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
This action is in response to papers filed 6/6/2025.
Claims 1, 3, 6, 9, 15, 22-23 have been amended.
Applicant’s election of Group I, [1] the detergent (14) is kept ready in a preparation buffer; [2] the detergent (14) is a nonionic detergent, and the nonionic detergent is Tween 80; [3] the detergent (14) is added before the start of fixation (13); [4] the hybridization buffer contains a buffer substance; [5] the hybridization buffer contains at least one salt; [6] detecting (16) comprises quantification; [7] the nucleic acid probe (11) is complementary RNA of a microorganism (1) to be detected; [8] the nucleic acid probe (11) is selected from molecular beacons; [9] a step for additional background reduction; [10] an additional initial step for improved living/dead differentiation by degradation of the target nucleic acids in dead microorganisms; [11] delivery and fixation occur concurrently; and [12] the detectable label (15) is selected from the group consisting of fluorescent labels. in the reply filed on 5/30/2023 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claims 2, 17, 19 withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 5/30/2023.
Claims 1, 3-7, 9-12, 14-16, 18, 20-23 are being examined.
The previous objection to the claims has been withdrawn.
Priority
The instant application was filed 02/12/2021, and claims foreign priority to EP102020103957.3, filed 02/14/2020. It is noted the foreign priority document is not in English.
Specification
The amendment filed 8/14/2024 is objected to under 35 U.S.C. 132(a) because it introduces new matter into the disclosure. 35 U.S.C. 132(a) states that no amendment shall introduce new matter into the disclosure of the invention. The added material which is not supported by the original disclosure is as follows: The specification has been amended to recite, “The detergent can, for example, also be a nonionic detergent, preferably Triton X-100 (2,4,4-trimethylpentan-2-yl)phenoxylethanol) or Tween 80 ( 2-{2-[3,4- bis(2-hydroxyethoxy)oxolan-2-yl]-2-(2-hydroxyethoxy)ethoxyt}ethyl (9E)-octadec-9- enoate)..” The response provides no indication where support for the amendment can be found. The response asserts “. Applicant respectfully asserts that these amendments are not “arguments of counsel” at least because IUPAC is an international standardized system for naming organic chemical compounds.” This is arguments of counsel not substantiated by evidence as the response has provide no evidence to substantiate the argument.
Applicant is required to cancel the new matter in the reply to this Office Action.
Response to Arguments
The response traverses the rejection asserting, “Applicant respectfully asserts that these amendments are not “arguments of counsel” at least because IUPAC is an international standardized system for naming organic chemical compounds.”. This is arguments of counsel not substantiated by evidence as the response has provide no evidence to substantiate the argument.
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 22are 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.
New matter
MPEP 2163 IB New or amended claims section II
With respect to newly added or amended claims, applicant should show support in the original disclosure for the new or amended claims. See, e.g., Hyatt v. Dudas, 492 F.3d 1365, 1370, n.4 (Fed. Cir. 2007) (citing MPEP § 2163.04 which provides that a "simple statement such as ‘applicant has not pointed out where the new (or amended) claim is supported, nor does there appear to be a written description of the claim limitation ‘___’ in the application as filed’ may be sufficient where the claim is a new or amended claim, the support for the limitation is not apparent, and applicant has not pointed out where the limitation is supported."); see also MPEP §§ 714.02 and 2163.06 ("Applicant should ... specifically point out the support for any amendments made to the disclosure."); and MPEP § 2163.04
Claim 22 has been amended to recite, “C2-[4-(2,4,4-trimethylpentan-2-yl)phenoxy]ethanol-G14H220(C2H4O) (wherein n=9-10) or 2-{2-[3,4-bis(2- hydroxyethoxy)oxolan-2-yl]-2-(2-hydroxyethoxy)ethoxy}ethyl (9E)-octadec-9-enoate..” The response asserts, “, “Applicant respectfully asserts that these amendments are not “arguments of counsel” at least because IUPAC is an international standardized system for naming organic chemical compounds.”. This argument has been thoroughly reviewed but is not considered persuasive as the response has provided no evidence to substantiate such an assertion. .
Response to Arguments
The response asserts, “, “Applicant respectfully asserts that these amendments are not “arguments of counsel” at least because IUPAC is an international standardized system for naming organic chemical compounds.”. This argument has been thoroughly reviewed but is not considered persuasive as the response has provided no evidence to substantiate such an assertion. .
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1, 3-12, 14-16, 18, 20-23 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 1 recites, “wherein fixation is not complete until the detergent is added.” Claim 1 later recites, "fixation of the microorganism occurs at least during the delivery of the nucleic acid probes such that the delivering of the nucleic acids probes and the fixation of the microorganisms takes place concurrently.” The recitation of “not complete” and “concurrently” are relative terms. The specification and claims do nod define how to differentiate not complete fixation from complete fixation. Further the specification and claims fail to provide how to differentiate fixation occurring concurrently or non-concurrently or how to reconcile the two limitations of the wherein clause.
Further the claim recites, “nontoxic denaturing substance.” The claim provides no guidance on how to differentiate a toxic nondenaturing substance from a nontoxic denaturing substance. Review of the specification did not reveal differentiate a toxic nondenaturing substance from a nontoxic denaturing substance. Thus the metes and bounds are unclear of what is required of a nontoxic denaturing substance.
Response to Arguments
The response traverses the previous rejections in view of the amendments. This is noted, however the amendments raised new issues.
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.
Claim(s) 1, 3-7, 9-12, 18, 21-23 is/are rejected under 35 U.S.C. 102(a)(1)/102(a)(2)as being anticipated by Fiandaca (USPGPUB 2007/0128646) as evidence by Kiebish (US 20180024132).
Claim 1 has been amended to recite, “nucleic acid probes comprising an optically detectable label.” The specification recites “nucleic acid ” 103 and provides no limiting definition. Kiebish teaches, “. In certain embodiments, the analyte comprises a nucleic acid and the probe comprises one or more synthetic single stranded nucleic acid molecules, e.g., a DNA molecule, a DNA-RNA hybrid, a PNA, or a modified nucleic acid molecule containing one or more artificial bases, sugars, or backbone moieties. .” (0555)Thus the broadest reasonable interpretation of an nucleic acid probe encompasses PNA.
With regards to claim 1, Fiandaca teaches, “0002 This invention is related to the field of probe based nucleic acid sequence detection, analysis and quantification. More specifically, this invention relates to the use of PNA probes in aqueous alcohol solutions for diagnostic applications. In one aspect, the invention enables sample preparation and analysis to be performed as a single step.” Fiandaca teaches, “0034) d. As used herein, the term “probe' means a polymer (e. g. a DNA, RNA, PNA, chimera or linked polymer) having a probing nucleobase sequence that is designed to sequence-specifically hybridize to a target sequence of interest.”
Fiandaca teaches, “0008] The present invention provides compositions, methods and kits for hybridizing a PNA probe to a target sequence. In one aspect, the invention features compositions in which at least one PNA probe is provided in combination with an aqueous alcohol solution that serves, for instance, as a specimen fixing and probe hybridization medium. The invention has a wide spectrum of important applications including use in pathogen detection assays.” Fiandaca teaches, “0075] The PNA probes may be designed to specifically bind nucleic acid targets, such as both DNA and RNA, including rRNA and mRNA. Non-limiting examples, include PNA probes for analysis of microorganisms and, for example, targeting species-specific rRNA sequences. For example the PNA probes may be targeting microorganisms potentially present in cervical swabs associated with women's health, such as but not limited to PNA probes targeting Chlamydia trachomatis and/or Neisseria gonorrhoeae (for examples of PNA probe nucleobase sequences see U.S. Pat. No. 6,169,169), Candida albicans (for example of PNA probe nucleobase sequences see Rigby et al. J. Clin. Microbiol. 40:2182-218(2002)), Gardnerella vaginalis, Trichomonas vaginalis and/or Streptococcus agalactia (Group B streptococci).”
Fiandaca teaches, “[0012] Practice of the invention can help avoid the time and expense of adding probe to a specimen after it is fixed. That is, the invention can be used, in one embodiment, to provide for essentially simultaneous fixation and hybridization of the PNA probe to target sequence. In this invention example, the need to use conventional assay steps involving the removal, exchange, inactivation and/or addition of chemicals needed for either fixation or hybridization is greatly reduced and often avoided.”
Fiandaca teaches, “[0024] An aqueous alcohol solution in accord with the invention can further include at least one of the following components: a buffering agent (eg., Tris, Hepes, PBS, etc); monovalent cation such as sodium or potassium; divalent cation such as calcium or magnesium ion; suitable anion such as acetate, chloride, fumarate, maleate, citrate, sulfate, phosphate, carbonate, etc.; cross-linking agent such as formaldehyde; chaotropic agent such as formamide; chelating agent such as EDTA; ionic or non-ionic detergent such as Triton-X-100, Nonidet P-40, SDS; stabilizer such as a polymer (eg., Ficoll 400, dextran salt, etc); or a preservative (eg., azide). In certain invention embodiments, one or more of the components may be present in trace amounts. For other applications, specific amounts of the components to be added to the solution will be informed by recognized parameters such as the sample for which detection of the target is needed, the assay format to be used, etc.”
Fiandaca teaches, “0034) d. As used herein, the term “probe' means a polymer (e. g. a DNA, RNA, PNA, chimera or linked polymer) having a probing nucleobase sequence that is designed to sequence-specifically hybridize to a target sequence of interest.”
Thus Fiandaca teaches delivering an oligonucleotide probe (RNA, DNA, PNA or chimera) to a microorganism in a fixative solution (alcohol) with a detergent and denaturing agent and detecting (claim 1 and 18, 0024).
With regards to claim 3, Fiandaca teaches the fixative solution has detergent and the probe and thus is a hybridization solution or preparation buffer (0024).
With regards to claim 4, Fiandaca teaches triton-x100, NP-40 and SDS.
With regards to claim 5, Fiandaca teaches the alcohol is added with the probe and thus is prior to fixation.
With regards to claim 6-7, Fiandaca teaches the use of chaotropic agents. Chaotropic agents are denaturing substance.
With regards to claim 9, Fiandaca teaches the use of salts (0024).
With regards to claim 10, Fiandaca teaches, “The assay may also be used to detect, identify and/or quantify microorganisms optionally present in the sample, such as, but not limited to, pathogens in cervical swabs; such as, but not limited to, Chlamydia trachomatis and human papilomavirus or bioterrorism.” (0115)
With regards to claim 11, 22, Fiandaca teaches probes complementary to rRNA, which is also complementary to DNA for rRNA. (0139)
With regards to claim 12 Fiandaca teaches use of optical labels (0044, 0045, 0070, 0120).
With regards to claim 22, Fiandaca teaches the use of TritonX100 (0024).
Response to Arguments
The response traverses the rejection asserting one of skill in the art would recognize nucleic acid is not a PNA. This argument is a little confusing as PNA is Peptide Nucleic Acid, thus a PNA is a nucleic acid. Further Kiebish (US 20180024132)
teaches, “. In certain embodiments, the analyte comprises a nucleic acid and the probe comprises one or more synthetic single stranded nucleic acid molecules, e.g., a DNA molecule, a DNA-RNA hybrid, a PNA, or a modified nucleic acid molecule containing one or more artificial bases, sugars, or backbone moieties. .” Further Li (20170275680) teaches, “ 0010] The probe nucleic acid molecules are typically single-stranded, or comprise at least a single-stranded region. In some embodiments, the probe nucleic acid molecules may also comprise a double-stranded region, or a triple-stranded region. The probe nucleic acid molecules may be formed from oligonucleotides, deoxyribonucleic acid (DNA), ribonucleic acid (RNA), or peptide nucleic acid (PNA). They may include both natural or artificial or synthetic nucleic acids. “ Further, LI (US2016/0304936)teaches, “[0037] The terms “polynucleotide,” “oligonucleotide,” “nucleic acid” and “nucleic acid molecule” are used herein to include a polymeric form of nucleotides of any length, either ribonucleotides or deoxyribonucleotides. This term refers only to the primary structure of the molecule. Thus, the term includes triple-, double- and single-stranded DNA, as well as triple-, double- and single-stranded RNA. It also includes modifications, such as by methylation and/or by capping, and unmodified forms of the polynucleotide. More particularly, the terms “polynucleotide,” “oligonucleotide,” “nucleic acid” and “nucleic acid molecule” include polydeoxyribonucleotides (containing 2-deoxy-D-ribose), polyribonucleotides (containing D-ribose), any other type of polynucleotide which is an N- or C-glycoside of a purine or pyrimidine base, and other polymers containing nonnucleotidic backbones, for example, polyamide (e.g., peptide nucleic acids (PNAs)) and polymorpholino (commercially available from the Anti-Virals, Inc., Corvallis, Oreg., as Neugene) polymers, and other synthetic sequence-specific nucleic acid polymers providing that the polymers contain nucleobases in a configuration which allows for base pairing and base stacking, such as is found in DNA and RNA. There is no intended distinction in length between the terms “polynucleotide,” “oligonucleotide,” “nucleic acid” and “nucleic acid molecule,” and these terms will be used interchangeably. Thus, these terms include, for example, 3′-deoxy-2′,5′-DNA, oligodeoxyribonucleotide N3′ P5′ phosphoramidates, 2′-O-alkyl-substituted RNA, double- and single-stranded DNA, as well as double- and single-stranded RNA, DNA:RNA hybrids, and hybrids between PNAs and DNA or RNA, and also include known types of modifications, for example, labels which are known in the art, methylation, “caps,” substitution of one or more of the naturally occurring nucleotides with an analog, internucleotide modifications such as, for example, those with uncharged linkages (e.g., methyl phosphonates, phosphotriesters, phosphoramidates, carbamates, etc.), with negatively charged linkages (e.g., phosphorothioates, phosphorodithioates, etc.), and with positively charged linkages (e.g., aminoalklyphosphoramidates, aminoalkylphosphotriesters), those containing pendant moieties, such as, for example, proteins (including nucleases, toxins, antibodies, signal peptides, poly-L-lysine, etc.), those with intercalators (e.g., acridine, psoralen, etc.), those containing chelators (e.g., metals, radioactive metals, boron, oxidative metals, etc.), those containing alkylators, those with modified linkages (e.g., alpha anomeric nucleic acids, etc.), as well as unmodified forms of the polynucleotide or oligonucleotide. “ Further Parish (US 2009/0044289)teaches, [0132] "Nucleic acid" as used herein refers to an oligonucleotide, polynucleotide, nucleotide and fragments or portions thereof, as well as to peptide nucleic acids (PNA), fragments, portions or antisense molecules thereof, and to DNA or RNA of genomic or synthetic origin which can be single- or double-stranded, and represent the sense or antisense strand. Where "nucleic acid" is used to refer to a specific nucleic acid sequence "nucleic acid" is meant to encompass polynucleotides that encode a polypeptide that is functionally equivalent to the recited polypeptide, e.g., polynucleotides that are degenerate variants, or polynucleotides that encode biologically active variants or fragments of the polypeptide, including polynucleotides having substantial sequence similarity or sequence identity relative to the sequences provided herein.” Further these are merely arguments of counsel not substantiated by evidence. As stated in the MPEP, 2145 “Arguments of Counsel”
“If a prima facie case of obviousness is established, the burden shifts to the applicant to come forward with arguments and/or evidence to rebut the prima facie case. See, e.g., In re Dillon, 919 F.2d 688, 692, 16 USPQ2d 1897, 1901 (Fed. Cir. 1990) (en banc). Rebuttal evidence and arguments can be presented in the specification, In re Soni, 54 F.3d 746, 750, 34 USPQ2d 1684, 1687 (Fed. Cir. 1995), by counsel, In re Chu, 66 F.3d 292, 299, 36 USPQ2d 1089, 1094-95 (Fed. Cir. 1995), or by way of an affidavit or declaration under 37 CFR 1.132, e.g., Soni, 54 F.3d at 750, 34 USPQ2d at 1687; In re Piasecki, 745 F.2d 1468, 1474, 223 USPQ 785, 789-90 (Fed. Cir. 1984). However, arguments of counsel cannot take the place of factually supported objective evidence. See, e.g., In re Huang, 100 F.3d 135, 139-40, 40 USPQ2d 1685, 1689 (Fed. Cir. 1996); In re De Blauwe, 736 F.2d 699, 705, 222 USPQ 191, 196 (Fed. Cir. 1984)..”
This should not be construed as an invitation for providing evidence.
The response on page 15 further alleges the teachings of Fiandaca require PNA which is not required of the claim. This argument has been thoroughly reviewed but is not considered persuasive as PNA is within the scope of a nucleic acid probe as the specification lacks a limiting definition of nuclei acid probe, while the art of u, LI, Parrish, and Ji demonstrate a PNA is within the scope of the nucleic acid probe.
The response further asserts MPEP 2111 asserting the broadest claims are to be given the broadest reasonable interpretation, not the broadest possible interpretation. This argument has been thoroughly reviewed but is not considered persuasive as the specification has not provided any definition and the art of Wu, LI, Parrish, and Ji demonstrate the art clearly demonstrate the art recognizes nucleic acid probes encompasses a PNA.
The response continues by arguing the claim requires a hybridization buffer containing a nontoxic denaturing substance. The response further alleges the alcohol solution of Fiandaca is toxic. This argument has been thoroughly reviewed but is not considered persuasive as the claim requires, “a hybridization buffer containing a nontoxic denaturing substance.” The claim does not require the fixative or the hybridization solution is not toxic. Further the specification does not define “nontoxic.” Thus it is unclear what non-toxic requires. Further it is unclear what nontoxic is relative to, as some microorganisms (yeast) produce alcohol and thus is not toxic to all microorganisms. Finally these are arguments of counsel not substantiated by evidence.
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."
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).
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) 1-7, 9-12, 14, 18, 21-23 is/are rejected under 35 U.S.C. 103 as being unpatentable over by Fiandaca (USPGPUB 2007/0128646) as evidence by Kiebish (US 20180024132) and Khoo (20180136210).
Claim 1 has been amended to recite, “nucleic acid probes comprising an optically detectable label.” The specification recites “nucleic acid ” 103 and provides no limiting definition. Kiebish teaches, “. In certain embodiments, the analyte comprises a nucleic acid and the probe comprises one or more synthetic single stranded nucleic acid molecules, e.g., a DNA molecule, a DNA-RNA hybrid, a PNA, or a modified nucleic acid molecule containing one or more artificial bases, sugars, or backbone moieties. .” (0555)Thus the broadest reasonable interpretation of an nucleic acid probe encompasses PNA.
With regards to claim 1, Fiandaca teaches, “0002 This invention is related to the field of probe based nucleic acid sequence detection, analysis and quantification. More specifically, this invention relates to the use of PNA probes in aqueous alcohol solutions for diagnostic applications. In one aspect, the invention enables sample preparation and analysis to be performed as a single step.” Fiandaca teaches, “0034) d. As used herein, the term “probe' means a polymer (e. g. a DNA, RNA, PNA, chimera or linked polymer) having a probing nucleobase sequence that is designed to sequence-specifically hybridize to a target sequence of interest.”
Fiandaca teaches, “0008] The present invention provides compositions, methods and kits for hybridizing a PNA probe to a target sequence. In one aspect, the invention features compositions in which at least one PNA probe is provided in combination with an aqueous alcohol solution that serves, for instance, as a specimen fixing and probe hybridization medium. The invention has a wide spectrum of important applications including use in pathogen detection assays.” Fiandaca teaches, “0075] The PNA probes may be designed to specifically bind nucleic acid targets, such as both DNA and RNA, including rRNA and mRNA. Non-limiting examples, include PNA probes for analysis of microorganisms and, for example, targeting species-specific rRNA sequences. For example the PNA probes may be targeting microorganisms potentially present in cervical swabs associated with women's health, such as but not limited to PNA probes targeting Chlamydia trachomatis and/or Neisseria gonorrhoeae (for examples of PNA probe nucleobase sequences see U.S. Pat. No. 6,169,169), Candida albicans (for example of PNA probe nucleobase sequences see Rigby et al. J. Clin. Microbiol. 40:2182-218(2002)), Gardnerella vaginalis, Trichomonas vaginalis and/or Streptococcus agalactia (Group B streptococci).”
Fiandaca teaches, “[0012] Practice of the invention can help avoid the time and expense of adding probe to a specimen after it is fixed. That is, the invention can be used, in one embodiment, to provide for essentially simultaneous fixation and hybridization of the PNA probe to target sequence. In this invention example, the need to use conventional assay steps involving the removal, exchange, inactivation and/or addition of chemicals needed for either fixation or hybridization is greatly reduced and often avoided.”
Fiandaca teaches, “[0024] An aqueous alcohol solution in accord with the invention can further include at least one of the following components: a buffering agent (eg., Tris, Hepes, PBS, etc); monovalent cation such as sodium or potassium; divalent cation such as calcium or magnesium ion; suitable anion such as acetate, chloride, fumarate, maleate, citrate, sulfate, phosphate, carbonate, etc.; cross-linking agent such as formaldehyde; chaotropic agent such as formamide; chelating agent such as EDTA; ionic or non-ionic detergent such as Triton-X-100, Nonidet P-40, SDS; stabilizer such as a polymer (eg., Ficoll 400, dextran salt, etc); or a preservative (eg., azide). In certain invention embodiments, one or more of the components may be present in trace amounts. For other applications, specific amounts of the components to be added to the solution will be informed by recognized parameters such as the sample for which detection of the target is needed, the assay format to be used, etc.”
Fiandaca teaches, “0034) d. As used herein, the term “probe' means a polymer (e. g. a DNA, RNA, PNA, chimera or linked polymer) having a probing nucleobase sequence that is designed to sequence-specifically hybridize to a target sequence of interest.”
Fiandaca does not specifically teach the use of a fluidic channel.
However, Koo teaches, “[0079] As will also be appreciated by those of skill in the art, the microfluidic device can further comprise other components upstream, downstream, or within a device. For example, one or more microfluidic devices can further comprise one or more collection devices (e.g., a reservoir), flow devices (e.g., a syringe, pump, pressure gauge, temperature gauge), analysis devices (e.g., a 96-well microtiter plate, a microscope), filtration devices (e.g., a membrane), e.g., for upstream or downstream analysis (e.g., immunostaining, polymerase chain reaction (PCR) such as reverse PCR, quantitative PCR), fluorescence (e.g., fluorescence in situ hybridization (FISH)), sequencing, and the like. An imaging system may be connected to the device, to capture images from the device, and/or may receive light from the device, in order to permit real time visualization of the isolation process and/or to permit real time enumeration of isolated cells. In one example, the imaging system may view and/or digitize the image obtained through a microscope when the device is mounted on a microscope slide. For instance, the imaging system may include a digitizer and/or camera coupled to the microscope and to a viewing monitor and computer processor.”
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 perform the method in a microfluidic system as taught by Khoo. The artisan would be motivated to use a microfluidic channel system to minimize the amount of reagents and samples required in the method. The artisan would have a reasonable expectation of success as the artisan is merely using known method and apparatus to perform a known method.
With regards to claim 3, Fiandaca teaches the fixative solution has detergent and the probe and thus is a hybridization solution (0024).
With regards to claim 4, Fiandaca teaches triton-x100, NP-40 and SDS.
With regards to claim 5, Fiandaca teaches the alcohol is added with the probe and thus is prior to fixation.
With regards to claim 6-7, Fiandaca teaches the use of chaotropic agents. Chaotropic agents are denaturing substance.
With regards to claim 9, Fiandaca teaches the use of salts (0024).
With regards to claim 10, Fiandaca teaches, “The assay may also be used to detect, identify and/or quantify microorganisms optionally present in the sample, such as, but not limited to, pathogens in cervical swabs; such as, but not limited to, Chlamydia trachomatis and human papilomavirus or bioterrorism.” (0115)
With regards to claim 11, 23Fiandaca teaches probes complementary to rRNA, which is also complementary to DNA for rRNA. (0139)
With regards to claim 12, 21 Fiandaca teaches use of optical labels including fluorescent labels (0044, 0045, 0070, 0120).
With regards to claim 22, Fiandaca teaches the use of TritonX100 (0024).
Response to Arguments
The response traverses the rejection in view of the alleged deficiencies of Fiandaca. These arguments are not persuasive for the reasons of record.
Claim(s) 1-7, 9-12, 15 18, 21-23 is/are rejected under 35 U.S.C. 103 as being unpatentable over Fiandaca (USPGPUB 2207/0128646) as evidence by Kiebish (US 20180024132) and Rigby (.USPGPUB 20030165856)
Claim 1 has been amended to recite, “nucleic acid probes comprising an optically detectable label.” The specification recites “nucleic acid ” 103 and provides no limiting definition. Kiebish teaches, “. In certain embodiments, the analyte comprises a nucleic acid and the probe comprises one or more synthetic single stranded nucleic acid molecules, e.g., a DNA molecule, a DNA-RNA hybrid, a PNA, or a modified nucleic acid molecule containing one or more artificial bases, sugars, or backbone moieties. .” (0555)Thus the broadest reasonable interpretation of an nucleic acid probe encompasses PNA.
With regards to claim 1, Fiandaca teaches, “0002 This invention is related to the field of probe based nucleic acid sequence detection, analysis and quantification. More specifically, this invention relates to the use of PNA probes in aqueous alcohol solutions for diagnostic applications. In one aspect, the invention enables sample preparation and analysis to be performed as a single step.” Fiandaca teaches, “0034) d. As used herein, the term “probe' means a polymer (e. g. a DNA, RNA, PNA, chimera or linked polymer) having a probing nucleobase sequence that is designed to sequence-specifically hybridize to a target sequence of interest.”
Fiandaca teaches, “0008] The present invention provides compositions, methods and kits for hybridizing a PNA probe to a target sequence. In one aspect, the invention features compositions in which at least one PNA probe is provided in combination with an aqueous alcohol solution that serves, for instance, as a specimen fixing and probe hybridization medium. The invention has a wide spectrum of important applications including use in pathogen detection assays.” Fiandaca teaches, “0075] The PNA probes may be designed to specifically bind nucleic acid targets, such as both DNA and RNA, including rRNA and mRNA. Non-limiting examples, include PNA probes for analysis of microorganisms and, for example, targeting species-specific rRNA sequences. For example the PNA probes may be targeting microorganisms potentially present in cervical swabs associated with women's health, such as but not limited to PNA probes targeting Chlamydia trachomatis and/or Neisseria gonorrhoeae (for examples of PNA probe nucleobase sequences see U.S. Pat. No. 6,169,169), Candida albicans (for example of PNA probe nucleobase sequences see Rigby et al. J. Clin. Microbiol. 40:2182-218(2002)), Gardnerella vaginalis, Trichomonas vaginalis and/or Streptococcus agalactia (Group B streptococci).”
Fiandaca teaches, “[0012] Practice of the invention can help avoid the time and expense of adding probe to a specimen after it is fixed. That is, the invention can be used, in one embodiment, to provide for essentially simultaneous fixation and hybridization of the PNA probe to target sequence. In this invention example, the need to use conventional assay steps involving the removal, exchange, inactivation and/or addition of chemicals needed for either fixation or hybridization is greatly reduced and often avoided.”
Fiandaca teaches, “[0024] An aqueous alcohol solution in accord with the invention can further include at least one of the following components: a buffering agent (eg., Tris, Hepes, PBS, etc); monovalent cation such as sodium or potassium; divalent cation such as calcium or magnesium ion; suitable anion such as acetate, chloride, fumarate, maleate, citrate, sulfate, phosphate, carbonate, etc.; cross-linking agent such as formaldehyde; chaotropic agent such as formamide; chelating agent such as EDTA; ionic or non-ionic detergent such as Triton-X-100, Nonidet P-40, SDS; stabilizer such as a polymer (eg., Ficoll 400, dextran salt, etc); or a preservative (eg., azide). In certain invention embodiments, one or more of the components may be present in trace amounts. For other applications, specific amounts of the components to be added to the solution will be informed by recognized parameters such as the sample for which detection of the target is needed, the assay format to be used, etc.”
Fiandaca teaches, “0034) d. As used herein, the term “probe' means a polymer (e. g. a DNA, RNA, PNA, chimera or linked polymer) having a probing nucleobase sequence that is designed to sequence-specifically hybridize to a target sequence of interest.”
Fiandaca does not specifically teach further reduction of background.
However, Rigby teaches, “[0090] A rapid, simple PNA FISH assay for detection of E. coli was developed. The method involves fixation of bacteria directly from culture, followed by hybridization with an E. coli specific PNA probe. The example described below demonstrate that this protocol can be used with a standard Flu (fluorescein) Labeled PNA Probe as well as a self-indicating fluorescein labeled PNA Linear Beacon. Additionally we have shown that the use of a Quencher Labeled PNA Probe, that is complementary to the E. coli specific PNA probes (both the Flu labeled PNA probe and the PNA Linear Beacon) and contains a dabcyl at the carboxyl terminus, is effective for the reduction of background.”
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 an additional step of reducing background. The artisan would be motivated as Rigby teaches the use of dabcyl allows for reduced background by altering fluorescence and thus improving sensitivity. Thea artisan would have a reasonable expectation of success as the artisan is merely using a known method to reduce background.
With regards to claim 3, Fiandaca teaches the fixative solution has detergent and the probe and thus is a hybridization solution (0024).
With regards to claim 4, Fiandaca teaches triton-x100, NP-40 and SDS.
With regards to claim 5, Fiandaca teaches the alcohol is added with the probe and thus is prior to fixation.
With regards to claim 6-7, Fiandaca teaches the use of chaotropic agents. Chaotropic agents are denaturing substance.
Claim 8 is indefinite as the claims and specification provide no context to differentiate toxic from nontoxic. Thus the broadest reasonable interpretation is any denaturing substance.
With regards to claim 8, Fiandaca teaches the use of chaotropic agents. Chaotropic agents are denaturing substance.
With regards to claim 9, Fiandaca teaches the use of salts (0024).
With regards to claim 10, Fiandaca teaches, “The assay may also be used to detect, identify and/or quantify microorganisms optionally present in the sample, such as, but not limited to, pathogens in cervical swabs; such as, but not limited to, Chlamydia trachomatis and human papilomavirus or bioterrorism.” (0115)
With regards to claim 11, 23Fiandaca teaches probes complementary to rRNA, which is also complementary to DNA for rRNA. (0139)
With regards to claim 12 Fiandaca teaches use of optical labels (0044, 0045, 0070, 0120).
With regards to claim 22, Fiandaca teaches the use of TritonX100 (0024).
Response to Arguments
The response traverses the rejection in view of the alleged deficiencies of Fiandaca. These arguments are not persuasive for the reasons of record.
Claim(s) 1-7, 9-12, 16, 18, 22-23 is/are rejected under 35 U.S.C. 103 as being unpatentable over Fiandaca (USPGPUB 2207/0128646) as evidence by Kiebish (US 20180024132) and Venkateswaran (USPGPUB20140155283)..
Claim 1 has been amended to recite, “nucleic acid probes comprising an optically detectable label.” The specification recites “nucleic acid ” 103 and provides no limiting definition. Kiebish teaches, “. In certain embodiments, the analyte comprises a nucleic acid and the probe comprises one or more synthetic single stranded nucleic acid molecules, e.g., a DNA molecule, a DNA-RNA hybrid, a PNA, or a modified nucleic acid molecule containing one or more artificial bases, sugars, or backbone moieties. .” (0555)Thus the broadest reasonable interpretation of an nucleic acid probe encompasses PNA.
With regards to claim 1, Fiandaca teaches, “0002 This invention is related to the field of probe based nucleic acid sequence detection, analysis and quantification. More specifically, this invention relates to the use of PNA probes in aqueous alcohol solutions for diagnostic applications. In one aspect, the invention enables sample preparation and analysis to be performed as a single step.” Fiandaca teaches, “0034) d. As used herein, the term “probe' means a polymer (e. g. a DNA, RNA, PNA, chimera or linked polymer) having a probing nucleobase sequence that is designed to sequence-specifically hybridize to a target sequence of interest.”
Fiandaca teaches, “0008] The present invention provides compositions, methods and kits for hybridizing a PNA probe to a target sequence. In one aspect, the invention features compositions in which at least one PNA probe is provided in combination with an aqueous alcohol solution that serves, for instance, as a specimen fixing and probe hybridization medium. The invention has a wide spectrum of important applications including use in pathogen detection assays.” Fiandaca teaches, “0075] The PNA probes may be designed to specifically bind nucleic acid targets, such as both DNA and RNA, including rRNA and mRNA. Non-limiting examples, include PNA probes for analysis of microorganisms and, for example, targeting species-specific rRNA sequences. For example the PNA probes may be targeting microorganisms potentially present in cervical swabs associated with women's health, such as but not limited to PNA probes targeting Chlamydia trachomatis and/or Neisseria gonorrhoeae (for examples of PNA probe nucleobase sequences see U.S. Pat. No. 6,169,169), Candida albicans (for example of PNA probe nucleobase sequences see Rigby et al. J. Clin. Microbiol. 40:2182-218(2002)), Gardnerella vaginalis, Trichomonas vaginalis and/or Streptococcus agalactia (Group B streptococci).”
Fiandaca teaches, “[0012] Practice of the invention can help avoid the time and expense of adding probe to a specimen after it is fixed. That is, the invention can be used, in one embodiment, to provide for essentially simultaneous fixation and hybridization of the PNA probe to target sequence. In this invention example, the need to use conventional assay steps involving the removal, exchange, inactivation and/or addition of chemicals needed for either fixation or hybridization is greatly reduced and often avoided.”
Fiandaca teaches, “[0024] An aqueous alcohol solution in accord with the invention can further include at least one of the following components: a buffering agent (eg., Tris, Hepes, PBS, etc); monovalent cation such as sodium or potassium; divalent cation such as calcium or magnesium ion; suitable anion such as acetate, chloride, fumarate, maleate, citrate, sulfate, phosphate, carbonate, etc.; cross-linking agent such as formaldehyde; chaotropic agent such as formamide; chelating agent such as EDTA; ionic or non-ionic detergent such as Triton-X-100, Nonidet P-40, SDS; stabilizer such as a polymer (eg., Ficoll 400, dextran salt, etc); or a preservative (eg., azide). In certain invention embodiments, one or more of the components may be present in trace amounts. For other applications, specific amounts of the components to be added to the solution will be informed by recognized parameters such as the sample for which detection of the target is needed, the assay format to be used, etc.”
Fiandaca teaches, “0034) d. As used herein, the term “probe' means a polymer (e. g. a DNA, RNA, PNA, chimera or linked polymer) having a probing nucleobase sequence that is designed to sequence-specifically hybridize to a target sequence of interest.”
Fiandaca does not specifically teaches determining living or dead.
However, Venkateswaran teaches, “[0093] In some embodiments, the detection system is able to measure the microbial diversity of complex communities without PCR amplification, and consequently, without the inherent biases associated with PCR amplification. In some embodiments, nucleic acid from dead cells is selectively removed before detection, such that detection is directed to determining the presence, absence, relative abundance, and/or quantity of live organisms in a sample, such as live members of one or more OTUs. Actively metabolizing cells typically contain about 20,000 or more ribosomes for protein assembly compared to quiescent or dead cells that have few. In some embodiments, rRNA can be purified directly from a sample and processed with no amplification step, thereby reducing or avoiding bias caused by preferential amplification of some sequences over others. Thus, in some embodiments, the signal from the analysis system can reflect the true number of rRNA molecules that are present in the samples. This can be expressed as the number of cells multiplied by the number of rRNA copies within each cell. The number of cells in a sample can then be inferred by several different methods, such as, for example, quantitative real-time PCR, or FISH (fluorescence in situ hybridization.). Then the average number of ribosomes within each cell can be calculated.”
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 determine alive and dead cells in the method. The artisan would be motivated as Venkateswaran suggests determining alive and dead cells by selectively removing nucleic acids from dead cells. The artisan would have a reasonable expectation of success as the artisan would be merely following the art of record.
With regards to claim 3, Fiandaca teaches the fixative solution has detergent and the probe and thus is a hybridization solution (0024).
With regards to claim 4, Fiandaca teaches triton-x100, NP-40 and SDS.
With regards to claim 5, Fiandaca teaches the alcohol is added with the probe and thus is prior to fixation.
With regards to claim 6-7, Fiandaca teaches the use of chaotropic agents. Chaotropic agents are denaturing substance.
Claim 8 is indefinite as the claims and specification provide no context to differentiate toxic from nontoxic. Thus the broadest reasonable interpretation is any denaturing substance.
With regards to claim 8, Fiandaca teaches the use of chaotropic agents. Chaotropic agents are denaturing substance.
With regards to claim 9, Fiandaca teaches the use of salts (0024).
With regards to claim 10, Fiandaca teaches, “The assay may also be used to detect, identify and/or quantify microorganisms optionally present in the sample, such as, but not limited to, pathogens in cervical swabs; such as, but not limited to, Chlamydia trachomatis and human papilomavirus or bioterrorism.” (0115)
With regards to claim 11, Fiandaca teaches probes complementary to rRNA, which is also complementary to DNA for rRNA. (0139)
With regards to claim 12 Fiandaca teaches use of optical labels (0044, 0045, 0070, 0120).
With regards to claim 22, Fiandaca teaches the use of TritonX100 (0024).
Response to Arguments
The response traverses the rejection in view of the alleged deficiencies of Fiandaca. These arguments are not persuasive for the reasons of record.
Claim(s) 1-7, 9-12, 18, 20, 22-23 is/are rejected under 35 U.S.C. 103 as being unpatentable over Fiandaca (USPGPUB 2207/0128646) as evidence by Kiebish (US 20180024132) and Dorsch (USPGPUB 20050032090)..
Claim 1 has been amended to recite, “nucleic acid probes comprising an optically detectable label.” The specification recites “nucleic acid ” 103 and provides no limiting definition. Kiebish teaches, “. In certain embodiments, the analyte comprises a nucleic acid and the probe comprises one or more synthetic single stranded nucleic acid molecules, e.g., a DNA molecule, a DNA-RNA hybrid, a PNA, or a modified nucleic acid molecule containing one or more artificial bases, sugars, or backbone moieties. .” (0555)Thus the broadest reasonable interpretation o