sheet 1 of 39, under “FIG. 1”, under “110b”, “110c”, and “110a”, and para. [0069]: “multiple different fluorophores […] arranged in a specified pattern and/or order”, and para. [0082]: “the ordering of the types of fluorophores on each probe is different, such that detecting the colors (or other identifying information, e.g., excitation spectrum, blinking dynamics) and locations of the fluorophores of a probe can facilitate identification of the probe”).
Wu teaches wherein the affinity reagent comprises an attachment site and wherein the linker structure comprises a complementary attachment site configured to attach to the attachment site of the affinity reagent, as in claim 2 (see, e.g., sheet 1 of 39, under “FIG. 1”, under “120b” and “130b”, and para. [0085]: “The backbone (e.g., 120a, 120b, 120c) of probes as described herein could be composed of a variety of materials or substances. For example, such backbones could be composed of single- or double-stranded DNA […] the staple strands are configured to bind, e.g., via covalent bonding or some other mechanism […] Different probes (e.g., probes having different numbers, types, spacings, and/or orderings of fluorophores) could be formed by using different staple strands and/or different sequences of base DNA to which such staple strands are configured to bind”).
Wu teaches wherein the linker structure is formed by oligonucleotides, as in claim 3 (see, e.g., para. [0085]: “backbones could be composed of single- or double-stranded DNA […] a DNA origami structure”).
Wu teaches a method for analyzing a sample, comprising:
Providing at least two markers according to claim 1, wherein the arrangement of the fluorescent dyes or the cleavage site at the linker structure is unique for each of the markers;
Introducing the markers into the sample;
Directing at least one first excitation light onto the sample in order to excite fluorescent dyes of the markers;
Generating at least one first readout from fluorescence light emitted by the excited fluorescent dyes located in a readout volume of the sample, as in claim 8 (see, e.g., providing markers - sheet 1 of 39, under “FIG. 1”, under “110b”, “110c”, and “110a”, and para. [0069]: “multiple different fluorophores […] arranged in a specified pattern and/or order”, and para. [0082]: “the ordering of the types of fluorophores on each probe is different, such that detecting the colors (or other identifying information, e.g., excitation spectrum, blinking dynamics) and locations of the fluorophores of a probe can facilitate identification of the probe”; introducing markers to a sample – para. [0004]: “A variety of systems and methods are provided to microscopically image a sample (e.g., a sample of biological tissue) in such a way that the identity of probes present in the sample can be determined. Such probes include two or more fluorophores having respective spectral properties (e.g., colors, emission spectra, absorption spectra) and respective relative locations within the probe such that the identity of the probe can be determined based on detected spectral properties (e.g., colors) and relative locations of fluorophores in the sample”; directing excitation light – para. [0077]: “a target environment could be imaged, according to the methods described herein, when illuminated by light at different wavelengths, e.g., wavelengths corresponding to different excitation wavelengths of respective different fluorophores of one or more probes”, and sheet 9 of 39, under “FIGURE 8”, under “LIGHT SOURCE 801”; generating a readout from the fluorescent dyes – para. [0005]: “generating, using the light sensor, a plurality of images of the target, wherein each image corresponds to a respective one of the plurality of periods of time; (iii) determining, based on the plurality of images, locations and colors of two or more fluorophores in the target; and (iv) determining, based on the determined colors and locations of the two or more fluorophores, an identity of a probe that is located in the target and that includes the two or more fluorophores”).
Wu teaches wherein generating the first and/or readout or the second readouts readout comprises separating the emission fluorescence light emitted by the excited fluorescent dyes or by the excited remaining fluorescent dyes into detection channels,
wherein the detection channels correspond to at least one emission characteristic, and wherein the emission characteristic is one of the following: an emission spectrum, a fluorescence intensity, or a fluorescence lifetime, as in claim 9 (see, e.g., para. [0079]: “The fluorophores could be distinguishable by differing with respect to an excitation spectrum, an excitation wavelength, an emission spectrum, an emission wavelength, a Raman spectrum, a fluorescence lifetime, or some other properties that may differ between different types of fluorophore”, and para. [0072]: “Such multiple images could then be used to determine the location and color of fluorophores in an environment (e.g., via deconvolution of the images, based on information about the directions, magnitudes, or other information about the wavelength-specific separation of the light represented in each of the images)”, and para. [0090]: “A correspondence between an individual light-sensitive element of such an array to light of a range of locations of a target at a range of corresponding wavelengths could be determined (e.g., by modeling or simulation of elements of such an imaging system, by empirical testing of such a system using one or more calibration targets having respective known patterns of spectrographic properties) and such a correspondence could be used to determine spectrographic information (e.g., a color) for one or more locations of an imaged target based on a number of images of the target taken while operating a chromatically dispersive element according to a respective number of different directions and/or magnitudes of spectral dispersion of the received light (e.g., via a process of deconvolution)”).
Wu teaches wherein each marker is configured such that each fluorescent dye corresponds to one detection channel of the first readout or the second readout, respectively, as in claim 10 (see, e.g., para. [0079]: “The fluorophores could be distinguishable by differing with respect to an excitation spectrum, an excitation wavelength, an emission spectrum, an emission wavelength, a Raman spectrum, a fluorescence lifetime, or some other properties that may differ between different types of fluorophore”, and para. [0072]: “Such multiple images could then be used to determine the location and color of fluorophores in an environment (e.g., via deconvolution of the images, based on information about the directions, magnitudes, or other information about the wavelength-specific separation of the light represented in each of the images)”, and para. [0090]: “A correspondence between an individual light-sensitive element of such an array to light of a range of locations of a target at a range of corresponding wavelengths could be determined (e.g., by modeling or simulation of elements of such an imaging system, by empirical testing of such a system using one or more calibration targets having respective known patterns of spectrographic properties) and such a correspondence could be used to determine spectrographic information (e.g., a color) for one or more locations of an imaged target based on a number of images of the target taken while operating a chromatically dispersive element according to a respective number of different directions and/or magnitudes of spectral dispersion of the received light (e.g., via a process of deconvolution)”).
Wu teaches wherein the fluorescent dyes of the markers are divided into sets of fluorescent dyes;
wherein the fluorescent dyes in a same set are capable of being excited by a same wavelength or by a same wavelength spectrum;
wherein at least one of the first excitation light and the second excitation light is directed at the sample in order to excite the fluorescent dyes of the respective set;
wherein at least one of the first readout and the second readout is generated from the fluorescence light emitted by the respective set of fluorescent dyes located in the readout volume of the sample, as in claim 11 (see, e.g., para. [0084]: “Quantum dots may be preferred, due to resistance to photobleaching and broad excitation spectra, such that multiple different quantum dots (e.g., quantum dots that emit light at respective different wavelengths in response to excitation) can be excited by illumination at a single wavelength”).
Wu teaches wherein the first excitation light and the second excitation light are directed onto the sample in a sequence temporally following each other, as in claim 12 (see, e.g., para. [0180]: “The method 1000 includes controlling a spatial light modulator (SLM) such that at least one of the gradient or magnitude of a controllable gradient of the refractive index of a refractive layer of the SLM are different during each of a plurality of period of time”).
Wu teaches wherein the first readout and/or the second readout comprises at least one image of the readout volume, or a readout signal data stream of the readout volume, or a readout image data stream of the readout volume, as in claim 14 (see, e.g., sheet 11 of 39, under “FIG. 11”).
Wu teaches further comprising capturing a hyperspectral image of the sample in order to generate the first readout and/or the second readout, as in claim 15 (see, e.g., para. [0096]: “such information could be determined for a plurality of regions across the target 200a allowing, e.g., hyperspectral imaging of the target”).
Wu teaches a device for analyzing a biological sample being adapted to carry out the method according to claim 8, as in claim 17 (see, e.g., para. [0092]: “The target 200a could be imaged by an imaging system as described elsewhere herein”, and sheet 8 of 39, under “FIGURE 8”).
Wu teaches comprising a microscope, a plate reader, a cytometer, an imaging cytometer, or a fluorescence activated cell sorter configured to generate the first readout and the second readouts readout, as in claim 18 (see, e.g., para. [0115]: “An SLM (e.g., 410) as described herein could be configured and operated as part of a variety of different imaging systems (e.g., bright-field microscopes, 4-pi microscopes, confocal microscopes, fluorescence microscopes, structured illumination microscopes, dark field microscopes, phase contrast microscopes) to provide controlled spectral dispersion of light for a variety of applications”).
Wu teaches the device according to claim 17, configured to determine an emission spectrum, as in claim 19 (see, e.g., para. [0088]: “Detecting the color of a fluorophore could include determining an emission spectrum, a characteristic wavelength, or some other characteristic(s) of the spectral content of light emitted from a fluorophore”).
Wu fails to teach a cleavage site arranged between two fluorescent dyes capable of being cut at the cleavage site by a cleaving agent in order to remove at least one of the fluorescent dyes from the marker, as in claim 1. Wu fails to teach introducing a cleaving agent in order to remove at least one fluorescent dye from a marker before directing a second excitation light and generating a second readout from the remaining fluorescent dyes, as in claim 8. Wu fails to teach the removed fluorescent dye is washed out of the sample before the second excitation light is directed into the sample, as in claim 13.
However, Mao teaches a marker with an affinity reagent and linker comprising at least two dyes with a cleavage site between the dyes, wherein the cleavage site is cleaved by a cleavage agent, specifically an enzymatic cleavage agent, in order to remove at least one dye, as in claims 1 and 4 (see, e.g., p. 6, lines 13-16: “Various embodiments are suitable for use with PCR to detect biomolecules other than nucleic acids by using an oligonucleotide-antibody conjugate wherein the antibody is specific for the biomolecules to be detected”, and p. 4, lines 8-10: “One embodiment includes oligonucleotides labeled with at least two photometric molecules”, and p. 27, lines 13-21: “In the presence of specific reagents or enzymes with 5'exonuclease activity the dye molecules are subsequently cleaved from the oligonucleotide [..] Maximal fluorescent increase is dependent on the cleavability of the phosphate backbone linking each neighboring dye pair by the 5'- exonuclease or an equivalent nuclease”, and p. 9, lines 16-17: “the spectra of three probes labeled with a
combination of FAM/FAM, FAM/CR110 and CR110/CR110 dye pairs”).
Mao teaches introducing a cleaving agent in order to remove at least one dye from a marker in a sample, as in claim 8 (see, e.g., p. 27, lines 13-21: “In the presence of specific reagents or enzymes with 5'exonuclease activity the dye molecules are subsequently cleaved from the oligonucleotide [..] Maximal fluorescent increase is dependent on the cleavability of the phosphate backbone linking each neighboring dye pair by the 5'- exonuclease or an equivalent nuclease”, and p. 9, lines 16-17: “the spectra of three probes labeled with a
combination of FAM/FAM, FAM/CR110 and CR110/CR110 dye pairs”).
Mao teaches the dye is removed, as in claim 13 (see, e.g., p. 27, lines 16-17: “Cleavage results in permanent separation of the dye molecules”).
Wu and Mao are analogous to the field of the claimed invention because they are both in the field of biomolecular probes. One of ordinary skill in the art before the effective filing date of the application would have found it obvious to use the cleavage site and cleaving agent of Mao in the method and device of Wu. An artisan would have been motivated to do so because Mao discloses that “Cleavage results in permanent separation of the dye molecules resulting in a large increase in fluorescence. Maximal fluorescent increase is dependent on the cleavability of the phosphate backbone linking each neighboring dye pair by the 5'exonuclease
or an equivalent nuclease” (see, p. 27, lines 16-21). An artisan would have had a reasonable expectation of success based on the given disclosures.
Claim 5 is rejected under 35 U.S.C. 103 as being unpatentable over Wu (cited above) and Mao (cited above), as applied to claims 1-4, 8-15, and 17-19 above, and further in view of Gupta (WO 2019152391 A1, published 2019-08-08).
Wu and Mao fail to teach the enzymatic cleavage site is a target site of a restriction enzyme, as in claim 5.
However, Gupta teaches the enzymatic cleavage site is a target site of a restriction enzyme, as in claim 5 (see, e.g., para. [0069]: “removal of the set of first tagging agents/ labels and additional sets of tagging agents may be accomplished using enzymes, such as exonucleases, endonucleases and restriction enzymes”).
Wu, Mao, and Gupta are analogous to the field of the claimed invention because they are all in the field of molecular probes. One of ordinary skill in the art before the effective filing date of the application would have found it obvious to substitute the enzymatic cleavage site of Gupta into the method of Wu as modified by Mao. An artisan would have found it obvious to simply substitute one enzymatic cleaving agent for another because they are functionally equivalent, especially because Gupta lists the enzymatic cleavage agent of Wu as modified by Mao in a list of enzymes with restriction enzymes. An artisan would have had a reasonable expectation of success based on the given disclosures.
Claim 6 is rejected under 35 U.S.C. 103 as being unpatentable over Wu (cited above) and Mao (cited above), as applied to claims 1-4, 8-15, and 17-19 above, and further in view of Beechem (US 20200040382 A1, published 2020-02-06).
Wu and Mao fail to teach the cleavage site is a photocleavage site, and the linker structure is capable of being cut at the cleavage site by photolysis, as in claim 6.
However, Beechem teaches the cleavage site is a photocleavage site, and the linker structure is capable of being cut at the cleavage site by photolysis, as in claim 6 (see, e.g., para. [0007]: “The cleavable linker may be photo-cleavable, which is cleaved by light provided by a suitable coherent light source (e.g., a laser and a UV light source) or a suitable incoherent light source (e.g., an arc-lamp and a light-emitting diode (LED))”).
Wu, Mao, and Beechem are analogous to the field of the claimed invention because they are all in the field of biomolecular probes. One of ordinary skill in the art before the effective filing date of the application would have found it obvious to substitute the cleavable site of Wu as modified by Mao with the photocleavable site of Beechem. An artisan would have been motivated to do so because Beechem discloses, “For probes including photo-cleavable linkers, the solid support (e.g., microscope slide) is placed in a microscope that is capable of providing excitation light at a wavelength capable of cleaving the photo-cleavable linker. A first region-of-interest (red line in panel B in FIG. 10 and ROIi in FIGS. 11 and 12) is excited with the light, thereby cleaving the photo-cleavable linker and releasing the signal oligonucleotides. […] By directing excitation light only to ROIi, signal oligonucleotides are only released from probes within ROIi and not from probes located outside of ROIi, which retain their signal oligonucleotides. Thus, signal oligonucleotides are collected only for probes that are bound to targets within ROIi, thereby permitting detection of the identities and quantities of the targets (proteins and/or nucleic acids) located within ROIi” (see, para. [0127]). An artisan would have understood the benefits of detecting the identities and quantities of targets within a specific region of interest. An artisan would have had a reasonable expectation of success based on the given disclosures.
Claim 7 is rejected under 35 U.S.C. 103 as being unpatentable over Wu (cited above) and Mao (cited above), as applied to claims 1-4, 8-15, and 17-19 above, and further in view of Acar (US 20180066031 A1, published 2018-03-08).
Wu and Mao fail to teach the enzymatic cleavage site is a proteolytic cleavage site capable of being cut by a protease, as in claim 7.
Acar teaches the enzymatic cleavage site is a proteolytic cleavage site capable of being cut by a protease, as in claim 7 (see, e.g., para. [0009]: “the peptide amphiphiles described herein comprise an enzymatically-cleavable linker flanked (e.g., one fluorophore on each side) by detectably-distinct fluorophores”, and para. [0006]: “an enzyme (e.g., cathepsin-B) cleavable linker”).
Wu, Mao, and Acar are analogous to the field of the claimed invention because they are all in the field of biomolecular probes. One of ordinary skill in the art before the effective filing date of the application would have found it obvious to substitute the cleavage site of Wu as modified by Mao with the cleavage site of Acar. An artisan would have found it obvious to simply substitute one cleaving site for another because they are functionally equivalent. An artisan would have had a reasonable expectation of success based on the given disclosures.
Claim 16 is rejected under 35 U.S.C. 103 as being unpatentable over Wu (cited above) and Mao (cited above), as applied to claims 1-4, 8-15, and 17-19 above, and further in view of the ProlongTM Gold and Diamond Antifade Mountants product information sheet (from Invitrogen, Pub. No. MAN0002469, Rev. F.0, published 2020-04-16).
Wu and Mao fail to teach stabilizing a fluorescence lifetime of at least one fluorescent dye by placing the dye in a shielded environment by co-crystallizing, as in claim 16.
ProlongTM teaches stabilizing a fluorescence lifetime of at least one fluorescent dye by placing the dye in a shielded environment by polymer-matrix embedding, as in claim 16 (see, e.g., p. 1, under “Product Description”: “ProLong™ Gold and Diamond Antifade Mountants are hard (curing) mountants that achieve an optimal refractive index of 1.46 after curing and can be used for long-term storage of slides. ProLong™ Diamond Mountant causes little or no quenching of fluorescent signal after mounting and is the ideal antifade solution for Alexa Fluor™ dyes, traditional dyes such as FITC and TRITC, and fluorescent proteins such as GFP and mCherry”, and p. 2, under “Fig. 1”, under panel “A”).
Wu, Mao, and ProlongTM are analogous to the field of the claimed invention because they are all in the field of fluorescent imaging. One of ordinary skill in the art before the effective filing date of the application would have found it obvious to add the shielded environment of ProlongTM to the fluorophores of Wu as modified by Mao. An artisan would have been motivated to do so because ProlongTM discloses, “ProLong™ Diamond Mountant causes little or no quenching of fluorescent signal after mounting and is the ideal antifade solution for Alexa Fluor™ dyes, traditional dyes such as FITC and TRITC, and fluorescent proteins such as GFP and mCherry” (see p. 1, under “Product Description). An artisan would have had a reasonable expectation of success based on the given disclosures.
Conclusion
No claims are allowed.
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/MICHAEL CAMERON SVEIVEN/ Examiner, Art Unit 1678
/GREGORY S EMCH/ Supervisory Patent Examiner, Art Unit 1678
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