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 .
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
Claims 1-2, 4, 9, 13 and 16-18 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Ray et al. ("Enhanced Fluorescence of Proteins and Label-Free Bioassays Using Aluminum Nanostructures", as cited in the IDS).
Regarding claim 1, the examiner is using broadest reasonable interpretation of "contaminating reagents" to comprise anything that can give off false signals for concentration or amounts of a target molecule (as taught by the specification, [0041]).
Ray et al. teaches a method of quantifying target molecules (see Abstract, disclosing label-free bioassays for detecting and observing binding interactions between proteins.) comprising the steps of: binding target molecules to a surface, wherein the target molecules are presented for a quantification assay (see pg. 6051, Results and Discussions, disclosing the aluminum nanostructured substrate were incubated in a phosphate buffer saline (PBS) solution of Bovine Serum Albumin (BSA) proteins with a concentration of 50 µg/mL which results in a monolayer of adsorbed protein.); cleaning the target molecules of contaminating reagents, wherein the target molecules remain bound to the surface (see pg. 6051, Results and Discussions, disclosing that after incubation for 1 hour at room temperature, the substrates were washed to remove the unbound proteins (i.e., removing contaminants that could otherwise result in potential false positives from interfering with measurements). BSA forms a adsorbed protein monolayer on the aluminum nanostructured substrate.); directly quantifying the target molecules, wherein the target molecules remain bound to the surface, wherein direct quantification of the target molecules is performed by measurement of intrinsic fluorescence of the target molecules (see pg. 6051, Results and Discussions, disclosing following the substrate wash, emission spectra of the BSA monolayer on quartz and aluminum nanostructured substrates is measured, and obtaining the characteristic fluorescence intensity.).
Regarding claim 2, Ray et al. teaches the method of Claim 1, further comprising storing or transporting the target molecules at least at room temperature, wherein the target molecules remain stable while bound to the surface (see pg. 6050, Experimental Section, disclosing that for deposition of proteins on the aluminum nanostructure surfaces and bare quartz substrates, direct deposition of proteins by noncovalent electrostatic immobilization of the proteins are performed. Immobilization, incubation, and measurements steps are all performed in phosphate buffer saline (PBS) at pH 7.4, while at room temperature.).
Regarding claim 4, Ray et al. teaches the method of Claim 1, wherein the direct quantification occurs by use of spectrophotometric techniques (See pg. 6050, Experimental Section, disclosing fluorescence spectra of mono- and multilayers of proteins on solid substrates were recorded using a Varian Cary Eclipse fluorescence spectrophotometer.)
Regarding claim 9, Ray et al. teaches the method of Claim 1, wherein the target molecules are bound on a surface presented on one or more selected from the group consisting of beads, membrane, packed column, monolithic column, glass beads and chromatographic beads (see pg. 6050, Experimental section, disclosing that proteins were deposited on a aluminum nanostructured surface, where aluminum nanostructures and metallic nanostructures are known in the art of fluorescence detection to be membranes.).
Regarding claim 13, Ray et al. teaches the method of Claim 1, wherein the direct quantification is performed by measuring protein fluorescence (see pg. 6051, Results and Discussions, disclosing following the substrate wash, emission spectra of the bovine serum albumin (BSA) protein monolayer on quartz and aluminum nanostructured substrates is measured, and obtaining the characteristic fluorescence intensity.).
Regarding claim 16, Ray et al. teaches the method of Claim 1, wherein the target molecules are proteins (see pg. 6051, Experimental Section, disclosing the proteins to be measured in the study are bovine serum albumin (BSA), biotinylated bovine serum albumin (BSA-bt), streptavidin (SA), and goat and rabbit immunoglobulins (IgG).).
Regarding claim 17, Ray et al. teaches the method of Claim 1, wherein the intrinsic fluorescence of tryptophan is measured (see Abstract, disclosing that intensities and lifetimes of several proteins with different numbers of tryptophan residues assembled on the surfaces of quartz or aluminum nanostructured films were measured.).
Regarding claim 18, Ray et al. teaches an apparatus for implementation of the method of Claim 1, wherein the device comprises: a protein immobilization spot (see pg. 6050, Experimental Section, disclosing that proteins were directly deposited onto aluminum nanostructured surfaces and bare quartz substrates by means of noncovalent electrostatic immobilization.); a UV light source (see pg. 6050, Experimental Section, disclosing the excitation wavelength in the frequency domain experiment was also 280 nm using modulated UV LED in the frequency range from 3 to 300 MHz.); and a detector (see pg. 6050, Experimental Section, disclosing fluorescence spectra of mono- and multilayers of proteins on solid substrates were recorded using a Varian Cary Eclipse fluorescence spectrophotometer.).
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 3, 5, 10 and 19-20 are rejected under 35 U.S.C. 103 as being unpatentable over Ray et al. as applied to claim 1 above, and further in view of Protifi ("S-Trap™", as cited in the IDS).
Regarding claim 3, Ray et al. fails to teach wherein the target molecules have a greater affinity for the surface than the affinity for the surface exhibited by the contaminating reagents.
However, in the analogous art of "S-Trap™", Protifi teaches S-Trap™ for sample processing for proteomics sample preparation. Multiple weak-affinity interactions hold undigested protein within the pores of derivatized silica S-Trap™. Captured proteins are present with maximal surface area allowing them to be washed fully free of all contaminants in only minutes (see Protifi, para. 1-2).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the label-free bioassay of Ray et al. to incorporate having multiple weak-affinity interactions in the derivatized silica S-Trap™ with target proteins to be captured and to be held in place for washing off the excess contaminants that aren't bound (as taught by Protifi), for the benefit of reducing additional outside influences on measurement results by preventing binding with contaminating reagents prior to washing it off.
Regarding claim 5, Ray et al. fails to teach wherein each step of the method is automated.
However, Protifi teaches using S-Trap™ sample processing as automatable 96-well plates, compatible with automated platforms including Tecan A200 positive pressure workstation and Agilent Bravo (see Protifi, para. 1, para. 4).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the label-free bioassay of Ray et al. to incorporate automating the method (as taught by Protifi), for the benefit of convenience, minimal prep time, and reproducibility of results (see Protifi, para. 4).
Regarding claim 10, Ray et al. teaches that the aluminum nanostructured substrate was incubated in a phosphate buffer saline (PBS) solution of Bovine Serum Albumin (BSA) proteins with a concentration of 50 µg/mL which results in a monolayer of adsorbed protein onto the aluminum nanostructured substrate (see Ray et al., pg. 6051, Results and Discussions).
Ray et al. fails to teach that the bound target molecules on the surface are washed of reducing reagents.
However, Protifi teaches S-Trap™ sample processing beginning with sample lysis and solubilization in 5% SDS, which are further denatured by acidification and subsequently exposed to a high concentration of methanol. Denatured, non-digested proteins are bound to the S-Trap via centrifugation, positive pressure or vacuum, where captured proteins are presented with maximal surface area to allow them to be washed fully free of all contaminants, such as PEG, glycerol, detergents, salts, Laemmli loading buffers, etc. (i.e., reducing and alkylating agents) (see Protifi, para. 1-2).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the washing of Ray et al. to incorporate washing off reducing reagents (as taught by Protifi), for the benefit of decreasing interfering contaminants from giving off false signals in protein fluorescing measurements.
Regarding claim 19, Ray et al. fails to teach wherein the apparatus comprises a 96-well plate.
However, Protifi teaches using S-Trap™ sample processing as automatable 96-well plates (see Protifi, para. 1).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the label-free bioassay of Ray et al. to incorporate a 96-well plate (as taught by Protifi), for the benefit of convenience, minimal prep time, and reproducibility of results (see Protifi, para. 4).
Regarding claim 20, Ray et al. fails to teach wherein the apparatus is automated.
However, Protifi teaches using S-Trap™ sample processing as automatable 96-well plates, compatible with automated platforms including Tecan A200 positive pressure workstation and Agilent Bravo (see Protifi, para. 1, para. 4).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the label-free bioassay of Ray et al. to incorporate automating the apparatus (as taught by Protifi), for the benefit of convenience, minimal prep time, and reproducibility of results (see Protifi, para. 4).
Claim 6 and 7 are rejected under 35 U.S.C. 103 as being unpatentable over Ray et al. as applied to claim 1 above, and further in view of Murphy et al. ("Automated Hydrophobic Interaction Chromatography Column Selection for Use in Protein Purification", as cited by the IDS).
Regarding claim 6, Ray et al. fails to teach wherein the surface is a C18 hydrophobic surface or optionally C4, C8, or other suitable hydrophobic surface.
However, in the analogous art of "Automated Hydrophobic Interaction Chromatography Column Selection for Use in Protein Purification", Murphy et al. teaches hydrophobic interaction chromatography (HIC) for purifying a given protein, as an automated method for scouting an optimal HIC media to be used in protein purification. Recombinant green fluorescent protein (GFP) is used as the target protein in purification, and several HIC medias are contemplated for automated column scouting, as pre-packed columns each containing one of several hydrophobic ligands (e.g., S-butyl, butyl (i.e., C4 hydrophobic surface), octyl (i.e., C8 hydrophobic surface), and phenyl) (see Murphy et al., Abstract).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the surfaces of Ray et al. to incorporate pre-packed columns containing hydrophobic ligands such as butyl and octyl (i.e., C4 and C8 hydrophobic surfaces, respectively), (as taught by Murphy et al.), for the benefit of being able to separate proteins and other biomolecules from a crude lysate based on the differences in hydrophobicity through the use of hydrophobic interaction chromatography (see Murphy et al., Abstract).
Regarding claim 7, Ray et al. fails to teach wherein the target molecules are bound to a surface by hydrophobic or hydrophilic chromatography.
However, Murphy et al. teaches that through hydrophobic interaction chromatography, hydrophobic moieties on the protein surface temporarily bind to a nonpolar ligand coupled to an inert, immobile matrix. The interaction between protein and ligand are highly dependent on the salt concentration of the buffer flowing through the chromatography column, with high ionic concentrations strengthening the protein-ligand interaction and making the protein immobile (i.e. bound inside the column) (see Murphy et al., Abstract).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the surface binding of target molecules of Ray et al. to incorporate hydrophobic interaction chromatography (as taught by Murphy et al.), for the benefit of being able to separate proteins and other biomolecules from a crude lysate based on the differences in hydrophobicity through the use of hydrophobic interaction chromatography (see Murphy et al., Abstract).
Claim 8 is rejected under 35 U.S.C. 103 as being unpatentable over Ray et al. as applied to claim 1 above, and further in view of Jungbauer et al. (US PG-Pub 20210149361 A1).
Regarding claim 8, Ray et al. fails to teach wherein the target molecules are bound to a surface by weak or strong ion exchange (cation or anion).
However, in the analogus art of real time monitoring of product purification, Jungbauer et al. teaches a method and device allowing for real-time determinization of concentration, purity and potency of a biological product during purification and or concentration processes. The method involves using an operational unit, which further comprises a chromatography unit, such as ion exchange chromatography. In a purification example using target protein basic fibroblast growth factor (FGF-2), carboxy methyl Sepharose fast flow, a weak cation-exchange resin, was a material used as a sorbent in the capture step of the FGF-2 (see Jungbauer et al., Abstract, [0002], [0031], [0267]).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the target molecule binding of Ray et al. to incorporate binding via weak ion exchange (as taught by Jungbauer et al.), for the benefit of online data monitoring of protein purification process to determine if it is within specification limits to allow for further processing (see Jungbauer et al., [0015]).
Claim 11 is rejected under 35 U.S.C. 103 as being unpatentable over Ray et al. as applied to claim 1 above, and further in view of Chen et al. ("Solid Phase Extraction of N‑Linked Glycopeptides Using Hydrazide Tip", as cited in the IDS).
Regarding claim 11, Ray et al. teaches that the aluminum nanostructured substrate was incubated in a phosphate buffer saline (PBS) solution of Bovine Serum Albumin (BSA) proteins with a concentration of 50 µg/mL which results in a monolayer of adsorbed protein onto the aluminum nanostructured substrate (see Ray et al., pg. 6051, Results and Discussions).
Ray et al. fails to teach that the bound target molecules on the surface are washed of aniline.
However, in the analogous art of "Solid Phase Extraction of N‑Linked Glycopeptides Using Hydrazide Tip", Chen et al. teaches using bovine fetuin as a standard glycoprotein in discovering sources of diagnoses in biomarkers. Hydrazide tips were utilized in N-linked glycopeptide isolation. In coupling the bovine fetuin with the hydrazide tip, 400 μL of bovine fetuin in oxidation buffer was oxidized with 15 mM sodium periodate for 1 h at room temperature in the dark followed by buffer exchange into a coupling buffer. After addition of 100 mM aniline, the fetuin samples were slowly pipetted through hydrazide tips for coupling. Protein concentration was determined using the bicinchoninic acid protein assay per the manufacturer’s protocol after removal of aniline (see Chen et al., Abstract, pg. 10671, Coupling Time for Glycoprotein to Hydrazine Tip).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the washing of Ray et al. to incorporate the removal of aniline from the surface (as taught by Chen et al.), for the benefit of reducing interfering reagents from affecting resulting protein concentration readings.
Claim 12 is rejected under 35 U.S.C. 103 as being unpatentable over Ray et al. as applied to claim 1 above, and further in view of Peters ("Miniaturization and improved throughput of the BCA concentration determination method", as cited in the IDS).
Regarding claim 12, Ray et al. fails to teach wherein the direct quantification is performed using a bicinchoninic acid assay.
However, in the analogous art of "Miniaturization and improved throughput of the BCA concentration determination method", Peters teaches determining total protein concentrations in comparing and standardizing biological samples. A colorimetric assay, such as bicinchoninic acid (BCA) protein assay, can be performed in white plates using fluorescence detection (see Peters, Introduction).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the direct quantification of Ray et al. to incorporate using bicinchoninic acid assay (as taught by Peters), for the benefit of exploiting the inherent fluorescence of white microplates. In presence of an absorbing solution, the inherent fluorescence is quenched and the decrease in fluorescent signal can be used to measure colorimetric assays (see Peters, Introduction).
Claims 14 and 15 are rejected under 35 U.S.C. 103 as being unpatentable over Ray et al. as applied to claim 1 above, and further in view of Ghisaidoobe et al. ("Intrinsic Tryptophan Fluorescence in the Detection and Analysis of Proteins: A Focus on Förster Resonance Energy Transfer Techniques", as cited in the IDS).
Regarding claim 14, Ray et al. fails to teach wherein the target molecules are nucleic acids.
However, in the analogous art of "Intrinsic Tryptophan Fluorescence in the Detection and Analysis of Proteins: A Focus on Förster Resonance Energy Transfer Techniques", Ghisaidoobe et al. teaches applications of intrinsic protein fluorescence, predominantly derived from tryptophan. Oligonucleotides (DNA and RNA) are used in the fluorescent labeling processes (see Ghisaidoobe et al., Abstract, pg. 22519 1. Introduction, pg. 22531/4. Intrinsic Förster Resonance Energy Transfer, Scheme 2).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the target molecule of Ray et al. to incorporate the target molecule further comprising a nucleic acid such as DNA or RNA (as taught by Ghisaidoobe et al.), for the benefit of being able to perform biomolecular fluorescence assay for RNA binding sites, which often displays Tryptophan residues (see Ghisaidoobe et al., pg. 22531/4. Intrinsic Förster Resonance Energy Transfer).
Regarding claim 15, Ray et al. fails to teach wherein the target molecules are RNA.
However, in the analogous art of "Intrinsic Tryptophan Fluorescence in the Detection and Analysis of Proteins: A Focus on Förster Resonance Energy Transfer Techniques", Ghisaidoobe et al. teaches applications of intrinsic protein fluorescence, predominantly derived from tryptophan. Oligonucleotides (DNA and RNA) are used in the fluorescent labeling processes (see Ghisaidoobe et al., Abstract, pg. 22519 1. Introduction, pg. 22531/4. Intrinsic Förster Resonance Energy Transfer, Scheme 2).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the target molecule of Ray et al. to incorporate the target molecule further comprising RNA (as taught by Ghisaidoobe et al.), for the benefit of being able to perform biomolecular fluorescence assay for RNA binding sites, which often displays Tryptophan residues (see Ghisaidoobe et al., pg. 22531/4. Intrinsic Förster Resonance Energy Transfer).
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Tracy C Colena whose telephone number is (571)272-1625. The examiner can normally be reached Mon-Thus 8:00am-5:00pm.
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/TRACY CHING-TIAN COLENA/Examiner, Art Unit 1797
/JENNIFER WECKER/Primary Examiner, Art Unit 1797
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