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 .
Claims Status
The amendment and remarks filed 05/26/2026 is entered. Claim 5 is cancelled. Claim 11-19 are new. Claims 1, 3, 4, 6, and 8 are amended. Claims 1-4, 6-19 are pending and under examination.
Withdrawn Objections/Rejections
Specification Objections
The previous objection to the specification regarding the references to color features is withdrawn in response to the Applicant’s amendment to the specification to remove the references to color and distinctly describe the features without adding new matter.
The previous objection to the specification regarding the incorporation-by-reference paragraph for the sequence listing is withdrawn in response to the Applicant’s amendment to the specification to include this paragraph without adding new matter.
The previous objection to the specification regarding missing sequence identifiers in the specification is withdrawn in response to the Applicant’s amendment to the specification to include this paragraph without adding new matter.
Claim Rejections - 35 USC § 112(b)
The previous 35 USC § 112(b) rejection to claims 1-10 is withdrawn in response to the Applicant’s amendment. Claim 5 is cancelled. Claims 1-4 and 6-10 are amended directly or by its dependency to remove the use of “preferably”.
Maintained Objections/Rejections
In response to the Applicant’s amendments, the previous 35 USC § 102 and 35 USC § 103 rejections are maintained and updated. New claims are included in the rejections, as appropriate.
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.
(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 1-2 and 11 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Wang et al (Wang, Z. et al, BirA*-protein A fusion protein based BioEnhancer amplifies western blot immunosignal, Electrophoresis 2021, 42, 793–799, published 03/2021), as evidenced by Branon et al (US 12110522 B2, filed 07/16/2020).
Regarding claim 1, Wang et al teaches a fusion polypeptide comprising a biotin ligase enzyme, BirA* (R118G-mutated protein BirA biotin ligase), fused to an immunoglobulin-binding bacterial protein, Protein A (Abstract). The proximity-dependent biotin identification protein BirA* is also referred to as BioID (p. 793, section: Introduction, column 1, paragraph 2), and the fusion protein of BirA* and Protein A is called BioEnhancer (p. 794, col. 1 , para. 2).
Instant SEQ ID NO: 1 is the 321 amino acid sequence for the wildtype BirA biotin ligase. Therefore, BirA* biotin ligase, disclosed as being characterized by having one point mutation (R118G) from the wildtype BirA biotin ligase (p. 793, col. 1, para. 2), has an amino acid sequence that has at least 90% sequence identity to amino acid sequence of instant SEQ ID NO: 1. To be further explicit, Branon et al teaches BirA-R118G (BioID), is a variant of BirA, by the point mutation R118G (col. 44, lines 18-21), which is the same as what Wang et al calls BirA*. Branon et al teaches BirA-R118G comprises of the amino acid sequence of SEQ ID NO: 9 (Sequence Listing, col. 81-83), which shares at least 90% sequence identity to instant SEQ ID NO: 1. Therefore, as evidenced by Branon et al, BioEnhancer taught by Wang et al meets the limitations of claim 1.
Claims 2 and 11 depends on claim 1. The teachings of Wang et al regarding claim 1 is incorporated in its entirety for claim 2 and 11, and further described, as is relevant to each claim, below.
Regarding claim 2, Wang et al further teaches that biotin ligase enzyme in the fusion polypeptide has proximity-dependent biotinylation activity (Abstract and Introduction, paragraphs 2 and 4).
Regarding claim 11, Wang et al teaches the immunoglobulin-binding bacterial protein is Protein A.
Claim Rejections - 35 USC § 103
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 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 1-2 and 11 are rejected under 35 U.S.C. 103 as being anticipated by Wang et al (Wang, Z. et al, BirA*-protein A fusion protein based BioEnhancer amplifies western blot immunosignal, Electrophoresis 2021, 42, 793–799, published 03/2021) in view of Branon et al (US 12110522 B2, filed 07/16/2020).
Regarding claim 1, Wang et al by itself already meets the limitations of the claim, as previously discussed in the 35 USC 102 rejection. Wang et al teaches a fusion polypeptide comprising a biotin ligase enzyme, BirA* (R118G-mutated protein BirA biotin ligase), fused to an immunoglobulin-binding bacterial protein, Protein A (Abstract). The proximity-dependent biotin identification protein BirA* is also referred to as BioID (p. 793, section: Introduction, column 1, paragraph 2), and the fusion protein of BirA* and Protein A is called BioEnhancer (p. 794, col. 1 , para. 2).
However, to address the other alternative embodiments in the claim, Wang et al does not explicitly teach the biotin ligase enzyme comprises the amino acid sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3.
However, Branon et al teaches engineered biotin ligases variants having increased promiscuous biotinylation activity capable of proximity labeling proteins in live cells (Abstract). Branon teaches:
Wildtype BirA biotin ligase comprising the amino acid sequence of SEQ ID NO: 7 (col. 24, lines 14-15; and Sequence Listing, col. 79-81), which has a 100% sequence match to instant SEQ ID NO: 1.
BirA-R118G (BioID), is a variant of BirA, by the point mutation R118G, which is the same as what Wang et al calls BirA*. BirA-R118G was developed for its higher promiscuity (col. 44, lines 18-21), and comprises of the amino acid sequence of SEQ ID NO: 9 (Sequence Listing, col. 81-83), which shares at least 90% sequence identity to instant SEQ ID NO: 1.
BirA-R118G was then engineered into BirA-R118S, which is more active than BirA-R118G, and BirA-R118S was subsequently used as the starting point for directed evolution (col. 44, lines 22-23). This resulted in the biotin ligases variants having increased promiscuous biotinylation activity capable of proximity labeling proteins in live cells in as little as 10 minutes (Abstract):
miniTurbo, with 12 mutations relative to wild-type BirA (col. 45, lines 32-33), comprising the amino acid sequence of SEQ ID NO 11 (col. 85), which shares 100% sequence identity to instant SEQ ID NO: 2; and
TurboID, with 14 mutations relative to wild-type BirA (col. 45, lines 38-39), comprising the amino acid sequence of SEQ ID NO 13 (col. 87), which shares 100% sequence identity to instant SEQ ID NO: 3.
Both miniTurbo and TurboID were more active than BioID (col. 46, lines 1-3).
Branon et al further teaches that in certain embodiments, the biotin ligase is linked to a peptide or protein that directs the biotin ligase to a subcellular region of interest (col. 6, lines 57-58). Branon et al also teaches that in some embodiment the biotin ligase is linked to an antibody specific for an epitope in the subcellular region of interest (col. 6, lines 63-65). Although Branon et al does not explicitly teach the biotin ligase is fused with an immunoglobulin-binding bacterial protein, this teaches these active biotin ligases can be linked to other active proteins while maintaining activity.
Claim 2 depends on claim 1. The teachings of Wang et al regarding claim 1 is incorporated in its entirety for claim 2, and further described, as is relevant to each claim, below.
Regarding claim 2, Wang et al further teaches that biotin ligase enzyme in the fusion polypeptide has proximity-dependent biotinylation activity (Abstract and Introduction, paragraphs 2 and 4).
Regarding claim 11, Wang et al teaches the immunoglobulin-binding bacterial protein is Protein A.
It would have been obvious to one skilled in the art, before the effective filing date of the instant application, to substitute the biotin ligase BirA-R118G/BirA*/BioID with the biotin ligase miniTurbo or TurboID, having the amino acid sequence of instant SEQ ID NO: 2 or 3, respectively, for their higher activity and promiscuity. It would have also been obvious to one skilled in the art, before the effective filing date of the instant application, to substitute the biotin ligase BirA-R118G/BirA*/BioID with the wildtype biotin ligase BirA, having the amino acid sequence of instant SEQ ID NO: 1, if this higher activity or promiscuity was not needed. These substitutions are further supported in light of Branon et al teachings that these biotin ligases are compatible with being linked to other active proteins.
One skilled in the art, before the effective filing date of the instant application, would be motivated to choose a biotin ligase that fits the needed activity and promiscuity level for their application. As these properties are well characterized for each biotin ligase, one skilled in the art would be motivated to choose high activity and promiscuous variants for applications that benefit from this, such as when speed and the ability to biotinylate all proteins are crucial. Conversely, in applications that does not require this promiscuity, such as with substrates that the wildtype biotin ligase already works sufficiently with, there is motivation to choose the wildtype biotin ligase.
One skilled in the art, before the effective filing date of the instant application, would have reasonable expectation of success because the substituted and substituting biotin ligases are known in the art to achieve proximity biotinylation, and the activity of these biotin ligases are characterized and compared to BioID, the substituted biotin ligase in Wang et al. It is reasonably expected that since like BioID fused to Protein A retains its proximity biotinylation activity, the substituting biotin ligases would also retain its function based on their similar sequence and active sites. In other words, the fused protein would similarly not impede on the active site of the biotin ligases when fused in the same way.
Claims 3-4, 6, 10, 12-19 are rejected under 35 U.S.C. 103 as being unpatentable over Wang et al (Wang, Z. et al, BirA*-protein A fusion protein based BioEnhancer amplifies western blot immunosignal, Electrophoresis 2021, 42, 793–799, published 03/2021), as evidenced by Branon et al (US 12110522 B2, filed 07/16/2020), as applied to claim 1 in the 35 USC 102 rejection above, and further in view of Farrell et al (US 9663814 B2, Farrell, M. et al, Proximity Assay for In Situ Detection of Targets, effectively filed 03/12/2013) and Choe et al (Choe, W. et al, Fc-Binding Ligands of Immunoglobulin G: An Overview of High Affinity Proteins and Peptides, Materials 2016, 9, 994, published 12/08/2016).
Claims 3-4, 6, 10, 12-19 are also rejected under 35 U.S.C. 103 as being unpatentable over Wang et al (Wang, Z. et al, BirA*-protein A fusion protein based BioEnhancer amplifies western blot immunosignal, Electrophoresis 2021, 42, 793–799, published 03/2021) in view of Branon et al (US 12110522 B2, filed 07/16/2020), as applied to claim 1 in the 35 USC 103 rejection above, and further in view of Farrell et al (US 9663814 B2, Farrell, M. et al, Proximity Assay for In Situ Detection of Targets, effectively filed 03/12/2013) and Choe et al (Choe, W. et al, Fc-Binding Ligands of Immunoglobulin G: An Overview of High Affinity Proteins and Peptides, Materials 2016, 9, 994, published 12/08/2016).
The teachings of the references regarding claim 1 is incorporated in its entirety for its dependent claims and further described below, as is relevant to each claim. In summary, the above 35 USC 102 rejection applied to claim 1 describe the teachings of the prior art to arrive at the claimed fusion polypeptide comprising a biotin ligase comprising 90% sequence identity of the amino acid sequence of SEQ ID NO: 1. The 35 USC 103 rejection applied to claim 1 describe the teachings of the prior art to arrive at the claimed fusion polypeptide comprising a biotin ligase comprising the amino acid sequence of SEQ ID NO: 1, 2, and 3.
Regarding claims 3-4 and 6-19, Wang et al further teaches an antibody, which is an immunoglobulin, directs the fusion polypeptide to the antibody target by way of the immunoglobulin-binding bacterial protein in the fusion polypeptide binding to the antibody (see section 3.2 BioEnhancer recognized IgG and added biotin tags to its proximal proteins, paragraph 3; and section 4.1 BioEnhancer inherits the primary antibody binding specificity). Wang et al teaches the fusion polypeptide and antibody are in a composition with the target (see section 3.2 BioEnhancer recognized IgG and added biotin tags to its proximal proteins, paragraph 3). Regarding claims 4 specifically, Wang et al teaches the antibody and fusion polypeptide is complexed (e.g. Figure 1).
Further regarding claims 12-13, 16-18 specifically, the immunoglobulin is a monoclonal antibody (Figure 1 and p. 794, Section: 2.1 Reagents, para. 1).
Further regarding claims 6-10 and 12-19, Wang et al further teaches a method of biotinylating a protein of interest and a method of proximity labeling of proteins in a sample of interest, wherein the method comprises of contacting or introducing the antibody and fusion polypeptide to its target protein and adding or contacting the target protein with biotin and ATP, wherein the antibody targets the fusion polypeptide to a target, and the biotin ligase biotinylates the antibody target protein or proteins in proximity to the biotin ligase (see section 3.2 BioEnhancer recognized IgG and added biotin tags to its proximal proteins, paragraph 3).
Regarding claims 6-7, the scope of the claims as written encompass the contacting the sample with the composition of claim 3, which encompasses compositions of the fusion protein and the antibody together but starting as separate entities, and compositions of the fusion protein complexed with the antibody as one entity. Wang et al teaches the method where the composition is the former, wherein the fusion protein eventually becomes complexed with the antibody, possibly both while in the composition before the antibody reaches its target and after the antibody reaches its target, meeting the claim limitations under the full scope of the claims.
However, Wang et al does not explicitly teach the antibody and fusion polypeptide is explicitly complexed before targeting to the antibody target.
Regarding claims 8-10 and 17-19, Wang et al does not explicitly teach a kit. Further regarding claim 10, Wang et al does not explicitly teach the kit further comprises of biotin or a derivative thereof, and ATP.
Regarding claims 6-7, 9, and 15 Wang et al teaches biotinylating a sample of interest by contacting the sample protein with the composition of claim 3 or wherein the immunoglobulin targets a protein, meeting the claim limitations under the scope of the claims, but does not explicitly teach the antibody targets the fusion polypeptide to a subcellular region of interest, which is an alternative limitation.
However, Branon et al also teaches that in some embodiment the biotin ligase is linked to an antibody specific for an epitope in the subcellular region of interest (col. 6, lines 63-65). Branon et al further shows that the biotin ligases themselves have promiscuous proximity biotinylation activity in subcellular compartments (col. 11, lines 60-66).
Branon et al does not explicitly teach the biotin ligase linked to an antibody, which serves to target it to an epitope site before promiscuous proximity biotinylation activity in subcellular compartments but teaches these biotin ligases fused to a peptide targeting sequence directing them to subcellular organelles (col. 12, lines 10-13).
Wang et al and Branon et al do not explicitly teach the kit.
However, Farrell et al also teaches the concept of biotin ligase targeted by an antibody for proximity-based biotinylation (Abstract, Figure 2). Farrell et al differs from the instant application claims by how the biotin ligase is bound to the antibody, as Farrell et al conjugates the thiol on the biotin ligase to a maleimide on the antibody, (Column 29, lines 60-67- Column 30, lines 55-56) instead of using an immunoglobulin-binding bacterial protein fused to the biotin ligase.
Farrell et al teaches that the antibody and biotin ligase are complexed before targeting the biotin ligase to the antibody target (Column 29, lines 60-67- Column 30, lines 55-56), as is relevant to claims 4, 6-7.
Farrell et al teaches a kit for biotinylating a protein of interest, comprising of a biotin ligase, an antibody, and further comprising biotin and ATP (Column 52, section VIII. Kits).
Farrell et al teaches that the targets for biotinylation can be in any cellular compartment (Column 2, line 3), which includes in a cell and subcellular regions.
Wang et al, Branon et al, and Farrell et al do not explicitly teach the motivation of using an immunoglobulin-binding bacterial protein as the method for binding a biotin ligase to an antibody for proximity-based biotinylation, as opposed to other methods of binding a biotin ligase to an antibody.
However, Choe et al further teaches the motivation of using an immunoglobulin-binding bacterial protein as the method for binding a ligand, such as a biotin ligase, to an immunoglobulin. Choe et al teaches that when an antibody is to be used in applications requiring binding to its cognate antigen, it is crucial that the Fab region of the antibody is not disturbed in order to enable binding of its cognate antigen (Section 1. Introduction, paragraph 2). As such, immunoglobulin-binding proteins that bind Fc regions of immunoglobulins are useful for these purposes.
Regarding claim 11, Wang et al teaches the immunoglobulin-binding bacterial protein is Protein A (Abstract). Choe et al teaches other immunoglobulin-binding bacterial protein are Protein G and Protein L (Abstract).
Regarding claim 14 and 19, Choe et al further teaches that Protein A binds to the Fc region of IgG (Section 2. Immunoglobulin Binding Proteins, paragraph 1) and Wang et al teaches the antibodies are IgG (p. 794, section: 2.1 Reagents, para. 1), which is also logical since Wang uses Protein A. Therefore, the immunoglobulin-binding bacterial protein (Protein A) would bind the antibody (IgG) in Wang et al, meeting the limitations of claim 19.
One skilled in the art, before the effective filing date of the instant application, would be motivated to use the fusion protein taught by Wang et al or the improved version with the substituted biotin ligases taught by Branon et al which have 100% sequence identity to instant SEQ ID NO: 2 and 3, and use it in a composition or complex with antibodies, as taught by Farrell et al, arriving at all the limitations of the claimed invention. The biotin ligases miniTurbo and TurboID are disclosed to being capable of proximity labeling of proteins in live cells due to their rapid biotinylation in 10 minutes. Even BirA* is reasonably likely to be able to achieve live cell biotinylation, just over a longer period of time of 6 hours. Further, Wang et al and Farrell et teach two different ways of complexing the biotin ligase to an antibody, but one skilled in the art is motivated to choose the method taught by Wang et based on the teachings of Choe et al that Fc-binding ligands are preferred for antibody conjugation when the antibody will be used for its binding function. Since the thiol-maleimide chemistry method of conjugation taught in Farrell et al is not specifically directed away from the Fab region of an antibody, but the immunoglobulin-binding bacterial protein taught by Wang et al, Protein A, is directed to the Fc region of IgG, and the antibody will be used for its targeting function, one skilled in the art, before the effective filing date of the instant application, would be motivated to adopt the structure taught by Wang et al in order to not disturb the binding activity of the antibody, which is crucial to the method of targeted biotinylation. Therefore, the fusion protein as taught by Wang et al or with a substituted biotin ligase is motivated.
One skilled in the art, before the effective filing date of the instant application, would have reasonable expectation of success with this improvement as the difference in conjugation strategy does not hinder the proximity-dependent biotinylation function of the antibody and biotin ligase, especially since Branon et al envisions these biotin ligases linked to antibodies still functioning in subcellular compartments.
Additionally, the conjugation method effects the order of binding between the different components in the method. The structure as taught by Farrell et al, using the thiol-maleimide chemistry to attach the biotin ligase to the antibody, teaches this structure complexed together before introduction to its target sample of interest. The structure as taught by Wang et al teaches the antibody and biotin ligase can be introduced to the target sample of interest as a composition, without complexing to each other first. However, it is possible to also complex the polypeptide to antibody before introduction to the target sample of interest.
The impact of the conjugation method between the biotin ligase and antibody has been shown to not preclude the functions of the biotin ligase and antibody, although the method used by Wang et al and the instant application theoretically precludes the antibody's function less than the method used by Farrell et al. Specifically, the differences in conjugation method does not preclude the structure taught by Wang et al from effectively functioning in a subcellular region. The differences in conjugation method does not preclude the structure taught by Wang et al to be placed into a kit as taught by Farrell et al, as there are methods to store and maintain the immunoglobulin-binding bacterial protein function, as is evidenced by the use of these binding proteins in antibody purification chromatography columns (Choe et al, Abstract). The antibody directed biotin ligase would therefore be expected to function as described in both references, meeting all the claimed limitations of the instant application.
Response to Arguments
Applicant's arguments filed 05/26/2026 have been fully considered but they are not persuasive for the reasons discussed below.
Claim Rejections - 35 USC § 102
Regarding the prior 35 USC § 102 rejection of claims 1-2, Applicant amends and argues regarding claim 1 that Wang et al does not teach the claimed biotin ligase according to the amended claim. However, as discussed in the maintained 35 USC § 102, Wang et al does teach a biotin ligase that is within the scope of amended claim 1, particular meeting the limitation of a biotin ligase that has at least 90% sequence identity to the amino acid sequence of instant SEQ ID NO: 1. Applicant argues that Wang et al does not teach TurboID enzyme, which has the amino acid sequence of SEQ ID NO: 3, but amended claim 1 is not limited to SEQ ID NO: 3, and thus not limited to TurboID as the biotin ligase enzyme. Although the Applicant does not argue this, the previous 35 USC § 102 rejection was also proper as the claim was even broader and only claimed a biotin ligase with any sequence limitation. Therefore, Wang et al teaches a product that is encompassed by the scope of claims 1 and 2.
Regarding claims 1-2, Applicant further argues that the product of Wang et al and the instant application operate in different technical contexts, i.e. with immobilized proteins versus cellular systems, respectively. However, this argument is invalid to the present claims which do not claim these limitations. In response to applicant's argument that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (i.e., its use in different technical contexts) are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993). The comparison is thus solely on the claimed limitations, and Wang et al meets all the claimed limitations of claims 1-2.
In response to the Applicant’s arguments being unpersuasive, the prior 35 USC § 102 rejections of claims 1-2 are maintained and updated.
Claim Rejections - 35 USC § 103
Regarding the prior 35 USC § 103 rejection of claims 3-10, Applicant argues that because Wang et al improperly rejected claim 1, which these claims depend on, the prior 35 USC § 103 rejection of claims 3-10 is also accordingly improper for lacking a proper foundation. However, the previously presented 35 USC § 102 rejection of claims 1-2 were proper and are still proper with the amendments to claim 1 for reasons discussed in the response to arguments for the 35 USC § 102 rejection.
Furthermore, Applicant wrongly limits the comparison of the structure taught by Wang et al to TurboID only, even though the scope of the claim encompasses SEQ ID NO: 1, 2, or 3, and sequences with at least 90% identity to SEQ ID NO: 1, 2, or 3. BirA* taught by Wang et al has at least 90% identity to SEQ ID NO: 1, having just one amino acid mutation from the 321 amino acid SEQ ID NO: 1. Applicant argues that SEQ ID NO: 1, 2, and 3 are TurboID enzymes or modifications thereof, which is misleading. In fact, SEQ ID NO: 1 is the wildtype BirA, SEQ ID NO: 2 is miniTurbo, and SEQ ID NO: 3 is TurboID, as previously discussed from Branon et al. Thus, the foundation is proper.
Applicant then argues that even if the combination of references previously presented was proper, they do not render the amended claims obvious because of the added limitations regarding the amino acid sequence of the biotin ligase. Again, the scope of the claim encompasses BirA* and therefore, Wang et al does meet the amended limitations regarding the sequences.
Applicant then argues that Wang provides no teaching, suggestion, or motivation to replace BirA* with a TurboID enzyme. Applicant argues that Farrell does not cure the deficiencies of Wang et al in that Farrell is silent about TurboID, let alone a fusion protein comprising TurboID fused to an immunoglobulin bacterial protein. Applicant further argues that Choe et al likewise does not cure the deficiencies of Wang et al. Again, the scope of the claim encompasses more than TurboID and encompasses BirA*. Therefore, no substitution is even needed to meet the limitations. In response to applicant's argument that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (i.e., its use in different technical contexts) are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993). The comparison is thus solely on the claimed limitations, and Wang et al meets all the claimed limitations of claims 1-2.
Even if the claims were directed to only SEQ ID NO: 2 (miniTurbo) and/or SEQ ID NO: 3 (TurboID), Branon et al provides the exact sequence for these biotin ligases and provides the advantages of these biotin ligases over BirA*, providing a motivation to substitute the base BirA* with one of these biotin ligases, as discussed in the updated 35 USC § 103 regarding these claims.
Applicant further argues that the structure from Farrell et al operates in a fundamentally different technical context of diagnostic assays instead of proximity biotinylation inside a living cell. In response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). Ferrel et al was combined with Wang et al, which already anticipates the claimed fusion protein, to teach the further limitations reciting complexing the fusion protein with an immunoglobulin via its immunoglobulin-binding bacterial protein. It is acknowledged that the structure of Farrell et al is different from the instantly claimed fusion protein and the fusion protein of Wang et al, but the concept of complexing with an antibody is applicable and transferable to the fusion protein of Wang et al to arrive at the claimed invention, as previously discussed in the maintained rejections.
Applicant further argues that Choe et al does not cure the deficiencies of Wang et al regarding the biotin ligase. However, that is irrelevant as Choe et al is used to teach the additional claimed limitations required regarding the immunoglobulin-binding protein, as discussed in the maintained rejection.
The Applicant further argues that a point of difference between the Wang et al and the other references compared to the instant invention is the biotinylation of a protein of interest or a subcellular region in a living cell without requiring transfection or genetic mutation (p 13 last paragraph – p. 14). The applicant further argues that the motivation to combine is flawed because the BirA*-based fusion protein taught by Wang et al has no indication that it could work in cellular systems. These arguments are flaw for three reasons.
Firstly, in response to applicant's argument that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (i.e., biotinylation of a subcellular region in a living cell without requiring transfection or genetic mutation) are not the only options recited in the claim. Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993). The claims also recite biotinylating a protein of interest in a cell, a subcellular region or a sample of interest, wherein the method comprises contacting the cell or sample with the composition. As such, the claims encompass the method of Wang et al because it includes a sample of interest and does not limit to only subcellular regions.
Finally, in response to applicant's argument that the BirA*-Protein A protein of Wang et al was used for a different application than subcellular targeting, separate from this previously discussed incorrect argued interpretation of the claim scope, a recitation of the intended use of the claimed invention must result in a structural difference between the claimed invention and the prior art in order to patentably distinguish the claimed invention from the prior art. If the prior art structure is capable of performing the intended use, then it meets the claim. As such, the fact that the BirA*-Protein A was used for in vitro targeting does not unequivocally mean it cannot be used for subcellular targeting.
Even if the claims were narrowed to the subcellular regions, the structure of Wang et al, comprising of BioID is still reasonably likely capable of targeting subcellular regions. Furthermore, the motivation to substitute BioID with miniTurbo or TurboID, to arrive at the other embodiments of the claimed, is still reasonably likely capable of targeting subcellular regions. This is because Branon et al teaches BioID, miniTurbo, and TurboID are all capable of biotinylating, just over different timescales. In timepoints of 10 minutes, 6 hours, and 18 hours, TurboID is able to biotinylate in 10 minutes, whereas BioID biotinylates did not biotinylate in 10 minutes but does in 6 hours. No time points in between 10 minutes and 6 hours were presented. As such, both would be expected to biotinylate, but BioID would need a longer time. In any case, these properties are expected for the structure taught by Wang et al or substituted with TurboID or miniTurbo, based on the properties of these biotin ligases taught by Branon et al.
In response to the Applicant’s arguments being unpersuasive, the prior 35 USC § 103 rejections of claims 3-10 are maintained and updated.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BONIRATH CHHAY whose telephone number is (571)272-0682. The examiner can normally be reached Mon-Thu 8AM-5PM EST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Bao-Thuy Nguyen can be reached at (571) 272-0824. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/BONIRATH CHHAY/Examiner, Art Unit 1645
June 12, 2026
/BAO-THUY L NGUYEN/Supervisory Patent Examiner, Art Unit 1677 June 15, 2026
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