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 1-30 are currently pending and under examination.
Priority
The instant application 18/426,101 filed on 1/29/24 is a CON of 18/332,469 filed 6/9/23, which is a CON of 18/048,552 filed 10/21/22, which is a CON of 17/695,494 filed 3/15/22, which is a CON of 17/392,655 filed 8/3/21, which is a CON of 17/129,106 filed 12/21/20, which is a CON of 16/543,351 filed 8/16/19, which claims domestic priority to provisional application 62/841,541 filed 5/1/19. The priority date is determined to be 5/1/19.
Claim Rejections - 35 USC § 112 – Indefiniteness
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 1-30 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.
Claims 1, 8, 15, 18, 27, and 29 recitations of “no greater than about”; “at least about”; and “less than about” are unclear because “no greater than”, “at least”, and “less than” typically indicate a maximum or minimum point. However, these terms are controverted by the term “about,” which implies that values above and below the indicated amount are permitted. Therefore, the juxtaposition of these two terms makes it unclear what maximum or minimum values are encompassed by the claim. See MPEP 2173.05(b)(III).
Claims 2-30 directly or indirectly depend upon claim 1 and are similarly indefinite.
Claim 3 is indefinite because dielectric constants are temperature dependent (see cited prior art Kabusa.com NPL document). The claims are indefinite because the same method infringes at one temperature but does not infringe at a different temperature.
Claim 7 is indefinite because it is unclear how the solvent can be present in an amount effective to denature a double stranded nucleic acid while claim 1 (upon which claim 7 depends) requires hybridization of two nucleic acids (i.e., to form a double stranded nucleic acid).
Claims 8-10 and 15-16 recite the limitation "the formulation". There is insufficient antecedent basis for this limitation in the claim. For purposes of compact prosecution, this term is interpreted as the “hybridizing composition” introduced within claim 1.
Claims 12-16 recite the limitation "molecular crowding agent". There is insufficient antecedent basis for this limitation in the claim which was first introduced within claim 11, not claim 1 as written. For purposes of compact prosecution, claims 12-16 are interpreted as depending from claim 11.
Claim 14 is indefinite because the recitation of “5k to 40k” has no molecular weight units.
Claims 18-19 recite the limitation "the additive for controlling melting temperature". There is insufficient antecedent basis for this limitation in the claim. For purposes of compact prosecution, claims 18-19 are interpreted as depending from claim 17.
Claim 20 is indefinite in the recitation of “NaOH, KOH”, as it is unclear how these strong bases can act as a buffer.
Claim 27 contains the trademark/trade name Cy3. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe a fluorescent synthetic dye within the cyanine family and, accordingly, the identification/description is indefinite.
Claim Rejections - 35 USC § 102
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, 4, 6-10, 24, and 29-30 are rejected under 35 U.S.C. 102(a)(1) and (a)(2) as being anticipated by Garimella et al. (2005; US 2005/0287560 A1), as evidenced by Kabusa.com (2015; "Dielectric Constants of Common Materials" retrieved via Wayback Machine; February 13, 2015; https://web.archive.org/web/20150213045628/https://www.kabusa.com/Dilectric-Constants.pdf) and, as applied to claim 6, as evidenced by Wang (2017; US 2017/0128380 A1) and, as applied to claim 7, as evidenced by Antoniou et al. (2003; US 2003/0061627 A1) and Koziel et al. (1999; US 5,859,336).
Relevant to claim 1, Garimella et al. teaches a method comprising providing a support having at least one surface bound probe, in the form of an attached capture probe, which is on a surface having a water contact angle of less than 45 degrees (paragraph 0204). The capture molecule is an oligonucleotide (e.g., paragraph 0055), and a target DNA molecule (e.g., a genomic target) is hybridized thereto, in the presence of the pH buffer SSC and the organic solvent formamide (paragraph 0481). Kabusa.com page 14 teaches formamide has a dielectric constant of 109 at 68°F.
Relevant to claims 2 and 4, Garimella et al. teaches the organic solvent is formamide (paragraph 0481; claim 4), which is polar aprotic (claim 2).
Relevant to claim 6, Garimella et al. teaches the organic solvent is formamide (paragraph 0481), which is miscible with water, as evidenced by Wang (paragraph 0098).
Relevant to claim 7, Garimella et al. teaches the organic solvent is formamide and is present at 18-70% (paragraph 0481), which is sufficient to denature a doubled stranded nucleic acid, as evidenced by the prior art of Antoniou et al., which teaches 50% formamide is sufficient to denature nucleic acids at 75oC (paragraph 0253), and the prior art of Koziel et al., which teaches 25% formamide is sufficient to denature oligomers (i.e., nucleic acids) at 95oC (column 17, lines 50-65). It is also noted that the claim does not actually contain an active method step of denaturation.
Relevant to claims 8-10, Garimella et al. teaches the organic solvent is present at 18-70% (paragraph 0481), which overlaps the ranges found in claims 8-9). In addition, the solvent ranges result in the buffer being no more than 82-30% of the total volume (claim 10).
Relevant to claim 24, Garimella et al. teaches covalent linkage to surfaces (paragraph 0007).
Relevant to claims 29-30, Garimella et al. teaches the hybridization step (i.e., the claimed contacting) occurs at 40oC, which is within the range of claim 30, and that the annealing (i.e., hybridization) occurs in about 5 minutes, which is within the range of claim 29 (paragraph 0481).
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 2-12, 15-21, and 23 are rejected under 35 U.S.C. 103 as being unpatentable over Garimella et al. (2005; US 2005/0287560 A1), as evidenced by Kabusa.com (2015; "Dielectric Constants of Common Materials" retrieved via Wayback Machine; February 13, 2015; https://web.archive.org/web/20150213045628/https://www.kabusa.com/Dilectric-Constants.pdf) and, as applied to claim 6, as evidenced by Wang (2017; US 2017/0128380 A1) and, as applied to claim 7, as evidenced by Antoniou et al. (2003; US 2003/0061627 A1) and Koziel et al. (1999; US 5,859,336) as applied to claims 1-2, 4, 6-10, 24, and 29-30 above, and further in view of Abravaya et al. (2017; US 2017/0198341 A1).
The teachings of Garimella et al. as evidenced by Kabusa.com, Wang, Antoniou et al., and Koziel et al. are described above as anticipating instant claims 1-2, 4, 6-10, 24, and 29-30. It is noted that while claims 2, 4, and 6-10 have been rejected as described in above section, the claims are also obvious using the interpretation outlined below.
Garimella et al. does not specifically teach the organic solvent having a dielectric constant of less than 40 (claim 3), which encompasses acetonitrile, which has a dielectric constant of 37.5, as evidenced by Kabusa.com page 1.
However, Abravaya et al. teach methods of DNA hybridization utilizing a buffer at pH 7, which is within the range of claim 23 (paragraph 0032) and includes one of HEPES, or Tris (claim 20; paragraph 0030). The buffer comprises formamide and acetonitrile (paragraph 0039), and thus comprises a polar organic solvent having a dielectric constant of less than 40, as well as a nitrile functionality and is miscible with water (claims 2-6). The solvent(s) have dielectric constants of at least 5 (claim 3; paragraph 0038), is present at about 50% of the buffer (paragraph 0040), and thus is in the ranges of claims 8-9, and therefore meet the buffer amounts of claim 10, and is sufficient to denature a double stranded nucleic acid (claim 7), as evidenced by the prior art of Antoniou et al., which teaches 50% formamide is sufficient to denature nucleic acids at 75oC (paragraph 0253), and the prior art of Koziel et al., which teaches 25% formamide is sufficient to denature oligomers (i.e., nucleic acids) at 95oC (column 17, lines 50-65). It is also noted that claim 7 does not actually require an active method step of denaturation.
Because the buffer contains both formamide and acetonitrile (paragraph 0039), the buffer is interpreted as comprising the organic solvent acetonitrile as well as the additive formamide, which is an additive for controlling the melting temperature of nucleic acids, as discussed in paragraph 0071 of the instant specification (claim 17), and further comprises the organic solvent of claim 21 in addition to the organic solvent required by claim 1. Because the total amounts of formamide and acetonitrile are about 50% (paragraph 0041), it would have been obvious to have formamide present in the ranges of claims 18-19 (i.e., about 2% to 50%).
The buffer further comprises the crowding agent dextran sulfate (claims 11-12; paragraph 0026) at about 10% (paragraph 0027), which is in the ranges of claims 15-16.
The courts have stated:
similar properties may normally be presumed when compounds are very close in structure. Dillon, 919 F.2d at 693, 696, 16 USPQ2d at 1901, 1904. See also In re Grabiak, 769 F.2d 729, 731, 226 USPQ 870, 871 (Fed. Cir. 1985) (“When chemical compounds have very close’ structural similarities and similar utilities, without more a prima facie case may be made.”). Thus, evidence of similar properties or evidence of any useful properties disclosed in the prior art that would be expected to be shared by the claimed invention weighs in favor of a conclusion that the claimed invention would have been obvious. Dillon, 919 F.2d at 697-98, 16 USPQ2d at 1905; In re Wilder, 563 F.2d 457, 461, 195 USPQ 426, 430 (CCPA 1977); In re Linter, 458 F.2d 1013, 1016, 173 USPQ 560, 562 (CCPA 1972) (see MPEP 2144.08(d)).
Therefore, the substitution of dextran sulfate for the claimed dextran would be considered an obvious variation over the prior art.
Abravaya et al. also teaches the buffer has the added advantage of being a reliable media for providing reproducible results (paragraph 0005). Thus, Abravaya et al. teaches the known techniques discussed above.
It is reiterated that the courts have stated where the claimed ranges overlap or lie inside the ranges disclosed by the prior art and even when the claimed ranges and prior art ranges do not overlap but are close enough that one skilled in the art would have expected them to have similar properties, a prima facie case of obviousness exists, and that the courts have also found that where 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.
Therefore, the claimed ranges merely represent an obvious variant and/or routine optimization of the values of the cited prior art.
It would therefore have been obvious to a person of ordinary skill in the art to have modified the method taught by Garimella et al. with the teachings of Abravaya et al. to arrive at the instantly claimed method with a reasonable expectation of success. The ordinary artisan would have been motivated to make the modification because said modification would have resulted in a method utilizing a buffer having the added advantage of being a reliable media for providing reproducible results as explicitly taught by Abravaya et al. (paragraph 0005). In addition, it would have been obvious to the ordinary artisan that the known techniques of Abravaya et al. could have been applied to the method of Garimella et al. with predictable results because the known techniques of Abravaya et al. predictably result in a useful buffer for nucleic acid hybridization.
Claims 11-16 are rejected under 35 U.S.C. 103 as being unpatentable over Garimella et al. (2005; US 2005/0287560 A1), as evidenced by Kabusa.com (2015; "Dielectric Constants of Common Materials" retrieved via Wayback Machine; February 13, 2015; https://web.archive.org/web/20150213045628/https://www.kabusa.com/Dilectric-Constants.pdf) and, as applied to claim 6, as evidenced by Wang (2017; US 2017/0128380 A1) and, as applied to claim 7, as evidenced by Antoniou et al. (2003; US 2003/0061627 A1) and Koziel et al. (1999; US 5,859,336) as applied to claims 1-2, 4, 6-10, 24, and 29-30 above, and further in view of Stone (1996; US 5,512,436).
The teachings of Garimella et al. as evidenced by Kabusa.com, Wang, Antoniou et al., and Koziel et al. are described above as anticipating instant claims 1-2, 4, 6-10, 24, and 29-30. It is noted that while claims 11-12 and 15-16 have been rejected as described above, the claims are also obvious using the interpretation outlined below.
Garimella et al. does not teach the crowding agent is polyethylene glycol (claim 13).
However, Stone teaches methods of hybridizing nucleic acids (i.e., polynucleotides) using polyethylene glycol (claims 11-13) or dextran sulfate (claims 11-12; Abstract). The preferred molecular weight of the glycol is 6000, and the dextran has a weight of 1K to 10,000K (column 2, lines 30-35), which overlap the range of claim 14. Stone also teaches the polyethylene glycol additive is present at 5-10% and the dextran is in around 10% (column 3, lines 50-60), which overlap the range of claims 15-16. Stone also teaches the additives have the added advantage of enhancing the hybridization rate (Abstract). Thus, Stone teaches the known techniques discussed above.
It is reiterated that the courts have stated similar properties may normally be presumed when compounds are very close in structure. Therefore, the substitution of dextran sulfate for the claimed dextran would be considered an obvious variation over the prior art.
It would therefore have been obvious to a person of ordinary skill in the art to have modified the method taught by Garimella et al. with the teachings of Stone to arrive at the instantly claimed method with a reasonable expectation of success. The ordinary artisan would have been motivated to make the modification because said modification would have resulted in a method having the added advantage of enhancing the hybridization rate as explicitly taught by Stone (Abstract). In addition, it would have been obvious to the ordinary artisan that the known techniques of Stone could have been applied to the method of Garimella et al. with predictable results because the known techniques of Stone predictably result in a useful additive for nucleic acid hybridization.
Claims 3-6, 20, 22, and 30 are rejected under 35 U.S.C. 103 as being unpatentable over Garimella et al. (2005; US 2005/0287560 A1), as evidenced by Kabusa.com (2015; "Dielectric Constants of Common Materials" retrieved via Wayback Machine; February 13, 2015; https://web.archive.org/web/20150213045628/https://www.kabusa.com/Dilectric-Constants.pdf) and, as applied to claim 6, as evidenced by Wang (2017; US 2017/0128380 A1) and, as applied to claim 7, as evidenced by Antoniou et al. (2003; US 2003/0061627 A1) and Koziel et al. (1999; US 5,859,336) as applied to claims 1-2, 4, 6-10, 24, and 29-30 above, and further in view of Singh et al. (2003; US 2003/0017461 A1).
The teachings of Garimella et al. as evidenced by Kabusa.com, Wang, Antoniou et al., and Koziel et al. are described above as anticipating instant claims 1-2, 4, 6-10, 24, and 29-30. It is noted that while claims 3-6, 20, and 30 have been rejected as described above, the claims are also obvious using the interpretation outlined below.
Garimella et al. does not teach MOPS buffers (claim 22).
However, Singe et al. teaches methods utilizing hybridization buffers, which include MOPS (claim 20) and organic solvents, including methanol, which has a dielectric constant of less than 40, as evidenced by Kabusa.com (claims 3-6; paragraph 0027). Because Singh et al. teaches solvents (i.e., plural) are added (paragraph 0027, it would have been obvious either to have methanol in addition to the formamide of Garimella et al., or to have both acetonitrile and methanol as taught by Singh et al. (claim 22; paragraph 0027). Singh et al also teaches hybridization at 30oC (paragraph 0028), which is in the range of claim 30, and that the buffer has the added advantage of enhanced stringency (paragraph 0027) which favors high specificity, which is a goal of Garimella et al. (e.g., paragraph 0283). Thus, Singh et al. teaches the known techniques discussed above.
It is reiterated that the courts have stated where the claimed ranges overlap or lie inside the ranges disclosed by the prior art and even when the claimed ranges and prior art ranges do not overlap but are close enough that one skilled in the art would have expected them to have similar properties, a prima facie case of obviousness exists, and that the courts have also found that where 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.
Therefore, the claimed ranges merely represent an obvious variant and/or routine optimization of the values of the cited prior art.
It would therefore have been obvious to a person of ordinary skill in the art to have modified the method taught by Garimella et al. with the teachings of Singh et al. to arrive at the instantly claimed method with a reasonable expectation of success. The ordinary artisan would have been motivated to make the modification because said modification would have resulted in a method utilizing a buffer having the added advantage of providing enhanced stringency as explicitly taught by Singh et al. (paragraph 0005), which favors high specificity, and which as a goal of Garimella et al. (e.g., paragraph 0283). In addition, it would have been obvious to the ordinary artisan that the known techniques of Singh et al. could have been applied to the method of Garimella et al. with predictable results because the known techniques of Singh et al. predictably result in a useful buffer for nucleic acid hybridization.
Claims 24-28 are rejected under 35 U.S.C. 103 as being unpatentable over Garimella et al. (2005; US 2005/0287560 A1), as evidenced by Kabusa.com (2015; "Dielectric Constants of Common Materials" retrieved via Wayback Machine; February 13, 2015; https://web.archive.org/web/20150213045628/https://www.kabusa.com/Dilectric-Constants.pdf) and, as applied to claim 6, as evidenced by Wang (2017; US 2017/0128380 A1) and, as applied to claim 7, as evidenced by Antoniou et al. (2003; US 2003/0061627 A1) and Koziel et al. (1999; US 5,859,336) as applied to claims 1-2, 4, 6-10, 24, and 29-30 above, and further in view of Pircher (2005; US 2005/0100951 A1).
The teachings of Garimella et al. as evidenced by Kabusa.com, Wang, Antoniou et al., and Koziel et al. are described above as anticipating instant claims 1-2, 4, 6-10, 24, and 29-30. It is noted that while claim 24 has been rejected as described above, the claims are also obvious using the interpretation outlined below.
While Garimella et al. teaches the surface is coated (paragraph 0002), Garimella et al. does not specifically teach the coating is a hydrophilic polymer (claim 25).
However, Pircher teaches methods wherein hydrogels of polyethylene glycol are coated on the surface of a biochip (claims 25 and 28), and oligonucleotide probes (paragraph 0004) are covalently immobilized therein (claim 24; paragraph 0050 and Abstract). Pircher teaches minimal non-specific binding of nucleic acids to the surface (claim 26; paragraph 0084), as well as minimal binding of non-specific Cy3 binding (claim 27; paragraphs 0090 and 0093). Pircher also teach the method has the added advantage of providing an immobilization surface that is optically clear and maximizes capture and detection (paragraph 0032). Thus, Pircher teaches the known techniques discussed above.
It is reiterated that the courts have stated where the claimed ranges overlap or lie inside the ranges disclosed by the prior art and even when the claimed ranges and prior art ranges do not overlap but are close enough that one skilled in the art would have expected them to have similar properties, a prima facie case of obviousness exists, and that the courts have also found that where 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.
Therefore, the claimed ranges merely represent an obvious variant and/or routine optimization of the values of the cited prior art.
It would therefore have been obvious to a person of ordinary skill in the art to have modified the method taught by Garimella et al. with the teachings of Pircher to arrive at the instantly claimed method with a reasonable expectation of success. The ordinary artisan would have been motivated to make the modification because said modification would have resulted in a method having the added advantage of providing an immobilization surface that is optically clear and maximizes capture and detection as explicitly taught by Pircher (paragraph 0032). In addition, it would have been obvious to the ordinary artisan that the known techniques of Pircher could have been applied to the method of Garimella et al. with predictable results because the known techniques of Pircher predictably result in a useful surface for nucleic acid hybridization.
Conclusion
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/SARAH JANE KENNEDY/Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
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