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 Status and Formal Matters
The instant response was filed 10/14/2025.
The instant response amended claims 1 has been amended.
Claims 1, 3, 13, 15 are pending.
Applicant’s election without traverse of group I, claims 1-14, Species 1: Tobacco etch virus (TEV) protease; Species 2: Beta-lactamase zymogen; and Species 3: Colorimetric substrate. Species 4: Claim 7 (the zymogen is B-lactamase zymogen and the colorimetric substrate is CENTA) in the reply filed on 2/20/2024 is acknowledged.
Claims 8-10, 15-21 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention or species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 2/20/2024.
Claims 1, 3-7, 13 are being examined.
The previous 102 rejection has been withdrawn in view of the certified translation of the foreign priority document.
Priority
The instant application was filed 04/02/2021 and is a national stage entry of PCT/KR2019/012891 with an international filing date: 10/02/2019 and claims foreign priority to KR10-2018-0119010, filed 10/05/2018.
Information Disclosure Statement
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Specification
The specification is objected to as failing to provide proper antecedent basis for the claimed subject matter. See 37 CFR 1.75(d)(1) and MPEP § 608.01(o). Correction of the following is required: Claim 1 has been amended to recite, “tobacco etch virus” and “(6R,7R)-3-[(3-carboxy- 4-nitrophenyl)sulfanylmethyll-8-oxo-7-[(2-thiophen-2-ylacetyl)aminol-5-thia-1- azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid”. Review and searching of the specification did not reveal antecedent basis for these limitations.
Summary
This is a new ground of objection.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1. 3, 13 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Further claim 1 has been amended to recite, “wherein the ssDNA- protease conjugate and the ssDNA-zymogen conjugate hybridize to the target nucleic acid at a distance of 3 nucleotides.” The response asserts support can be found in {0011}, {0031-0034} of the PGPUB. However, the description of figure 3 c states, “FIG. 3c shows the optimal conditions of the nucleotide spacer between the target nucleic-acid binding sites of the ssDNA-protease conjugate and the ssDNA-zymogen conjugate according to the present invention.” Further the response of 1/10/2025 asserts support can be found in paragraph 121 of the instant specification. This is confusing as paragraph 121 teaches
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This teaching is limited to Beta-lactamase zymogen conjugated to the 5’ end of ssDNA [86] and TEV-protease conjugated to the 3’ end of a single stranded DNA. [89] Thus the teachings are limited to a single example and do not provide support for the breadth of the claims. The response continues by providing arguments with respect to the specific example. These arguments have been thoroughly reviewed but is not considered persuasive as the teachings are limited to a single example and does not provide support for the full breadth of the claims.
Response to Arguments
The rejection with respect to the ranges of MgCl2 and temperature have been withdrawn in view of the amendment.
The response does not specifically address the issue with respect to the wherein clause, thus the rejection is maintained.
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.
Claim(s)1, 3, 13 is/are rejected under 35 U.S.C. 103 as being unpatentable over Stein (WO2016065415), Polayes (.Methods m Molecular Medicine, Vol 13 Molecular Diagnosis of Infectious Diseases (1998) pages 169-183), Lee (KR 20140121949 A), Bebrone (ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, June 2001, p. 1868-1871), Singh (Chem. Soc. Rev., 2010, 39, 2054–2070).
All references to Lee are to the English translation provided through P2E2 search.
Stein teaches, “This invention relates to biosensors. More particularly, this invention relates to a biosensor comprising a non-protease enzyme activity that is suitable for selective detection of one or more target molecules. The biosensor may be used to detect molecules in biological, clinical, environmental and industrial samples. The biosensor may also relate to the field of synthetic biology such as for constructing artificial cellular or extracellular signaling networks” (page 1)
Stein teaches, “In one aspect, the invention relates to a biosensor that comprises a first molecular component and a second molecular component, wherein the first molecular component comprises: a first binding partner, an amino acid sequence of an enzyme that is not a protease; and an inhibitor of the enzyme; and the second molecular component comprises: a second binding partner and an amino acid sequence capable of facilitating at least partial release of inhibition of the enzyme of the first molecular component by the inhibitor to thereby switch the enzyme of the first molecular component from a catalytically inactive to a catalytically active state.” (page 2-3)
Stein teaches, “Suitably, the first binding partner and the second binding partner are different molecules (e.g. proteins, nucleic acids, sugars, lipids or combinations of these although without limitation thereto) or are different portions, parts, segments, moieties, domains, regions, sub-sequences or fragments of the same molecule.” (page 4, lines 16-19)Stein teaches, “The term "nucleic acid" as used herein designates single-or double-stranded mRNA, RNA, cRNA, RNAi, siRNA and DNA inclusive of cDNA, mitochondrial DNA (mtDNA) and genomic DNA.”
Stein teaches, “In this regard, the target molecule may be any ligand, analyte, epitope, domain, fragment, subunit, moiety or combination thereof, such as a protein inclusive of antibodies and antibody fragments, antigens, phosphoproteins, glycoproteins, lipoproteins and glycoproteins, lipid, phospholipids, carbohydrates inclusive of simple sugars, disaccharides and polysaccharides, nucleic acids, nucleoprotein or any other molecule or analyte. These include drugs and other pharmaceuticals including antibiotics, chemotherapeutic agents and lead compounds in drug design and screening, molecules and analytes typically found in biological samples such as biomarkers, tumour and other antigens, receptors, DNA-binding proteins inclusive of transcription factors, hormones, neurotransmitters, growth factors, cytokines, receptors, metabolic enzymes, signaling molecules, nucleic acids such as DNA and RNA, membrane lipids and other cellular components, pathogen-derived molecules inclusive of viral, bacterial, protozoan, fungal and worm proteins, lipids, carbohydrates and nucleic acids, although without limitation thereto.” (page 20, lines 11-24).
Stein teaches, “It will be appreciated from the foregoing that the biosensor disclosed herein is comprises a non-protease enzyme that is capable of switching from a catalytically inactive state to a catalytically active state in response to a binding interaction or event that occurs between the first and second binding partners, such as when binding a target molecule. Suitably, the catalytically active enzyme is capable of reacting with a substrate molecule to produce a detectable signal. The detectable signal may be or include chromogenic, fluorescent, light (e.g. bioluminescent), electrical, radioactive and other detectable signals.”
Stein teaches, “In one general embodiment, the amino acid sequence of the second molecular component is of a protease. According to this general embodiment, the protease of the second molecular component is capable of proteolytically cleaving a protease cleavage site in the first molecular component. Suitably, this cleavage event is capable of facilitating at least partial release of inhibition of the enzyme of the first molecular component by the inhibitor to thereby switch the enzyme of the first molecular component from a catalytically inactive to a catalytically active state.” (page 3).
Stein does not specifically teach ssDNA-protease conjugate and zymogen or the MgCl2 or temperature required of the claims.
However, Stein teaches the use of an inactive enzyme and protease that are brought into proximity by a binding event.
Stein teaches, “Co-localization of the first and second molecular components upon binding or interaction between the first binding partner, the second binding partner and in some cases a target molecule, spatially localizes this low or basal protease activity in the proximity of the first molecular component to enable cleavage of the protease cleavage site in the first molecular component, thereby facilitate switching of the enzyme of the first molecular component from a catalytically inactive state to a catalytically active state.” (page 15)
MPEP 2144.05 II A States:
II. ROUTINE OPTIMIZATION
A. Optimization Within Prior Art Conditions or Through Routine Experimentation
Generally, differences in concentration or temperature will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration or temperature is critical. “[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation.” In reAller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955)
Therefore it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims the teachings of Stein encompass providing zymogen and protease in an orientation to allow for interaction to allow for activation including 3 nucleotides apart of instant claims. The artisan would be motivated to optimize and/or design choice to allow detect nucleic acids by use of a protease and an inactivate enzyme (zymogen). The artisan would have a reasonable expectation as the artisan is merely using methods taught by Stein. (claims 1, 3)
Lee teaches, “The Rheb-binding protein complex was then subjected to a TEV
cleavage reaction (100 U TEV enzyme, 10 mM Tris-HCl pH 8.0, 150 mM sodium chloride, 0.3% NP-40, 20 mM MgCl2 , 0.5 mMEDTA, .sub.0.5 mM DTT” )page 4, section 4.1).
Polayes teaches, “rTEV protease IS active over a broad temperature range (4°C-37°C)..” (3.4 page 178). Polayes teaches Tev Polayes teaches 50 mM MgCl2 reaction butter (materials)
MPEP 2144.05 II A States:
II. ROUTINE OPTIMIZATION
A.Optimization Within Prior Art Conditions or Through Routine Experimentation
Generally, differences in concentration or temperature will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration or temperature is critical.
Therefore it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to provide at least 20 mm MgCl2 and perform the protease cleavage assay at 37oC. The artisan would be motivated to find the best reaction conditions. The artisan would have a reasonable expectation of success as the artisan is merely using known conditions to start the optimization of the reaction taught by Stein.
While Stein teaches the use of TEV protease and an inactivated beta lactamase linked to nucleic acids which hybridize to detect a nucleic acid, Stein does not teach the use of CENTA as a substrate and detection at 405 nm, use of magnesium chloride or the temperature of the assay..
However, Berbone teaches CENTA is a chromogenic substrate for beta lactamases (title, abstract, throughout). Berbone teaches detection at 405 absorbance. (figure 2).
Therefore it would have been prima facie obvious to one of skill in the art prior to the effective filing date of the claims to use CENTA as a substrate for beta lactamase. The artisan would be motivated as Berbone teaches, “These experiments demonstrate that CENTA is a readily obtained chromogenic substrate which can conveniently be used in kinetic studies of b-lactamases and for the detection of these enzymes in bacterial crude extracts or in chromatographic fractions during enzyme purification. It can also be easily used in high-throughput screening tests for the selection of new b-lactamase inactivators” The artisan would have a reasonable expectation of success as the artisan is merely using a known substrate for a known enzyme.
While the prior art teaches , Stein teaches the detection of a nucleic acid target, he does not specifically teach how or where the TEV protease and Zymogen are attached.
However, Singh teaches, “ONs are conjugated mostly at 5’-or3’-termini because of their easy accessibility.”
Therefore it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to attach the protease to the 5’ and zymogen at the 3’ end. The artisan would be motivated as Singh teaches conjugation to nucleotide sequence at the 5’ and 3’ end. The artisan would be further motivated to provide orientation of the zymogen and protease to provide greatest activity. The artisan would have a reasonable expectation of success as the artisan is merely using known means of attaching zymogens and proteases to nucleic acid sequences.
With regards to claim 3, Stein teaches, “Activation of the protease may be actuated on an effector comprising an enzymatic or structural protein domain operably linked to an auto inhibitory domain via a linker containing a cleavage site of the said protease” (page 30, lines 7-9). Stein teaches, “As will be described in more detail in the Examples, ~-lactamase cleavage of nitrocefin results in an increase in detectable signal measured as an increases in absorbance at A620.” (page 23).
Stein claims TEV protease (claim 18) (page 11, line 20).
Stein teaches,” ~-lactamase amino acid sequences are underlined, the amino acid sequence of the protease cleavage site is bolded and the amino acid sequence of the auto inhibitor peptide is double-underlined.” (page 31, lines 17-19).
Stein teaches, “As will be described in more detail in the Examples, ~-lactamase cleavage of nitrocefin results in an increase in detectable signal measured as an increase in absorbance at A620.” (page 23).
Stein teaches, “A "primer" is usually a single-stranded oligonucleotide, preferably having 15-50 contiguous nucleotides, which is capable of annealing to a complementary nucleic acid "template" and being extended in a template-dependent fashion by the action of a DNA polymerase such as Taq polymerase,”
Stein does not specifically teach amplification.
Therefore it would have bene prima facie obvious to one of ordinary skill of the
art to use primer extension and Taq polymerase to Stein to amplify the sequence via
polymerase chain reaction. The artisan would be motivated as amplify the target
nucleic acid sequence to increase the likelihood it is present in a high enough concentration to be detected. The artisan would have a reasonable expectation of
success as the artisan is merely using known methods to amplify nucleic acids.
Response to Arguments
The response traverses the rejection asserting Stein does not teach detection of nucleic acids. This argument has been thoroughly reviewed but is not considered persuasive as Stein teaches, “In this regard, the target molecule may be any ligand, analyte, epitope, domain, fragment, subunit, moiety or combination thereof, such as a protein inclusive of antibodies and antibody fragments, antigens, phosphoproteins, glycoproteins, lipoproteins and glycoproteins, lipid, phospholipids, carbohydrates inclusive of simple sugars, disaccharides and polysaccharides, nucleic acids, nucleoprotein or any other molecule or analyte..” (page 20, lines 11-24).
The response continues by asserting Stein does not describe the importance of any conditions. 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). Further the cited prior art renders the limitations obvious.
The response continues by providing arguments with respect to 37oC. Polayes teaches, “rTEV protease IS active over a broad temperature range (4°C-37°C)..” (3.4 page 178). The response continues by providing arguments to the AcTEV product sheet. This argument is not considered persuasive as the claims are not limited to AcTEV product, further the response has not provided the alleged product sheet. Thus this is arguments of counsel not substantiated by evidence. Further the art of Polayes teaches, “rTEV protease IS active over a broad temperature range (4°C-37°C)..” (3.4 page 178).
The response continues by providing arguments to the temperature of TEV. This argument has been thoroughly reviewed but is not considered persuasive as Polayes teaches, “rTEV protease IS active over a broad temperature range (4°C-37°C)..” (3.4 page 178). Chen (Engineering of TEV Protease for Manipulation of Biosystems , 2013) teaches, “TEVp is active over a wide range salt concentrations and temperatures from 4 °C to 37 °C, with optimum activity at around 30 °C, while retaining appreciable activity at 4 °C and 37 °C (73, 74).” (page 12)
The response continues by asserting Polayes teaches away from the claims from the temperature conditions. This argument has been thoroughly reviewed but is not considered persuasive as Polayes teaches, “rTEV protease IS active over a broad temperature range (4°C-37°C)..” (3.4 page 178). Chen (Engineering of TEV Protease for Manipulation of Biosystems , 2013) teaches, “TEVp is active over a wide range salt concentrations and temperatures from 4 °C to 37 °C, with optimum activity at around 30 °C, while retaining appreciable activity at 4 °C and 37 °C (73, 74).” (page 12)
The response continues by providing argues with respect to a meta-analysis of MgCl2 concentration and DNA hybridization , but does not provide the article references. Thus this is not persuasive as it appears to be arguments of counsel not substantiated by evidence.
The response continues by providing arguments with respect to alleged unexpected results and teaching away. This argument MPEP 2123 states:
“[t]he prior art’s mere disclosure of more than one alternative does not constitute a teaching away from any of these alternatives because such disclosure does not criticize, discredit, or otherwise discourage the solution claimed….” In re Fulton, 391 F.3d 1195, 1201, 73 USPQ2d 1141, 1146 (Fed. Cir. 2004).
Depuy Spine, Inc. v. Medtronic Sofamor Danek, Inc., 567 F.3d 1314 (Fed. Cir. 2009). The courts indicated a reference that does "not criticize, discredit, or otherwise discourage investigation into the invention claimed," does not teach away.”
In the instant case the response has provided no evidence any of the relied on references discourage, discredit or otherwise discourage the claimed invention.
First, MPEP 716.01(c) makes clear that "The arguments of counsel cannot take the place of evidence in the record. In re Schulze , 346 F.2d 600, 602, 145 USPQ 716, 718 (CCPA 1965). Examples of attorney statements which are not evidence and which must be supported by an appropriate affidavit or declaration include statements regarding unexpected results, commercial success, solution of a long - felt need, inoperability of the prior art, invention before the date of the reference, and allegations that the author(s) of the prior art derived the disclosed subject matter from the applicant." Here, the statements regarding the unexpected results must be supported by evidence, not argument.
This should not be construed as an invitation for providing evidence. As further stated in the MPEP 716.01 regarding the timely submission of evidence:
A) Timeliness.
Evidence traversing rejections must be timely or seasonably filed to be entered and entitled to consideration. In re Rothermel, 276 F.2d 393, 125 USPQ 328 (CCPA 1960). Affidavits and declarations submitted under 37 CFR 1.132 and other evidence traversing rejections are considered timely if submitted:
(1) prior to a final rejection,
(2) before appeal in an application not having a final rejection, or
(3) after final rejection and submitted
(i) with a first reply after final rejection for the purpose of overcoming a new ground of rejection or requirement made in the final rejection, or
(ii) with a satisfactory showing under 37 CFR 1.116(b) or 37
CFR 1.195, or
(iii) under 37 CFR 1.129(a).
Thus the rejection is maintained.
Summary
No claims are allowed.
Conclusion
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 STEVEN C POHNERT PhD whose telephone number is (571)272-3803. The examiner can normally be reached Monday- Friday about 6:00 AM-5:00 PM, every second Friday off.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Anne Gussow can be reached at (571)272-6047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/Steven Pohnert/Primary Examiner, Art Unit 1683
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