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 .
Status of the Claims
Claims 1-25 and 27-29 are pending.
Claims 14-18 and 28-29 are withdrawn.
Election/Restrictions
Applicant’s election without traverse of Group I, directed to a resynthesis kit comprising a thermophilic phosphatase and a polymerase, in the reply filed on 17 March 2026 is acknowledged. Applicant also elected, without traverse, the following species: a thermophilic glycosylase and a thermophilic exonuclease.
Claims 14-18 and 28-29 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention or species, there being no allowable generic or linking claim.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 17 March, 2026.
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)(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, 7, 24, and 27 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by JP 2019511010A (filed 9 February 2019).
JP 2019511010A teaches a system and method for analyzing nucleic acids. JP 2019511010A teach components for their method including a thermophilic phosphatase [00205] and a polymerase [00204]. Both the polymerase and the thermophilic phosphatase are in the same section of the disclosure for preparing a nucleic acid library from nucleic acids. [00204]. While claim 1 recites a resynthesis kit, the components are a thermophilic phosphatase and a polymerase which are taught by JP 2019511010A.
Regarding claim 7, JP 2019511010A teaches the use of Taq polymerase. [00222].
Regarding claim 24, JP 2019511010A teaches the use of dNTPs. [00218]. The instant specification states: The resynthesis kit may further comprise a nucleotide triphosphate (NTP). Preferably, the nucleotide triphosphate may be a deoxynucleotide triphosphate (dNTP). [00122].
Regarding claim 27, JP 2019511010A teaches the kit of claim 1. Where the only difference between a prior art product and a claimed product is printed matter that is not functionally related to the product, the content of the printed matter will not distinguish the claimed product from the prior art. In re Ngai, 367 F.3d 1336, 1339, 70 USPQ2d 1862, 1864 (Fed. Cir. 2004). (Claim at issue was a kit requiring instructions and a buffer agent. The Federal Circuit held that the claim was anticipated by a prior art reference that taught a kit that included instructions and a buffer agent, even though the content of the instructions differed.) See also In re Gulack, 703 F.2d 1381, 1385-86, 217 USPQ 401, 404 (Fed. Cir. 1983). (“Where the printed matter is not functionally related to the substrate, the printed matter will not distinguish the invention from the prior art in terms of patentability…[T]he critical question is whether there exists any new and unobvious functional relationship between the printed matter and the substrate.”)
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 3, 4, 5, and 21 is/are rejected under 35 U.S.C. 103 as being unpatentable over JP 2019511010A (filed 9 February 2019) in view of Zappa et al. (Applied and Environmental Microbiology, 2001) as evidenced by Q9UZV2 (Pyrococcus abyssi (strain GE5/Orsay) alkaline phosphatase sequence, uploaded 2000).
The teachings of JP 2019511010A as applied to claims 1, 7, 24, and 27 under 35 USC 102(a)(2) are applied to claims 3, 4, 5, and 21. JP 2019511010A does not teach the limitations recited in claims 3, 4, 5, and 21.
Regarding claims 3, 4, and 21, Zappa et al. characterize the highly thermostable alkaline phosphatase from Pyrococcus abyssi. Zappa et al. state the strain used is the Orsay strain Q9UZV2. (see organism and growth conditions on page 4504). The Q9UZV2 sequence is identical to SEQ ID NO: 1 from base 2 to the end. (see alignment below). The Q9UZV2 comprises extra bases between base 1 and base 2 of SEQ ID NO: 1 and is therefore a functional variant.
2 SPSGVRNVIILIGDGMGFSQLQLTKLVYGHLNMEDFPYTGIELTDSLSGEVTDSAAAGTA 61
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
23 SPSGVRNVIILIGDGMGFSQLQLTKLVYGHLNMEDFPYTGIELTDSLSGEVTDSAAAGTA 82
62 IATGVKTYNRMISTTNVTGKLVNLTTLLEIAQMLGKATGLVTTTRITHATPAVFASHVPD 121
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
83 IATGVKTYNRMISTTNVTGKLVNLTTLLEIAQMLGKATGLVTTTRITHATPAVFASHVPD 142
122 RDMEEEIARQLILHNVTVLMGGGREKFSEEVLKLAEDYGYSIVYTREDLEKVKDGKVLGL 181
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
143 RDMEEEIARQLILHNVTVLMGGGREKFSEEVLKLAEDYGYSIVYTREDLEKVKDGKVLGL 202
182 FAEGHLPYVLDRSEEDVSLLEMTKKAIEILEKNPNGFFLMIEGGRIDHACHANDVASIVA 241
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
203 FAEGHLPYVLDRSEEDVSLLEMTKKAIEILEKNPNGFFLMIEGGRIDHACHANDVASIVA 262
242 ETKEFDDVVGYVLDYARRRGDTLVIVLADHETGGLGIGLNYGHSVDIDSIRRIDASIEEM 301
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
263 ETKEFDDVVGYVLDYARRRGDTLVIVLADHETGGLGIGLNYGHSVDIDSIRRIDASIEEM 322
302 SKEIKSGGDIRDVIRRHTGLELTDEEVKEIEEAKNSTNKYALGNIIGEIISKKLGVGFVS 361
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
323 SKEIKSGGDIRDVIRRHTGLELTDEEVKEIEEAKNSTNKYALGNIIGEIISKKLGVGFVS 382
362 HKHTGEPVPLLAYGPGAENFVGFKHHVDTAKVIAKLMIFGDRSISFTIKGVSKIKGDVTG 421
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
383 HKHTGEPVPLLAYGPGAENFVGFKHHVDTAKVIAKLMIFGDRSISFTIKGVSKIKGDVTG 442
422 DYRVDERDAYATLMLLLGDLVDTELENIADMDNNGIIDLLDVMAILQASS 471
||||||||||||||||||||||||||||||||||||||||||||||||||
443 DYRVDERDAYATLMLLLGDLVDTELENIADMDNNGIIDLLDVMAILQASS 492
Regarding claims 5, Zappa et al. teach that the alkaline phosphatase assay was carried out at 70°C and therefore has a denaturation temp above 40°C.
Claim(s) 2 is/are rejected under 35 U.S.C. 103 as being unpatentable over JP 2019511010A (filed 9 February 2019) in view of Zappa et al. (Journal of Inorganic Biochemistry, 2004).
The teachings of JP 2019511010A as applied to claims 1, 7, 24, and 27 under 35 USC 102(a)(2) are applied to claim 2. JP 2019511010A does not teach the concentration range recited in claim 2.
Zappa et al. teach the use of P. abyssi alkaline phosphatase at a concentration of 4.5µM (5-10 µg in 20 µL) in an assay. Zappa et al. used this standard amount for routine activity assays. Therefore, one of ordinary skill in the art would use a range that is known for routine assays in the kit taught by JP 2019511010A as a starting point. It is noted that 4.5µM is within the range recited in claim 2, however, one of ordinary skill in the art would optimize this amount based on the type of reaction.
Claim(s) 6 and 8 is/are rejected under 35 U.S.C. 103 as being unpatentable over JP 2019511010A (filed 9 February 2019) in view of Innis et al. (PNAS, 1988).
The teachings of JP 2019511010A as applied to claims 1, 7, 24, and 27 under 35 USC 102(a)(2) are applied to claims 6 and 8. JP 2019511010A does not teach the amount of polymerase recited in claim 6 or the denaturation temperature of Taq polymerase.
Innis et al. teach DNA sequencing with Taq polymerase. Enzyme amounts are not typically recited as M but instead as U (units). The examiner calculated, from the information provided by Innis et al., that each U of Taq polymerase is 4.25 µM. (See enzymes under materials). Innis et al. adds 5 units/µL for a total of 50 units in 10 µL which is 212.5 µM.
Regarding claim 8, Innis et al. teach the denaturation temperature of Taq polymerase is above 40°C. (see extension-termination reaction).
Therefore, one of ordinary skill in the art would be motivated to use known amounts of Taq polymerase in the kit taught by JP 2019511010A as JP 2019511010A already teaches the inclusion of Taq polymerase in the kit.
Claim(s) 9 and 11-13 is/are rejected under 35 U.S.C. 103 as being unpatentable over JP 2019511010A (filed 9 February 2019) in view of Q58134-OGG1_METJA (Methanocaldococcus jannaschii strain DNA glycosylase, uploaded 1996).
The teachings of JP 2019511010A as applied to claims 1, 7, 24, and 27 under 35 USC 102(a)(2) are applied to claims 9 and 11-13. JP 2019511010A does not teach a thermophilic glycosylase of claim 9 and the limitations of claims 11-13.
Q58134-OGG1_METJA teaches SEQ ID NO: 2, the DNA glycosylase from Methanocaldococcus jannaschii. See alignment below:
1 MMLIKKIEELKNSEIKDIIDKRIQEFKSFKNKSNEEWFKELCFCILTANFTAEGGIRI 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
1 MMLIKKIEELKNSEIKDIIDKRIQEFKSFKNKSNEEWFKELCFCILTANFTAEGGIRIQK 60
61 EIGDGFLTLPREELEEKLKNLGHRFYRKRAEYIVLARRFKNIKDIVESFENEKVAREFLV 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
61 EIGDGFLTLPREELEEKLKNLGHRFYRKRAEYIVLARRFKNIKDIVESFENEKVAREFLV 120
121 RNIKGIGYKEASHFLRNVGYDDVAIIDRHILRELYENNYIDEIPKTLSRRKYLEIENILR 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
121 RNIKGIGYKEASHFLRNVGYDDVAIIDRHILRELYENNYIDEIPKTLSRRKYLEIENILR 180
181 DIGEEVNLKLSELDLYIWYLRTGKVLK 207
|||||||||||||||||||||||||||
181 DIGEEVNLKLSELDLYIWYLRTGKVLK 207
JP 2019511010A teaches the use of glycosylase. [00158]. The claim would have been obvious to one of ordinary skill in the skill because the substitution of one known element for another would have yielded predictable results.
Claim(s) 10 is/are rejected under 35 U.S.C. 103 as being unpatentable over JP 2019511010A (filed 9 February 2019) in view of Q58134-OGG1_METJA (Methanocaldococcus jannaschii strain DNA glycosylase, uploaded 1996) as applied to claims 9 and 11-13 above, and further in view of Sebera et al. (Nucleic Acids Research, 2017).
The teachings of JP 2019511010A in view of in view of Q58134-OGG1_METJA as applied to claims 9 and 11-13 above are applied to claim 10. JP 2019511010A in view of Q58134-OGG1_METJA does not teach the concentration of glycosylase as recited in claim 10. Sebera et al. teach assays with hOGG1, an 8-oxoguanine DNA glycosylase. Q58134-OGG1_METJA teaches an 8-oxoguanine DNA glycosylase. Sebera et al. teaches an in vitro assay that uses 3.33µM of glycosylase. (The in vitro assay of hOGG1 catalytic assay, page 5233). Sebera et al. shows results of the assay in figure 4b.
Based on the activity assay taught by Sebera et al., using the same glycosylase as 8-oxoguanine DNA glycosylase, one of skill in the art would be motivated to use the same amount of glycosylase that is shown to be effective in the kit taught by JP 2019511010A in view of in view of Q58134-OGG1_METJA.
Claim(s) 22 and 23 is/are rejected under 35 U.S.C. 103 as being unpatentable over JP 2019511010A (filed 9 February 2019) in view of Q58134-OGG1_METJA (Methanocaldococcus jannaschii strain DNA glycosylase, uploaded 1996) as applied to claims 9 and 11-13 above, and further in view of Gasteyer et al. (US 8,793,895 B2).
The teachings of JP 2019511010A in view of in view of Q58134-OGG1_METJA as applied to claims 9 and 11-13 above are applied to claim 10. JP 2019511010A in view of Q58134-OGG1_METJA does not teach that the glycosylase is lyophilized or that it includes a salt and trehalose.
Gasteyer et al. teach a method of lyophilizing a material. (claim 1). The method is an improvement on pharmaceutical lyophilization processes and can be applied to any material processing. (Col 4 line 64-Col 5 line 9). Gasteyer et al. describes the pharmaceutically acceptable carrier including any and all solvents, salt, or other materials that would be known to one of skill in the art. (Col. 11, lines 15-48). Gasteyer et al. teach the use of excipients like trehalose. (Example 8).
All the claimed elements were known in the prior art and one skilled in the art could have combined the elements. Lyophilization of materials was known in the art as well as the components necessary for a suitable carrier. Therefore, it would have been obvious to one of ordinary skill in the art to provide the required components of a kit in a lyophilized form to store the components.
Claim(s) 19 and 20 is/are rejected under 35 U.S.C. 103 as being unpatentable over JP 2019511010A (filed 9 February 2019) in view of Gasteyer et al. (US 8,793,895 B2) and Raj (Biotech Articles, 2014).
The teachings of JP 2019511010A as applied to claims 1, 7, 24, and 27 under 35 USC 102(a)(2) are applied to claims 19 and 20. JP 2019511010A teaches an exonuclease [00183], does not teach a lyophilized formulation comprising the thermophilic phosphatase, a salt, a detergent, and any one or more of magnesium chloride, acetate, or sulfate.
Gasteyer et al. teach a method of lyophilizing a material. (claim 1). The method is an improvement on pharmaceutical lyophilization processes and can be applied to any material processing. (Col 4 line 64-Col 5 line 9). Gasteyer et al. describes the pharmaceutically acceptable carrier including any and all solvents, surfactants, salt, or other materials that would be known to one of skill in the art. (Col. 11, lines 15-48).
Raj et al. reviews why salt and magnesium chloride are necessary for PCR. Salt functions by reducing the repulsion between the negatively charged DNA strands and the primer and template. MgCl2 affects the specificity and efficiency of the reaction and is identified as a critical component.
All the claimed elements were known in the prior art and one skilled in the art could have combined the elements. Lyophilization of materials was known in the art as well as the components necessary for sequencing and repair assays. Therefore, it would have been obvious to one of ordinary skill in the art to provide the required components of a kit in a lyophilized form to store the components.
Claim(s) 1, 3-5, 7, 21, 24, and 27 is/are rejected under 35 U.S.C. 103 as being unpatentable over Boutell et al. (US 2020/019578 A1) in view of Zappa et al. (Applied and Environmental Microbiology, 2001) as evidenced by Q9UZV2 (Pyrococcus abyssi (strain GE5/Orsay) alkaline phosphatase sequence, uploaded 2000).
Boutell et al. teach methods and compositions for paired end sequencing. Boutell et al. teach a method that uses a phosphatase, a polymerase, and a glycosylase. (see claims 1-11 for example). Boutell et al. teach the use of Taq polymerase which is identified by Boutell et al. as thermostable. [0116]. The instant specification defines thermophilic and thermostable the same way. [0090]. Boutell et al. does not teach a thermophilic phosphatase.
Zappa et al. characterize the highly thermostable alkaline phosphatase from Pyrococcus abyssi. Zappa et al. teach that the P. abyssi alkaline phosphatase is the most thermostable alkaline phosphatase described so far. (page 4510). Zappa et al. teach that P. abyssi alkaline phosphatase has greater efficiency than E. coli alkaline phosphatase and should be studied to elucidate its potential in molecular biology applications. (page 4510). Therefore, one of ordinary skill art would have been motivated to utilize the P. abyssi alkaline phosphatase in the method taught by Boutell et al. because it showed a high efficiency in a dephosphorylation assay. The claim would have been obvious because the substitution of one alkaline phosphatase for a highly efficient alkaline phosphatase would have yielded predictable results.
Regarding claims 3, 4, 5, and 21 Zappa et al. state the strain use is the Orsay strain Q9UZV2. (see organism and growth conditions on page 4504). The Q9UZV2 sequence is identical to SEQ ID NO: 1 from base 2 to the end. (see alignment below). The Q9UZV2 comprises extra bases between base 1 and base 2 of SEQ ID NO: 1 and is therefore a functional variant.
2 SPSGVRNVIILIGDGMGFSQLQLTKLVYGHLNMEDFPYTGIELTDSLSGEVTDSAAAGTA 61
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
23 SPSGVRNVIILIGDGMGFSQLQLTKLVYGHLNMEDFPYTGIELTDSLSGEVTDSAAAGTA 82
62 IATGVKTYNRMISTTNVTGKLVNLTTLLEIAQMLGKATGLVTTTRITHATPAVFASHVPD 121
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
83 IATGVKTYNRMISTTNVTGKLVNLTTLLEIAQMLGKATGLVTTTRITHATPAVFASHVPD 142
122 RDMEEEIARQLILHNVTVLMGGGREKFSEEVLKLAEDYGYSIVYTREDLEKVKDGKVLGL 181
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
143 RDMEEEIARQLILHNVTVLMGGGREKFSEEVLKLAEDYGYSIVYTREDLEKVKDGKVLGL 202
182 FAEGHLPYVLDRSEEDVSLLEMTKKAIEILEKNPNGFFLMIEGGRIDHACHANDVASIVA 241
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
203 FAEGHLPYVLDRSEEDVSLLEMTKKAIEILEKNPNGFFLMIEGGRIDHACHANDVASIVA 262
242 ETKEFDDVVGYVLDYARRRGDTLVIVLADHETGGLGIGLNYGHSVDIDSIRRIDASIEEM 301
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
263 ETKEFDDVVGYVLDYARRRGDTLVIVLADHETGGLGIGLNYGHSVDIDSIRRIDASIEEM 322
302 SKEIKSGGDIRDVIRRHTGLELTDEEVKEIEEAKNSTNKYALGNIIGEIISKKLGVGFVS 361
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
323 SKEIKSGGDIRDVIRRHTGLELTDEEVKEIEEAKNSTNKYALGNIIGEIISKKLGVGFVS 382
362 HKHTGEPVPLLAYGPGAENFVGFKHHVDTAKVIAKLMIFGDRSISFTIKGVSKIKGDVTG 421
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
383 HKHTGEPVPLLAYGPGAENFVGFKHHVDTAKVIAKLMIFGDRSISFTIKGVSKIKGDVTG 442
422 DYRVDERDAYATLMLLLGDLVDTELENIADMDNNGIIDLLDVMAILQASS 471
||||||||||||||||||||||||||||||||||||||||||||||||||
443 DYRVDERDAYATLMLLLGDLVDTELENIADMDNNGIIDLLDVMAILQASS 492
Regarding claim 5, Zappa et al. teach that the alkaline phosphatase assay was carried out at 70°C and therefore has a denaturation temp above 40°C.
Regarding claim 24, Boutell et al. teaches the use of dNTPs. [0108]. The instant specification states: The resynthesis kit may further comprise a nucleotide triphosphate (NTP). Preferably, the nucleotide triphosphate may be a deoxynucleotide triphosphate (dNTP). [00122].
Regarding claim 27, Boutell et al. in view of Zappa et al. as evidenced by Q9UZV2 teaches the kit of claim 1. Where the only difference between a prior art product and a claimed product is printed matter that is not functionally related to the product, the content of the printed matter will not distinguish the claimed product from the prior art. In re Ngai, 367 F.3d 1336, 1339, 70 USPQ2d 1862, 1864 (Fed. Cir. 2004). (Claim at issue was a kit requiring instructions and a buffer agent. The Federal Circuit held that the claim was anticipated by a prior art reference that taught a kit that included instructions and a buffer agent, even though the content of the instructions differed.) See also In re Gulack, 703 F.2d 1381, 1385-86, 217 USPQ 401, 404 (Fed. Cir. 1983). (“Where the printed matter is not functionally related to the substrate, the printed matter will not distinguish the invention from the prior art in terms of patentability…[T]he critical question is whether there exists any new and unobvious functional relationship between the printed matter and the substrate.”)
Claim(s) 2 is/are rejected under 35 U.S.C. 103 as being unpatentable over Boutell et al. (US 2020/019578 A1) in view of Zappa et al. (Applied and Environmental Microbiology, 2001) as evidenced by Q9UZV2 (Pyrococcus abyssi (strain GE5/Orsay) alkaline phosphatase sequence, uploaded 2000) as applied to claims 1, 3-5, 7, 21, 24, and 27 above, and further in view of Zappa et al. (Journal of Inorganic Biochemistry, 2004).
The teachings of Boutell et al. in view of Zappa et al. as evidenced by Q9UZV2 as applied to claims 1, 3-5, 7, 24, and 27 are applied to claim 2. Boutell et al. in view of Zappa et al. as evidenced by Q9UZV2 does not teach the concentration range recited in claim 2.
Zappa et al. teach the use of P. abyssi alkaline phosphatase at a concentration of 4.5µM (5-10 µg in 20 µL) in an assay. Zappa et al. used this standard amount for routine activity assays. Therefore, one of ordinary skill in the art would use a range that is known for routine assays in the kit taught by Boutell et al. in view of Zappa et al. as evidenced by Q9UZV2 as a starting point. It is noted that 4.5µM is within the range recited in claim 2, however, one of ordinary skill in the art would optimize this amount based on the type of reaction.
Claim(s) 6 and 8 is/are rejected under 35 U.S.C. 103 as being unpatentable over Boutell et al. (US 2020/019578 A1) in view of Zappa et al. (Applied and Environmental Microbiology, 2001) as evidenced by Q9UZV2 (Pyrococcus abyssi (strain GE5/Orsay) alkaline phosphatase sequence, uploaded 2000) further in view of Innis et al. (PNAS, 1988).
The teachings of Boutell et al. in view of Zappa et al. as evidenced by Q9UZV2 as applied to claims 1, 3-5, 7, 24, and 27 are applied to claim 6 and 8. Boutell et al. in view of Zappa et al. as evidenced by Q9UZV2 does not teach the amount of polymerase recited in claim 6 or the denaturation temperature of Taq polymerase.
Innis et al. teach DNA sequencing with Taq polymerase. Enzyme amounts are not typically recited as M but instead as U (units). The examiner calculated, from the information provided by Innis et al., that each U of Taq polymerase is 4.25 µM. (See enzymes under materials). Innis et al. adds 5 units/µL for a total of 50 units in 10 µL which is 212.5 µM.
Regarding claim 8, Innis et al. teach the denaturation temperature of Taq polymerase is above 40°C. (see extension-termination reaction).
Therefore, one of ordinary skill in the art would be motivated to use know amounts of Taq polymerase in the kit taught by of Boutell et al. in view of Zappa et al. as evidenced by Q9UZV2 as Boutell et al. already teaches the inclusion of Taq polymerase in the kit.
Claim(s) 9 and 11-13 is/are rejected under 35 U.S.C. 103 as being unpatentable over Boutell et al. (US 2020/019578 A1) in view of Zappa et al. (Applied and Environmental Microbiology, 2001) as evidenced by Q9UZV2 (Pyrococcus abyssi (strain GE5/Orsay) alkaline phosphatase sequence, uploaded 2000) further in view of Q58134-OGG1_METJA (Methanocaldococcus jannaschii strain DNA glycosylase, uploaded 1996).
The teachings of Boutell et al. in view of Zappa et al. as evidenced by Q9UZV2 as applied to claims 1, 3-5, 7, 24, and 27 are applied to claim 9 and 11-13. Boutell et al. in view of Zappa et al. as evidenced by Q9UZV2 does not teach a thermophilic glycosylase of claim 9 and the limitations of claims 11-13.
Q58134-OGG1_METJA teaches SEQ ID NO: 2, the DNA glycosylase from Methanocaldococcus jannaschii. See alignment below:
1 MMLIKKIEELKNSEIKDIIDKRIQEFKSFKNKSNEEWFKELCFCILTANFTAEGGIRI 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
1 MMLIKKIEELKNSEIKDIIDKRIQEFKSFKNKSNEEWFKELCFCILTANFTAEGGIRIQK 60
61 EIGDGFLTLPREELEEKLKNLGHRFYRKRAEYIVLARRFKNIKDIVESFENEKVAREFLV 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
61 EIGDGFLTLPREELEEKLKNLGHRFYRKRAEYIVLARRFKNIKDIVESFENEKVAREFLV 120
121 RNIKGIGYKEASHFLRNVGYDDVAIIDRHILRELYENNYIDEIPKTLSRRKYLEIENILR 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
121 RNIKGIGYKEASHFLRNVGYDDVAIIDRHILRELYENNYIDEIPKTLSRRKYLEIENILR 180
181 DIGEEVNLKLSELDLYIWYLRTGKVLK 207
|||||||||||||||||||||||||||
181 DIGEEVNLKLSELDLYIWYLRTGKVLK 207
Boutell et al. teaches the use of glycosylase. [00158]. The claim would have been obvious to one of ordinary skill in the skill because the substitution of one known element for another would have yielded predictable results.
Claim(s) 10 is/are rejected under 35 U.S.C. 103 as being unpatentable over Boutell et al. (US 2020/019578 A1) in view of Zappa et al. (Applied and Environmental Microbiology, 2001) as evidenced by Q9UZV2 (Pyrococcus abyssi (strain GE5/Orsay) alkaline phosphatase sequence, uploaded 2000) in view of Q58134-OGG1_METJA (Methanocaldococcus jannaschii strain DNA glycosylase, uploaded 1996) as applied to claims 9 and 11-13 above, and further in view of Sebera et al. (Nucleic Acids Research, 2017).
The teachings of over Boutell et al. in view of Zappa et al. as evidenced by Q9UZV2 in view of Q58134-OGG1_METJA as applied to claims 9 and 11-13 above are applied to claim 10. Boutell et al. in view of Zappa et al. as evidenced by Q9UZV2 in view of Q58134-OGG1_METJA does not teach the concentration of glycosylase as recited in claim 10. Sebera et al. teach assays with hOGG1, an 8-oxoguanine DNA glycosylase. Q58134-OGG1_METJA teaches an 8-oxoguanine DNA glycosylase. Sebera et al. teaches an in vitro assay that uses 3.33µM of glycosylase. (The in vitro assay of hOGG1 catalytic assay, page 5233). Sebera et al. shows results of the assay in figure 4b.
Based on the activity assay taught by Sebera et al., using the same glycosylase as 8-oxoguanine DNA glycosylase, one of skill in the art would be motivated to use the same amount of glycosylase that is shown to be effective in the kit taught by Boutell et al. in view of Zappa et al. as evidenced by Q9UZV2 in view of Q58134-OGG1_METJA.
Claim(s) 22 and 23 is/are rejected under 35 U.S.C. 103 as being unpatentable over Boutell et al. (US 2020/019578 A1) in view of Zappa et al. (Applied and Environmental Microbiology, 2001) as evidenced by Q9UZV2 (Pyrococcus abyssi (strain GE5/Orsay) alkaline phosphatase sequence, uploaded 2000) in view of Q58134-OGG1_METJA (Methanocaldococcus jannaschii strain DNA glycosylase, uploaded 1996) and Sebera et al. (Nucleic Acids Research, 2017)as applied to claims 9 and 11-13 above, and further in view of Gasteyer et al. (US 8,793,895 B2).
The teachings of Boutell et al. in view of Zappa et al. as evidenced by Q9UZV2 in view of Q58134-OGG1_METJA and Sebera et al. as applied to claims 9 and 11-13 above are applied to claim 10. These do not teach that the glycosylase is lyophilized or that it includes a salt and trehalose.
Gasteyer et al. teach a method of lyophilizing a material. (claim 1). The method is an improvement on pharmaceutical lyophilization processes and can be applied to any material processing. (Col 4 line 64-Col 5 line 9). Gasteyer et al. describes the pharmaceutically acceptable carrier including any and all solvents, salt, or other materials that would be known to one of skill in the art. (Col. 11, lines 15-48). Gasteyer et al. teach the use of excipients like trehalose. (Example 8).
All the claimed elements were known in the prior art and one skilled in the art could have combined the elements. Lyophilization of materials was known in the art as well as the components necessary for a suitable carrier. Therefore, it would have been obvious to one of ordinary skill in the art to provide the required components of a kit in a lyophilized form to store the components.
Claim(s) 19 and 20 is/are rejected under 35 U.S.C. 103 as being unpatentable over Boutell et al. (US 2020/019578 A1) in view of Zappa et al. (Applied and Environmental Microbiology, 2001) as evidenced by Q9UZV2 (Pyrococcus abyssi (strain GE5/Orsay) alkaline phosphatase sequence, uploaded 2000) further in view of Gasteyer et al. (US 8,793,895 B2) and Raj (Biotech Articles, 2014).
The teachings of Boutell et al. in view of Zappa et al. as evidenced by Q9UZV2 as applied to claims 1, 3-5, 7, 24, and 27 are applied to claim 19 and 20. Boutell et al. teaches an exonuclease [claim 14 and 15], does not teach a lyophilized formulation comprising the thermophilic phosphatase, a salt, a detergent, and any one or more of magnesium chloride, acetate, or sulfate.
Gasteyer et al. teach a method of lyophilizing a material. (claim 1). The method is an improvement on pharmaceutical lyophilization processes and can be applied to any material processing. (Col 4 line 64-Col 5 line 9). Gasteyer et al. describes the pharmaceutically acceptable carrier including any and all solvents, surfactants, salt, or other materials that would be known to one of skill in the art. (Col. 11, lines 15-48).
Raj et al. reviews why salt and magnesium chloride are necessary for PCR. Salt functions by reducing the repulsion between the negatively charged DNA strands and the primer and template. MgCl2 affects the specificity and efficiency of the reaction and is identified as a critical component.
All the claimed elements were known in the prior art and one skilled in the art could have combined the elements. Lyophilization of materials was known in the art as well as the components necessary for sequencing and repair assays. Therefore, it would have been obvious to one of ordinary skill in the art to provide the required components of a kit in a lyophilized form to store the components.
Conclusion
No claims are allowed.
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/MINDY G BROWN/Patent Examiner, Art Unit 1683
/ANNE M. GUSSOW/Supervisory Patent Examiner, Art Unit 1683
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