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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 04/02/2026 has been entered.
Response to Amendment
The Amendment filed 04/02/2026 has been entered. Claims 1-8, 10, and 12-21 remain pending in the application. Claims 1-8 and 16-17 are withdrawn. Applicant’s amendments to the claims have overcome each and every objection previously set forth in the Final Office Action mailed 11/26/2025. New grounds of rejections necessitated by amendments are discussed below.
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 10, 13, 15, and 19-20 are rejected under 35 U.S.C. 103 as being unpatentable over Hoffmann (EP2618130A1; cited in the IDS filed 07/05/2022) and Bastiaens et al. (US 20150064713 A1) and Koike et al. (US 20090185181 A1).
Regarding claim 10, Hoffmann teaches a method of detecting molecular interactions associated with target samples (abstract teaches a method of detection of binding affinities, i.e. molecular interactions, of target samples), comprising:
- providing a biomolecular detection device for analyzing a target sample (abstract and Figs. 1-3 teach a device for detection of binding affinities of target samples is provided; paragraph [0002] teaches detection of molecules, proteins, DNA, i.e. biomolecules), the device comprising
an evanescent illuminator (Fig. 1, coherent light 1, grating 4, planar waveguide 2; paragraph [0027], “evanescent field”) with an optical coupling unit (Fig. 1, grating 4) configured for generating an evanescent field from coherent light (paragraph [0027]) with a predefined wavelength on a first surface of the evanescent illuminator (paragraph [0027]; Fig. 1, outer surface 5),
the first surface of the evanescent illuminator comprising a template nanopattern (Fig. 1, predetermined lines 9; paragraph [0008] teaches the lines are distanced in a range of 100 – 1000nm, therefore is interpreted as a template nanopattern), containing a coherent arrangement of a plurality of predetermined lines (Fig. 1, teaches predetermined lines 9 in a coherent arrangement; paragraph [0008] teaches the lines are distanced in a range of 100 – 1000nm) along which membrane recognition elements for a protein are arranged (paragraphs [0007], [0027] teach binding sites to which target samples can bind are arranged on the lines; paragraphs [0008],[0030] teach binding sites can include capture molecules for binding of molecules, proteins, DNA, therefore is are recognition element for a protein),
wherein the membrane recognition elements are configured to bind protein for forming a transmembrane nanopattern based on the template nanopattern of the evanescent illuminator (paragraphs [0008],[0030] teaches the binding sites comprise capture molecules, such as proteins, to bind target samples along the lines, thus is for forming a transmembrane nanopattern based on the template nanopattern of the evanescent illuminator), such that light of the evanescent field is scattered by the protein bound to the membrane recognition elements (paragraph [0030] teaches light in the evanescent field is scattered by the target samples bound to the capture molecules of the binding sites), and
wherein the predetermined lines are arranged such that light scattered by the target samples bound to the membrane recognition elements constructively interferes at a predefined detection site with a difference in optical path length that is an integer multiple of the predefined wavelength of the coherent light (abstract and paragraphs [0007],[0031],[0036] teach scattered light from target samples bound to the binding sites constructively interferes at a predetermined detection location with a difference in optical path length which is an integer multiple of the predetermined wavelength);
- applying a target sample to the membrane recognition elements (paragraph [0025] and Fig. 1 shows target samples 8 are applied to the capture molecules 7);
- generating a beam of coherent light at a predefined beam generation location relative to the plurality of predetermined lines (Figs. 1-2 and paragraph [0025] teaches coupling coherent light into the planar waveguide such that the coherent light propagates along the waveguide, therefore a beam of coherent light is generated at a location relative to the lines), the beam of coherent light having a predefined wavelength (paragraph [0025]) and being incident on the membrane recognition elements (paragraph [0027] teaches the coherent light propagates along the waveguide and is scattered by the target samples bound to the binding sites within the measurement zone, therefore the coherent light is incident on the capture molecules of the binding sides) in a manner that diffracted portions of the incident beam of coherent light constructively interfere at the predefined detection site relative to the plurality of predetermined lines (abstract and paragraph [0007],[0024],[0025],[0036] teaches the scattered light constructively interferes at predetermined detection locations) with a difference in optical path length that is an integer multiple of the predefined wavelength of the coherent light (abstract and paragraph [0007],[0024],[0025] teach scattered light constructively interferes at a predetermined detection location with a difference in optical path length which is an integer multiple of the predetermined wavelength) to provide a signal representative of the membrane recognition elements with the target sample bound thereto at the predefined detection site (paragraph [0025] teaches detecting light at the predetermined location is by target samples bound to binding sites, therefore the light provides a signal representative of the capture molecules bound to target samples at predefined locations); and
- measuring the signal representative for the membrane recognition elements with the target sample bound thereto (paragraph [0025] teaches detecting light, i.e. measuring the signal, at the predetermined location is by target samples bound to binding sites).
While Hoffmann teaches biosensors for detection of binding affinities or processes of different target samples like molecules, proteins or DNA (paragraph [0002]), Hoffmann fails to teach: the method of detecting molecular interactions associated with cells; biomolecular detection device for analyzing a cell; wherein the membrane recognition elements are configured to bind the binder structure of the transmembrane protein for forming a transmembrane nanopattern within the cell based on the template nanopattern of the evanescent illuminator; the plurality of predetermined lines along which membrane recognition elements for a binder structure of a transmembrane protein of the cell are arranged; wherein the membrane recognition elements are configured to bind the binder structure of the transmembrane protein for forming a transmembrane nanopattern within the cell based on the template nanopattern of the evanescent illuminator, such that light of the evanescent field is scattered by the cell bound to the membrane recognition elements; wherein the predetermined lines are arranged such that light scattered by the cell bound to the membrane recognition elements constructively interferes at a predefined detection site with a difference in optical path length that is an integer multiple of the predefined wavelength of the coherent light;
- applying the cell to the membrane recognition elements, wherein the cell comprises a membrane and at least one transmembrane protein with an extracellular or extravesicular binder structure, optionally where at least one transmembrane protein is laterally diffused along the membrane;
- aligning the at least one transmembrane protein of the cell according to the template nanopattern of the first surface of the evanescent illuminator, such that a transmembrane nanopattern is formed in the membrane of the cell, wherein the transmembrane nanopattern corresponds at least partially to the template nanopattern of the first surface of the evanescent illuminator;
- the beam of coherent light being incident on the membrane recognition elements with the bound transmembrane protein in a manner that diffracted portions of the incident beam of coherent light constructively interfere at the predefined detection site relative to the plurality of predetermined lines with a difference in optical path length that is an integer multiple of the predefined wavelength of the coherent light to provide a signal representative of the membrane recognition elements with the transmembrane protein of the cell bound thereto at the predefined detection site; and
- measuring the signal representative for the membrane recognition elements with the transmembrane protein of the cell bound thereto, wherein the measured signal is dependent on the mass of the transmembrane protein and of the mass of any binding partner bound to the transmembrane protein.
Bastiaens teaches methods and systems for determining a reaction between transmembrane receptor and an intracellular interaction partner thereof within a cell (abstract), wherein a transmembrane receptor designates a protein capable of spanning a membrane of a cell (paragraphs [0022]-[0023]). Bastiaens teaches known challenges of studying protein reactions of cells, such as studying multiple intracellular molecular reactions in parallel in an individual living cell (paragraph [0002]), wherein the solution to this challenge is achieved by the methods and systems as described (paragraph [0002]). Bastiaens teaches membrane recognition elements configured to bind a binder structure of the transmembrane protein for forming a transmembrane nanopattern within the cell based on a template pattern (Figs. 1B, 2, 5,7 teaches antibody-DNA complexes, i.e. membrane recognition elements, binding to a binder structure of transmembrane proteins that forms a transmembrane nanopattern within the cell based on a template pattern of the antibody-DNA complexes). Bastiaens teaches in the case of objective-based TIRF detection of chimeric transmembrane receptor recruitment and reaction, preferably interaction, a material of suitable refractive index and thickness must be selected to allow formation of the evanescent wave (paragraph [0051]), and interaction with probes can be monitored via tracking and spectral analysis of nanostructures via evanescent wave (paragraph [0170]). Bastiaens teaches the method of determining reaction between a transmembrane receptor and an intracellular interaction partner thereof within a cell includes: applying a cell to the membrane recognition elements (Fig. 1 and paragraph [0003] teaches providing a cell and contacting the cell with compounds, i.e. membrane recognition elements, bound to a surface), wherein the cell comprises a membrane (Fig. 2 shows a plasma membrane of a cell) and at least one transmembrane protein with an extracellular or extravesicular binder structure (Figs. 1-3 and 5 shows at least one transmembrane protein with an extracellular binder structure, which binds to the membrane recognition element on a surface of a support) and where at least one transmembrane protein is laterally diffused along the membrane (Figs. 1-3 and 5 shows at least one transmembrane protein laterally diffused along the plasma membrane of the cell); and aligning the at least one transmembrane protein of the cell according to the template pattern of a first surface of the support (Fig. 1b and paragraph [0003] teaches contacting the cell with at least two different extracellular compounds bound to a surface of a support, which is interpreted as alignment of the transmembrane protein of the cell with a pattern of the extracellular components in a pattern on a surface of the support), such that a transmembrane pattern is formed in the membrane of the cell (Fig. 1b shows a pattern of the transmembrane proteins in the membrane of the cell), wherein the transmembrane pattern corresponds at least partially to the template pattern of the first surface of the support (Fig. 1b shows the transmembrane proteins correspond to the pattern of the antibody-DNA complexes of the support). Bastiaens teaches rearranging and/or exchanging extracellular compounds in order to generate a surface to which the cell can be contacted (paragraph [0056]). Bastiaens teaches the sensor is a sensitive biological element, such as cell receptors, and can include optical detectors (paragraph [0148]). Bastiaens teaches detecting change of a label or energy transfer, which is indicative of a reaction (paragraph [0003]). Bastiaens teaches a correlation of the detected signal to a chimeric transmembrane receptor is unambiguously possible in connection with the knowledge of the position or coordinate of an area comprising a specific extracellular compound on a support (paragraph [0042]). Bastiaens teaches the invention provides advantages, such as identifying novel protein interactions, the ability to dynamically manipulate the cellular context during the experiment, the identification of new protein interactions in individual, living, intact cells, such dynamic, transient interactions, which might be elusive in other, standard methods (paragraph [0069]). Bastiaens the invention allows for analysis of the behavior of cells (paragraph [0070]). Bastiaens teaches micropatterns can be scaled down to nanosized dimensions (paragraph [0186]).
Since Bastiaens teaches determining a reaction between a protein bound to a membrane recognition elements on a surface and nanosized patterns, similar to Hoffmann, and Bastiaens teaches a known problem in the art of studying protein reactions in living cells (paragraph [0002]), it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Hoffmann to incorporate Bastiaens’s teachings of membrane recognition elements configured to bind a binder structure of the transmembrane protein for forming a transmembrane nanopattern within the cell based on a template pattern (Figs. 1B, 2, 5,7), interaction with probes can be monitored via tracking and spectral analysis of nanostructures via evanescent wave (paragraph [0170]), rearranging and/or exchanging extracellular compounds in order to generate a surface to which the cell can be contacted (paragraph [0056]), and applying a cell to membrane recognition elements and aligning the transmembrane proteins of a cell (Figs. 1-2 and paragraph [0003]) to provide: the method of detecting molecular interactions associated with cells; biomolecular detection device for analyzing a cell; wherein the membrane recognition elements are configured to bind the binder structure of the transmembrane protein for forming a transmembrane nanopattern within the cell based on the template nanopattern of the evanescent illuminator; the plurality of predetermined lines along which membrane recognition elements for a binder structure of a transmembrane protein of the cell are arranged; wherein the membrane recognition elements are configured to bind the binder structure of the transmembrane protein for forming a transmembrane nanopattern within the cell based on the template nanopattern of the evanescent illuminator, such that light of the evanescent field is scattered by the cell bound to the membrane recognition elements; wherein the predetermined lines are arranged such that light scattered by the cell bound to the membrane recognition elements constructively interferes at a predefined detection site with a difference in optical path length that is an integer multiple of the predefined wavelength of the coherent light; - applying the cell to the membrane recognition elements, wherein the cell comprises a membrane and at least one transmembrane protein with an extracellular or extravesicular binder structure, optionally where at least one transmembrane protein is laterally diffused along the membrane; - aligning the at least one transmembrane protein of the cell according to the template nanopattern of the first surface of the evanescent illuminator, such that a transmembrane nanopattern is formed in the membrane of the cell, wherein the transmembrane nanopattern corresponds at least partially to the template nanopattern of the first surface of the evanescent illuminator;- the beam of coherent light being incident on the membrane recognition elements with the bound transmembrane protein in a manner that diffracted portions of the incident beam of coherent light constructively interfere at the predefined detection site relative to the plurality of predetermined lines with a difference in optical path length that is an integer multiple of the predefined wavelength of the coherent light to provide a signal representative of the membrane recognition elements with the transmembrane protein of the cell bound thereto at the predefined detection site; and - measuring the signal representative for the membrane recognition elements with the transmembrane protein of the cell bound thereto. Doing so would have a reasonable expectation of successfully identifying novel protein interactions of cells, the ability to dynamically manipulate the cellular context during the experiment, the identification of new protein interactions in individual, living, intact cells, such dynamic, transient interactions, which might be elusive in other, standard methods (Bastiaens, paragraph [0069]), and thus allow for analysis of the behavior of cells (Bastiaens, paragraph [0070]).
Furthermore, the claimed limitations are obvious because all of the claimed elements were known in the prior art and one skilled in the art could have combined the elements (i.e. the claimed method of detecting molecular interactions with cells and binding of a binder structure of a transmembrane protein of the cell to the membrane recognition elements) by known methods with no change in their respective functions (i.e. detection of molecular interactions), and the combinations yielded nothing more than predictable results (i.e. providing the method of detecting molecular interactions with cells and binding of a binder structure of a transmembrane protein of the cell to the membrane recognition elements as claimed and the methods of “applying the cell…”, “aligning…”, “generating a beam…”, and “measuring” would yield nothing more than the obvious and predictable result of enabling analysis of the behavior of cells). See MPEP 2143(A).
Modified Hoffman fails to teach: wherein the measured signal is dependent on the mass of the transmembrane protein and of the mass of any binding partner bound to the transmembrane protein.
Hoffman teaches detecting of binding affinities using evanescent field (paragraph [0007]) and signal is dependent on target molecules bound to capture molecules at the detection location (paragraph [0015]).
Bastiaens teaches detection includes recording signals generated by labels and shape and size of the labels (paragraph [0060]). Bastiaens teaches quantification of interaction can be performed by measuring signal intensity generated by labels (paragraph [0105]). Bastiaens interaction with probes can be monitored via tracking and spectral analysis of nanostructures via evanescent wave (paragraph [0170]).
Koike teaches a method for measuring a surface plasmon resonance for easy detection of proteins and determination whether a peptide is phosphorylated or not in biological materials (abstract). Koike teaches SPR is known to generate an evanescent wave on a total reflection surface (paragraph [0013]). Koike teaches known measurement principles of SPR measuring includes reflected light intensity is dependent on variation of mass of a compound bound, which is therefore measured as measurement data from a strength of reflected light (paragraph [0047]).
Since Koike teaches measurement of bound compounds based on evanescence and total reflection, similar to modified Hoffmann, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of measuring of modified Hoffmann to incorporate Bastiaens’ teachings of quantifying interaction based on signal intensity via spectral analysis of evanescent wave (paragraphs [0105],[0170]) and Koike’s teachings of known methods of measuring changes in light intensity that is dependent on mass of a compound bound based on evanescence wave (paragraphs [0013],[0047]) to provide: wherein the measured signal is dependent on the mass of the transmembrane protein and of the mass of any binding partner bound to the transmembrane protein. Doing so would have a reasonable expectation of successfully improving characterization and analysis of the transmembrane protein and any binding partner based on the measured signal.
Regarding claim 13, Hoffmann further teaches wherein the target sample is specific to an capture molecule being arranged along the predefined lines of the evanescent illuminator of the biomolecular detection device (paragraph [0030] teaches the binding sites comprises capture molecules are capable of binding the target samples along the predetermined lines, therefore the capture molecules are specific to the target samples).
Modified Hoffmann fails to teach: wherein the binder structure of the transmembrane protein is specific to an antibody being arranged along the predefined lines of the evanescent illuminator of the biomolecular detection device.
Bastiaens teaches membrane recognition elements configured to bind a binder structure of the transmembrane protein for forming a transmembrane nanopattern within the cell based on a template pattern (Figs. 1B, 2, 5,7 teaches antibody-DNA complexes, i.e. membrane recognition elements, binding to a binder structure of transmembrane proteins that forms a transmembrane nanopattern within the cell based on a template pattern of the antibody-DNA complexes). Bastiaens teaches binding structures of transmembrane proteins are specific to antibodies arranged on a support (Fig. 1B). Bastiaens teaches the invention provides advantages, such as identifying novel protein interactions, the ability to dynamically manipulate the cellular context during the experiment, the identification of new protein interactions in individual, living, intact cells, such dynamic, transient interactions, which might be elusive in other, standard methods (paragraph [0069]). Bastiaens the invention allows for analysis of the behavior of cells (paragraph [0070]).
Since Bastiaens teaches determining a reaction between a protein bound to a membrane recognition elements on a surface and nanosized patterns, similar to Hoffmann, and Bastiaens teaches a known problem in the art of studying protein reactions in living cells (paragraph [0002]), it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of modified Hoffmann to incorporate Bastiaens’s teachings of membrane recognition elements, such as antibodies, configured to bind a binder structure of the transmembrane protein (Figs. 1B, 2, 5,7) to provide: wherein the binder structure of the transmembrane protein is specific to an antibody being arranged along the predefined lines of the evanescent illuminator of the biomolecular detection device. Doing so would have a reasonable expectation of successfully identifying novel protein interactions of cells, the ability to dynamically manipulate the cellular context during the experiment, the identification of new protein interactions in individual, living, intact cells, such dynamic, transient interactions, which might be elusive in other, standard methods (Bastiaens, paragraph [0069]), and thus allow for analysis of the behavior of cells (Bastiaens, paragraph [0070]).
Regarding claim 15, modified Hoffmann fails to teach: wherein additionally, optionally simultaneously (interpreted as not required due to the term “optionally”), a fluorescent and/or bioluminescent signal is recorded.
Bastiaens teaches that using corresponding probes as first and second labels additionally provides the option to assess whether the reaction (being preferably a binding) between potential intracellular interaction, preferably binding partner and chimeric transmembrane receptor is direct or indirect on the basis of a comparison of fluorescent intensities in view of suitable control samples; and to this end, modifications of FRET such as BRET (bioluminescence resonance energy transfer) are also envisaged (paragraph [0042]). Bastiaens teaches one can relatively quantify the interactions taking place when comparing e.g. fluorescence intensities of the signal(s) detected at different measurement points, different points being different locations in space and/or time (paragraph [0062]). Bastiaens teaches identifying fluorescent properties allows a multiplexed biosensor (paragraph [0067]). Bastiaens teaches the use of fluorescent proteins can used to identify new, i.e. unknown protein reactions, preferably interactions (paragraph [0068]). Bastiaens teaches the invention provides advantages, such as identifying novel protein interactions, the ability to dynamically manipulate the cellular context during the experiment, the identification of new protein interactions in individual, living, intact cells, such dynamic, transient interactions, which might be elusive in other, standard methods (paragraph [0069]). Bastiaens the invention allows for analysis of the behavior of cells (paragraph [0070]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of modified Hoffmann to incorporate the teachings of measuring fluorescence of Bastiaens (paragraphs [0042],[0062],[0067]-[0068]) to provide: wherein additionally, optionally simultaneously, a fluorescent and/or bioluminescent signal is recorded. Doing so would have a reasonable expectation of successfully improving multiplexing of the sensor and detection of interactions at different space and time (Bastiaens, paragraphs [0062],[0067]), identifying novel protein interactions of cells, the ability to dynamically manipulate the cellular context during the experiment, the identification of new protein interactions in individual, living, intact cells, such dynamic, transient interactions, which might be elusive in other, standard methods (Bastiaens, paragraphs [0068]-[0069]), and thus allow for improved analysis of the behavior of cells (Bastiaens, paragraph [0070]).
Regarding claim 19, modified Hoffmann fails to teach: wherein membrane recognition elements of multiple different predetermined lines bind to the same cell.
Hoffmann teaches binding sites comprise capture molecules that bind target samples along the predetermined lines, i.e. multiple different predetermined lines (paragraph [0030]).
Bastiaens teaches membrane recognition elements configured to bind a binder structure of the transmembrane protein for forming a transmembrane nanopattern within the cell based on a template pattern (Figs. 1B, 2, 5,7 teaches antibody-DNA complexes, i.e. membrane recognition elements, binding to a binder structure of transmembrane proteins that forms a transmembrane nanopattern within the cell based on a template pattern of the antibody-DNA complexes). Bastiaens teaches a correlation of the detected signal to a chimeric transmembrane receptor is unambiguously possible in connection with the knowledge of the position or coordinate of an area comprising a specific extracellular compound on a support (paragraph [0042]). Bastiaens teaches the invention provides advantages, such as identifying novel protein interactions, the ability to dynamically manipulate the cellular context during the experiment, the identification of new protein interactions in individual, living, intact cells, such dynamic, transient interactions, which might be elusive in other, standard methods (paragraph [0069]). Bastiaens the invention allows for analysis of the behavior of cells (paragraph [0070]). Bastiaens teaches micropatterns can be scaled down to nanosized dimensions (paragraph [0186]). Bastiaens teaches different membrane recognition elements bind to the same cell (Fig. 1B).
Since Bastiaens teaches determining a reaction between a protein bound to a membrane recognition elements on a surface and nanosized patterns, similar to Hoffmann, and Bastiaens teaches a known problem in the art of studying protein reactions in living cells (paragraph [0002]), it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of modified Hoffmann to incorporate Bastiaens’s teachings of membrane recognition elements configured to bind a binder structure of the transmembrane protein for forming a transmembrane nanopattern within the cell based on a template pattern, and the membrane recognition elements bind to the same cell (Figs. 1B, 2, 5,7) to provide: wherein membrane recognition elements of multiple different predetermined lines bind to the same cell. Doing so would have a reasonable expectation of successfully identifying novel protein interactions of cells, the ability to dynamically manipulate the cellular context during the experiment, the identification of new protein interactions in individual, living, intact cells, such dynamic, transient interactions, which might be elusive in other, standard methods (Bastiaens, paragraph [0069]), and thus allow for analysis of the behavior of cells (Bastiaens, paragraph [0070]).
Regarding claim 20, Hoffmann further teaches wherein a distance between two directly adjacent predetermined line is between 2 to 100 times smaller than the cell (paragraph [0008] teaches the distance between adjacent predetermine lines range from 100-1000 nm, which is interpreted as between 2 to 100 times smaller than a cell; note that the instant application, specification, page 10, lines 16-19, describes the distance between adjacent lines to be less than 1.5 um, therefore the BRI of a distance “2 to 100 times smaller than the cell” includes distances less than 1.5 um; note that the specific distance and the size of the cell is not claimed).
Claims 12 and 18 are rejected under 35 U.S.C. 103 as being unpatentable over Hoffmann in view of Bastiaens and Koike as applied to claim 10 above, and further in view of Fang et al. (US 20090142790 A1).
Regarding claim 12, modified Hoffmann fails to explicitly teach: wherein a cell is applied to the membrane recognition elements and wherein before generating the beam of coherent light the cell is modified such that only parts of the cell membrane remain on the biomolecular detection device.
Bastiaens teaches a cell is applied to the membrane recognition elements (Figs. 1B, 2, 5,7 teaches antibody-DNA complexes, i.e. membrane recognition elements, binding to a binder structure of transmembrane proteins that forms a transmembrane nanopattern within the cell based on a template pattern of the antibody-DNA complexes). Bastiaens teaches only parts of the cell membrane remain on a biomolecular detection device (Fig. 1B shows the cell membrane remaining on a device). Bastiaens teaches rearranging and/or exchanging extracellular compounds in order to generate a surface to which the cell can be contacted (paragraph [0056]). Bastiaens teaches the invention provides advantages, such as identifying novel protein interactions, the ability to dynamically manipulate the cellular context during the experiment, the identification of new protein interactions in individual, living, intact cells, such dynamic, transient interactions, which might be elusive in other, standard methods (paragraph [0069]). Bastiaens the invention allows for analysis of the behavior of cells (paragraph [0070]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of modified Hoffmann to incorporate the teachings of applying a cell to membrane recognition elements of Bastiaens (Figs. 1B, 2, 5,7) and the teachings of the cell membrane remaining on a biomolecular detection device of Bastiaens (Fig. 1B) to provide: wherein a cell is applied to the membrane recognition elements and wherein the cell is modified such that only parts of the cell membrane remain on the biomolecular detection device. Doing so would have a reasonable expectation of successfully identifying novel protein interactions of cells, the ability to dynamically manipulate the cellular context during the experiment, the identification of new protein interactions in individual, living, intact cells, such dynamic, transient interactions, which might be elusive in other, standard methods (Bastiaens, paragraph [0069]), and thus allow for positioning and analysis of the behavior of cells on the device (Bastiaens, paragraph [0070]).
Modified Hoffmann fails to teach: wherein before generating the beam of coherent light the cell is modified such that only parts of the cell membrane remain on the biomolecular detection device.
Fang teaches methods for using a label free optical biosensor for performing cell arrays (abstract). Fang teaches a method of providing the biosensor, placing cells on the biosensor, applying solutions, and then interrogating the biosensor to monitor cell response (Fig. 8). Fang teaches an optical system includes an interrogation system for generating and controlling light beams to illuminate the sensor (paragraphs [0005],[0322]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of modified Hoffmann to incorporate the teachings of placing cells on a biosensor before interrogating the biosensor with light of Fang (Fig. 8; paragraphs [0005],[0322]) and the teachings of the cell membrane remaining on a biomolecular detection device of Bastiaens (Fig. 1B) to provide: wherein before generating the beam of coherent light the cell is modified such that only parts of the cell membrane remain on the biomolecular detection device. Doing so would have a reasonable expectation of successfully allowing for proper arrangement of the desired cell for analysis on the device prior to analysis via light.
Regarding claim 18, modified Hoffmann fails to teach: wherein after aligning the transmembrane protein and forming of the transmembrane nanopattern, the cell is modified such that only parts of the cell membrane remain on the biomolecular detection device.
Fang teaches methods for using a label free optical biosensor for performing cell arrays (abstract). Fang teaches a method of providing the biosensor, placing cells on the biosensor, applying solutions, and then interrogating the biosensor to monitor cell response (Fig. 8). Fang teaches an optical system includes an interrogation system for generating and controlling light beams to illuminate the sensor (paragraphs [0005],[0322]). Fang teaches the method includes culturing cells on a biosensor, washing the cells, and then recording a signal with the biosensor (paragraph [0676]). Fang teaches a step of rinsing the cells (paragraph [0677]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of modified Hoffmann to incorporate the teachings of placing cells on a biosensor, and then applying solution, washing, and/or rinsing the cells of Fang (Fig. 8; paragraphs [0676],[0677]) to provide: wherein after aligning the transmembrane protein and forming of the transmembrane nanopattern, the cell is modified such that only parts of the cell membrane remain on the biomolecular detection device. Doing so would have a reasonable expectation of successfully ensuring that only the desired cells to be analyzed, e.g. parts of the cell membrane, remain on the device for analysis via washing or rinsing, therefore improving analysis of the cell.
Claim 14 is rejected under 35 U.S.C. 103 as being unpatentable over Hoffmann in view of Bastiaens and Koike as applied to claim 10 above, and further in view of Rassman et al. (US 20030224370 A1).
Regarding claim 14, modified Hoffmann fails to teach: wherein a protein of interest of the biomolecular interaction comprises a high-mass moiety (note that instant specification describes a “high-mass moiety” has having a molecular weight of 150 kDa or more; therefore, the BRI of high-mass moiety includes molecular weight of 150 kDa or more).
Bastiaens teaches proteins of choice comprising quantum dots, labeled nanospheres, or color-coded beads that allows for localization of the proteins to fiduciary marks to enable measurement of multiple interactions of intracellular, fluorescently labeled binding partners (paragraph [0168]; Figs. 1-2). Bastiaens teaches beads are known in the art and nanoparticles traditionally comprises metals, such as cadmium or zinc, which can be tuned to emit a desired color of light (paragraph [0114]).
Rassman teaches a probe-target reaction is made more recognizable by the provision of a mass-enhancing and/or evanescent-field-perturbing amplifier element which reacts uniquely with and binds to the probe-target pair to provide increased mass (abstract). Rassman teaches if protein targets are used, enhancement with gold nanoparticles will amplify signals when probed with evanescent techniques (paragraph [0124]), wherein a gold nanoparticle is interpreted as a high-mass moiety.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Hoffmann to incorporate the teachings of a protein of choice comprising nanoparticles, such as metallic nanoparticles to be tuned to emit a desired light of Bastiaens (paragraph [0114],[0168]; Figs. 1-2) and the teachings of a protein target comprising gold nanoparticles, i.e. high-mass moiety, to amplify signals of Rassman (paragraph [0124]) to provide: wherein a protein of interest of the biomolecular interaction comprises a high-mass moiety. Doing so would have a reasonable expectation of successfully improving amplification of signals when probed with evanescent techniques as discussed by Rassman (paragraph [0124]).
Claim 21 is rejected under 35 U.S.C. 103 as being unpatentable over Hoffmann in view of Bastiaens and Koike as applied to claim 10 above, and further in view of Sippel et al. (US 7029905 B1).
Regarding claim 21, modified Hoffmann fails to teach: wherein a plurality of the transmembrane proteins laterally diffuse through the cellular membrane and are spatially locked in position by binding to the membrane recognition elements, thereby forming the transmembrane nanopattern in the cell which corresponds at least partially to the template nanopattern.
Bastiaens teaches a plurality of the transmembrane proteins are spatially locked in position by binding to the membrane recognition elements, thereby forming the nonpattern in the cell which corresponds at least partially to the template nanopattern (Fig. 1B shows transmembrane proteins of the cell are spatially locked in position by binding to the antibody-DNA complexes to thereby form a pattern in the cell that corresponds to the pattern of the antibody-DNA complexes).
Sippel teaches methods of detecting specific interactions between membrane receptor and a ligand of a cell (abstract). Sippel teaches the membrane receptor comprises transmembrane receptors (column 4, lines 62-67). Sippel teaches that as a result of ligand binding to the binding section of the membrane receptor, there is a translocation of a protein onto the cell membrane (column 6, lines 39-45), thus causing lateral diffusion of the transmembrane proteins through the cellular membrane to spatially lock the transmembrane proteins in position by binding to a ligand (Fig. 2a). Sippel teaches cells are immobilized on a solid carrier for detecting and measuring membrane receptor-ligand interactions (column 21, lines 49-55).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of modified Hoffmann to incorporate the teachings of transmembrane proteins spatially locking in position by binding to the membrane recognition elements, thereby forming the nonpattern in the cell which corresponds at least partially to the template nanopattern of Bastiaens (Fig. 1B) and the teachings of lateral diffusion of transmembrane proteins to lock the transmembrane proteins in a position when binding to a ligand of Sippel (Fig. 2a; column 6, lines 39-45) to provide: wherein a plurality of the transmembrane proteins laterally diffuse through the cellular membrane and are spatially locked in position by binding to the membrane recognition elements, thereby forming the transmembrane nanopattern in the cell which corresponds at least partially to the template nanopattern. Doing so would have a reasonable expectation of successfully allowing for desired binding of the transmembrane proteins with the membrane recognition elements according to the nanopattern of the device.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
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Claim 10 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 18 of copending Application No. 17/767,810 (herein, “App ‘810”) in view of Bastiaens et al. (US 20150064713 A1) and Koike et al. (US 20090185181 A1).
Regarding claim 10, App ‘810 recites a method of detecting molecular interactions associated with cells (claim 18), comprising:
- providing a biomolecular detection device for analyzing a cell (claim 18, recites providing a “biomolecular detection device”, and the method is for detecting interactions in a cell, i.e. for analyzing a cell), the device comprising an evanescent illuminator with an optical coupling unit configured for generating an evanescent field from coherent light (L) with a predefined wavelength on a first surface of the evanescent illuminator, the first surface of the evanescent illuminator comprising a template nanopattern, containing a coherent arrangement of a plurality of predetermined lines along which membrane recognition elements for a binder structure of a transmembrane protein of the cell are arranged, wherein the membrane recognition elements are configured to bind the binder structure of the transmembrane protein for forming a transmembrane nanopattern within the cell based on the template nanopattern of the evanescent illuminator, such that light of the evanescent field is scattered by the cell bound to the membrane recognition elements, and wherein the predetermined lines are arranged such that light scattered by the cell bound to the membrane recognition elements constructively interferes at a predefined detection site with a difference in optical path length that is an integer multiple of the predefined wavelength of the coherent light (claim 18);
- applying the cell to the membrane recognition elements (claim 18), wherein the cell comprises a membrane and at least one transmembrane protein with an extracellular or extravesicular binder structure (claim 18 recites applying the cell to membrane recognition elements, and the membrane recognition elements bind to binder structures of transmembrane proteins of the cell; therefore, the cell is implied to comprise a membrane and at least one transmembrane protein with an extracellular or extravesicular binder structure), optionally where at least one transmembrane protein is laterally diffused along the membrane (interpreted as not required due to the term “optionally”);
- generating a beam of coherent light at a predefined beam generation location relative to the plurality of predetermined lines, the beam of coherent light having a predefined wavelength and being incident on the membrane recognition elements with the bound transmembrane protein in a manner that diffracted portions of the incident beam of coherent light constructively interfere at the predefined detection site relative to the plurality of predetermined lines with a difference in optical path length that is an integer multiple of the predefined wavelength of the coherent light to provide a signal representative of the membrane recognition elements with the transmembrane protein of the cell bound thereto at the predefined detection site (claim 18); and
- measuring the signal representative for the membrane recognition elements with the transmembrane protein of the cell bound thereto (claim 18).
App ‘810 fails to recite: - aligning the at least one transmembrane protein of the cell according to the template nanopattern of the first surface of the evanescent illuminator, such that a transmembrane nanopattern is formed in the membrane of the cell, wherein the transmembrane pattern corresponds at least partially to the template nanopattern of the first surface of the evanescent illuminator; and wherein the measured signal is dependent on the mass of the transmembrane protein and of the mass of any binding partner bound to the transmembrane protein.
Bastiaens teaches methods and systems for determining a reaction between transmembrane receptor and an intracellular interaction partner thereof within a cell (abstract), wherein a transmembrane receptor designates a protein capable of spanning a membrane of a cell (paragraphs [0022]-[0023]). Bastiaens teaches known challenges of studying protein reactions of cells, such as studying multiple intracellular molecular reactions in parallel in an individual living cell (paragraph [0002]), wherein the solution to this challenge is achieved by the methods and systems as described (paragraph [0002]). Bastiaens teaches membrane recognition elements configured to bind a binder structure of the transmembrane protein for forming a transmembrane nanopattern within the cell based on a template pattern (Figs. 1B, 2, 5,7 teaches antibody-DNA complexes, i.e. membrane recognition elements, binding to a binder structure of transmembrane proteins that forms a transmembrane nanopattern within the cell based on a template pattern of the antibody-DNA complexes). Bastiaens teaches in the case of objective-based TIRF detection of chimeric transmembrane receptor recruitment and reaction, preferably interaction, a material of suitable refractive index and thickness must be selected to allow formation of the evanescent wave (paragraph [0051]), and interaction with probes can be monitored via tracking and spectral analysis of nanostructures via evanescent wave (paragraph [0170]). Bastiaens teaches the method of determining reaction between a transmembrane receptor and an intracellular interaction partner thereof within a cell includes: applying a cell to the membrane recognition elements (Fig. 1 and paragraph [0003] teaches providing a cell and contacting the cell with compounds, i.e. membrane recognition elements, bound to a surface), wherein the cell comprises a membrane (Fig. 2 shows a plasma membrane of a cell) and at least one transmembrane protein with an extracellular or extravesicular binder structure (Figs. 1-3 and 5 shows at least one transmembrane protein with an extracellular binder structure, which binds to the membrane recognition element on a surface of a support) and where at least one transmembrane protein is laterally diffused along the membrane (Figs. 1-3 and 5 shows at least one transmembrane protein laterally diffused along the plasma membrane of the cell); and aligning the at least one transmembrane protein of the cell according to the template pattern of a first surface of the support (Fig. 1b and paragraph [0003] teaches contacting the cell with at least two different extracellular compounds bound to a surface of a support, which is interpreted as alignment of the transmembrane protein of the cell with a pattern of the extracellular components in a pattern on a surface of the support), such that a transmembrane pattern is formed in the membrane of the cell (Fig. 1b shows a pattern of the transmembrane proteins in the membrane of the cell), wherein the transmembrane pattern corresponds at least partially to the template pattern of the first surface of the support (Fig. 1b shows the transmembrane proteins correspond to the pattern of the antibody-DNA complexes of the support). Bastiaens teaches rearranging and/or exchanging extracellular compounds in order to generate a surface to which the cell can be contacted (paragraph [0056]). Bastiaens teaches the sensor is a sensitive biological element, such as cell receptors, and can include optical detectors (paragraph [0148]). Bastiaens teaches detecting change of a label or energy transfer, which is indicative of a reaction (paragraph [0003]). Bastiaens teaches a correlation of the detected signal to a chimeric transmembrane receptor is unambiguously possible in connection with the knowledge of the position or coordinate of an area comprising a specific extracellular compound on a support (paragraph [0042]). Bastiaens teaches the invention provides advantages, such as identifying novel protein interactions, the ability to dynamically manipulate the cellular context during the experiment, the identification of new protein interactions in individual, living, intact cells, such dynamic, transient interactions, which might be elusive in other, standard methods (paragraph [0069]). Bastiaens the invention allows for analysis of the behavior of cells (paragraph [0070]). Bastiaens teaches micropatterns can be scaled down to nanosized dimensions (paragraph [0186]).
Since Bastiaens teaches determining a reaction between a protein bound to a membrane recognition elements on a surface and nanosized patterns, similar to App ‘810, and Bastiaens teaches a known problem in the art of studying protein reactions in living cells (paragraph [0002]), it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of App ‘810 to incorporate Bastiaens’s teachings of membrane recognition elements configured to bind a binder structure of the transmembrane protein for forming a transmembrane nanopattern within the cell based on a template pattern (Figs. 1B, 2, 5,7), interaction with probes can be monitored via tracking and spectral analysis of nanostructures via evanescent wave (paragraph [0170]), rearranging and/or exchanging extracellular compounds in order to generate a surface to which the cell can be contacted (paragraph [0056]), and applying a cell to membrane recognition elements and aligning the transmembrane proteins of a cell (Figs. 1-2 and paragraph [0003]) to provide: aligning the at least one transmembrane protein of the cell according to the template nanopattern of the first surface of the evanescent illuminator, such that a transmembrane nanopattern is formed in the membrane of the cell, wherein the transmembrane pattern corresponds at least partially to the template nanopattern of the first surface of the evanescent illuminator. Doing so would have a reasonable expectation of successfully ensuring placement of the cell on the surface of the illuminator, thus allowing for identifying novel protein interactions of cells, the ability to dynamically manipulate the cellular context during the experiment, the identification of new protein interactions in individual, living, intact cells, such dynamic, transient interactions, which might be elusive in other, standard methods (Bastiaens, paragraph [0069]), and thus allow for analysis of the behavior of cells (Bastiaens, paragraph [0070]).
Modified App ‘810 fails to recite wherein the measured signal is dependent on the mass of the transmembrane protein and of the mass of any binding partner bound to the transmembrane protein.
Bastiaens teaches detection includes recording signals generated by labels and shape and size of the labels (paragraph [0060]). Bastiaens teaches quantification of interaction can be performed by measuring signal intensity generated by labels (paragraph [0105]). Bastiaens interaction with probes can be monitored via tracking and spectral analysis of nanostructures via evanescent wave (paragraph [0170]).
Koike teaches a method for measuring a surface plasmon resonance for easy detection of proteins and determination whether a peptide is phosphorylated or not in biological materials (abstract). Koike teaches SPR is known to generate an evanescent wave on a total reflection surface (paragraph [0013]). Koike teaches known measurement principles of SPR measuring includes reflected light intensity is dependent on variation of mass of a compound bound, which is therefore measured as measurement data from a strength of reflected light (paragraph [0047]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of measuring of modified Hoffmann to incorporate Bastiaens’ teachings of quantifying interaction based on signal intensity via spectral analysis of evanescent wave (paragraphs [0105],[0170]) and Koike’s teachings of known methods of measuring changes in light intensity that is dependent on mass of a compound bound based on evanescence wave (paragraphs [0013],[0047]) to provide: wherein the measured signal is dependent on the mass of the transmembrane protein and of the mass of any binding partner bound to the transmembrane protein. Doing so would have a reasonable expectation of successfully improving characterization and analysis of the transmembrane protein and any binding partner.
This is a provisional nonstatutory double patenting rejection.
Response to Arguments
Applicant’s arguments, see pages 8-12, filed 04/02/2026, with respect to the rejections of claims 10-15 and 18-21 under 35 U.S.C. 103, specifically regarding amended claim 1, have been fully considered and are persuasive. Therefore, the rejection has been withdrawn. However, upon further consideration, a new ground(s) of rejection is made in view of Hoffmann (EP2618130A1; cited in the IDS filed 07/05/2022) and Bastiaens et al. (US 20150064713 A1) and Koike et al. (US 20090185181 A1).
Applicant's arguments, see page 11, filed 04/02/2026, with respect to the nonstatutory double patenting rejection of claim 10 have been fully considered but they are not persuasive. Additionally, upon further consideration of the amended claim 10, a new ground(s) of rejection is made in view of Application No. 17/767,810 (herein, “App ‘810”) in view of Bastiaens et al. (US 20150064713 A1) and Koike et al. (US 20090185181 A1).
In response to applicant’s argument that App ‘810 does not recite a transmembrane nanopattern, the examiner disagrees. Claim 18 of App ‘810 recites “transmembrane nanopattern within the cell”. Thus, the nonstatutory double patenting rejection of claim 10 is maintained.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Gollier et al. (US 20050070027 A1) teaches a method of using a double resonance effect within a grating coupled waveguide sensor for label-independent detection of biological and chemical agents within a sensing region at increased sensitivity (abstract). Gollier teaches detecting analytes using evanescent field and waveguides (paragraphs [0044],[0055]). Gollier teaches a light source populates a mode of the waveguide and provides the evanescent optical field that penetrates into a medium to be sensed, wherein a change in the mass or refractive index of the sensor medium causes a corresponding change in the properties of the field in the optical confinement layer; wherein targets that bind with probe materials on the surface of the sensor alters the refractive index and the evanescent field, measured (paragraph [0056]).
Bailey et al. (US 20130295688 A1) teaches systems and methods for detecting an analyte of interest including an optical sensor and capture probe attached to a surface of the optical sensor (abstract). Bailey teaches optical sensors based on refractive index-based sensing schemes in which mass of bound analytes, in combination with other factors such as capture probe affinity and surface density, contributes to the observed signal and measured sensitivity (paragraph [0090]).
Schasfoort et al. (WO 2012070942 A1) teaches an apparatus for SPR scanning (abstract). Schasfoort teaches SPR is a well known optical technique, which can be based on a linear relationship between change in reflected light intensity and the mass of the bound analyte (page 1, lines 8-12, 29-32).
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/HENRY H NGUYEN/Primary Examiner, Art Unit 1758
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