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 .
Priority
This application, filed August 11, 2022, is a national stage application of PCT/EP2021/053534, filed February 12, 2021, which claims priority to foreign priority application FR2001479, filed February 14, 2020.
Status of the Application
Applicant’s communication, received February 26, 2026, wherein claims 22, 25, 30, and 31 are amended and new claims 32-38 are added, is acknowledged.
Claims 16-38 are pending and examined on the merits herein.
Withdrawn Objections
Applicant’s amendment, received February 26, 2026, with respect to the objection to claim 25 for minor informalities, has been fully considered and found to be persuasive to remove the objection because claim 25 is amended to correct these minor informalities. Therefore the objection is withdrawn.
Withdrawn Rejections
Applicant’s amendment, received February 26, 2026, with respect to the rejection of claims 22-23 under 35 USC § 102 as anticipated by Kemp, as evidenced by Volkmer and Sezenov, has been fully considered and found to be persuasive to remove the rejection because claim 22 is amended to require the final concentration of potassium salt ranges from about 8 mM to about 190 mM, which Kemp does not teach. Therefore the rejection is withdrawn.
Applicant’s amendment, received February 26, 2026, with respect to the rejection of claims 22-23 under 35 USC § 102 as anticipated by Chen, as evidenced by Volkmer, Sezenov, and Advanced Minerals, has been fully considered and found to be persuasive to remove the rejection because claim 22 is amended to require the final concentration of potassium salt ranges from about 8 mM to about 190 mM, which the embodiments of Chen cited in the previous rejection do not address. Therefore the rejection is withdrawn.
Applicant’s amendment, received February 26, 2026, with respect to the rejection of claims 16-23 under 35 USC § 103 as unpatentable over Chen, has been fully considered and found to be persuasive to remove the rejection of claims 22 and 23 because claim 22 is amended to require the final concentration of potassium salt ranges from about 8 mM to about 190 mM, which the embodiments of Chen cited in the previous rejection do not address. Therefore the rejection is withdrawn.
Applicant’s amendment, received February 26, 2026, with respect to the rejection of claims 22-23 under 35 USC § 103 as unpatentable over Arad in view of Kemp, as evidenced by Milo, has been fully considered and found to be persuasive to remove the rejection of claims 22 and 23 because claim 22 is amended to require the final concentration of potassium salt ranges from about 8 mM to about 190 mM, which the combination of Arad and Kemp does not teach. Therefore the rejection is withdrawn.
Applicant’s amendment, received February 26, 2026, with respect to the rejection of claims 24, 26, and 28-30 under 35 USC § 103 as unpatentable over Arad in view of Kemp and Krupey, has been fully considered and found to be persuasive to remove the rejection because independent claim 22 is amended to require the final concentration of potassium salt ranges from about 8 mM to about 190 mM, which the combination of Arad, Kemp, and Krupey does not teach. Therefore the rejection is withdrawn.
Applicant’s amendment, received February 26, 2026, with respect to the rejection of claims 25 and 27 under 35 USC § 103 as unpatentable over Arad in view of Kemp, Krupey, and Chen has been fully considered and found to be persuasive to remove the rejection because independent claim 22 is amended to require the final concentration of potassium salt ranges from about 8 mM to about 190 mM, which the combination of Arad, Kemp, Krupey, and Chen does not teach. Therefore the rejection is withdrawn.
Applicant’s amendment, received February 26, 2026, with respect to the rejection of claim 25 under 35 USC § 103 as unpatentable over Arad in view of Kemp, Krupey, and Goldsborough has been fully considered and found to be persuasive to remove the rejection because independent claim 22 is amended to require the final concentration of potassium salt ranges from about 8 mM to about 190 mM, which the combination of Arad, Kemp, Krupey, and Goldsborough does not teach. Therefore the rejection is withdrawn.
Applicant’s amendment, received February 26, 2026, with respect to the rejection of claims 28-31 under 35 USC § 103 as unpatentable over Arad in view of Kemp and Corstjens has been fully considered and found to be persuasive to remove the rejection because independent claim 22 is amended to require the final concentration of potassium salt ranges from about 8 mM to about 190 mM, which the combination of Arad, Kemp, and Corstjens does not teach. Therefore the rejection is withdrawn.
Claim Interpretation
The term “complex sample” recited in the present claims is interpreted consistent with its definition in the specification (see p. 6), which states that complex sample “relates to a sample which can comprise, in addition to the nucleic acids of interest, other constituents”.
The following rejection is modified from the previous Office Action, necessitated by Applicant’s amendment narrowing claim 22 to require the final concentration of potassium salt ranges from about 8 mM to about 190 mM.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 22-23 are rejected under 35 U.S.C. 102(a)(1) and 35 U.S.C. 102(a)(2) as being anticipated by Chen (U.S. pre-grant publication no. US 20090227011 A1; of record).
Claim 22 is drawn to a method for extracting nucleic acids from a complex sample, comprising the steps of a) through e) recited in the claim, and claim 23 requires the complex sample is a biological sample, environmental sample, or food sample.
Chen teaches novel methods to purify plasmid DNA from host cells (cover page, Abstract, lines 1-2). Chen teaches that in their method, following a standard lysis procedure that releases plasmid DNA from the host cells, two sequential precipitation procedures separate plasmid DNA from essentially all impurities of the host cells (cover page, Abstract, lines 2-5).
Chen teaches that in an embodiment of their method, alkaline lysis of the host cells step comprises re-suspending harvested host cells by centrifugation or filtration in a buffer solution of Sol. I (e.g., 50 mM Tris-HCl, 10 mM EDTA, pH 8.0) and then lysing the cells by adding a Sol. II (e.g., 0.2 NaOH and 1 % SDS), further teaching that the exact formulations for Sol. I and Sol. II are not limited (p. 3, [0026], lines 4-10). Chen teaches that following the lysis step, host cell impurities are precipitated from the lysate by adding a first solution comprising salts of at least one monovalent cation and at least one divalent cation, and that in an embodiment, the first solution comprises potassium and manganese ions, and that in an embodiment, the addition of the first solution occurs simultaneously with addition of a neutralization buffer (p. 3, [0028], lines 1-9).
In addition, Chen teaches an exemplary process for DNA purification that includes the steps of 1. Re-suspension of the host cells in Sol. I of 50 mM Tris-HCl, 10 mM EDTA, pH 8.0; 2. Lysis of the cells by adding equal volume of Sol. II of 0.2 M NaOH, 1 % SDS; 3. Neutralizing the lysate with equal volume of Sol. III of 2.0 M acetic acid, 0.6 M potassium acetate, 0.4 M manganese chloride, 0.4 M calcium chloride; 4. Obtaining clarified lysate by centrifugation or filtration (p. 6, [0055]-[0059]), 5. Precipitating plasmid DNA from the clarified lysate by adding PEG 8000 to a final concentration of 4%; 6. Collecting the plasmid DNA precipitation by centrifugation or filtration; and 7. Optionally dissolving the plasmid DNA in water, and precipitate the plasmid DNA again by adding calcium chloride to a final and concentration of 40 mM and PEG 8000 to a final concentration of 4%, and collect the final plasmid DNA precipitation by centrifugation or filtration (p. 6, [0059]-[0062]).
Finally, Chen teaches a specific example for isolating plasmid DNA from E. coli (p. 11, Example 8, [0191]-[0204]) (emphasis added). This process includes growing a 20 L culture of E. coli (p. 11, [0192]), filtering the cells using 20 grams of Celpure® filter aid (p. 11, [0193]), resuspending the Celpure®-bacteria cake in one liter of Sol. I [50 mM Tris-HCl, 10 mM EDTA, pH 8.0] (p. 11, [0194]), adding one liter of Sol. II [0.2M NaOH and 1 % SDS] to lyse the bacteria (p. 11, [0195]), adding one liter of Sol. III [2.0M HAc, 0.6M KAc, 0.4M MnCl2, 0.4 M CaCl2] (p. 11, [0196]), filtering the lysate (p. 11, [0197]), adding 40% PEG 8000 to the clarified lysate, mixing, filtering the mixture through a 0.1 micron filter membrane (p. 11, [0198] and [0199]), and finally adding water to the filter, collecting the filtrate, adding water again, and collecting the filtrate again (p. 11, [0200]). Chen further teaches an additional precipitation and wash step, before adding water to dissolve the plasmid DNA (p. 11, [0201]-[0204]). These steps satisfy the limitations of present claim 22.
Chen discloses Sol. I as 50 mM Tris-Cl, pH 8.0 and 10 mM EDTA, Sol II as 0.2 M NaOH and 1 % SDS, and Sol III as 2.0M HAc, 0.6M KAc, 0.4M MnCl2, 0.4 M CaCl2. Therefore, ignoring the volume of the cell pellet, the solution in which the cells are lysed in Example 8 above is a 2 L solution that includes 0.5% SDS, as required by step a) of claim 22. In addition, after adding Sol III, the resulting solution is a 3 L solution that includes approximately 0.2 M (200 mM) potassium salt.
These concentrations above do not include a volume of a cell pellet or filter aid. However, considerations of those volumes would be expected to increase the total volume and further reduce concentration. Accordingly, the concentrations of SDS and potassium salt above would be considered upper limits of the concentration actually present in the method of Chen, and consideration of these volumes would reduce the actual concentrations of SDS and potassium salt.
As defined in the specification, "about" referring to a value, means more or less 10% of said value (p. 6, Definitions section). Therefore, a concentration of about 190 mM would include conditions of 200 mM potassium, as taught by Chen.
As stated, the conditions disclosed by Chen satisfy all conditions of claims 22-23.
Response to Applicant’s arguments: With respect to the previous rejection of claims 22-23 under 35 U.S.C. § 102 as anticipated by Chen, Applicant argues that the paragraphs commented from the outstanding Office Action in in Chen (Example 8, paragraphs [0191]-[0200]) do not disclose the final concentrations of the potassium salt as defined in original claim 22 and now amended claims. Applicant argues that the Office Action provides a theoretical estimate which entirely relies on two postulates, assuming that: (i) the volume of the bacterial pellet is negligible, and (ii) the final amount corresponds to the arithmetic sum of potassium salt content in stock solutions from Chen, corresponding to a 200 mM potassium salt solution. Applicant argues that postulate (i) is speculative and that postulate (ii) is inapplicable to Chen, which explicitly states on paragraph [0027], that volume ratios are variable and can be optimized.
Applicant’s arguments have been fully considered but they are not found persuasive. As described in the above rejection, Chen discloses a specific example, Example 8, which would provide a concentration of 200 mM potassium salt solution. Applicant argues that this concentration assumes the volume of the bacterial pellet is negligible, and thus the final concentration of potassium salt is not known. However, any volume of bacterial culture would reduce the concentration of potassium salt such that this concentration falls within the claimed range. The Office has not identified conditions in which the conditions of Example 8 would not have a potassium concentration within the claimed range, and Applicant has not provided a persuasive argument to rebut the potassium concentration present in Example 8 of Chen as inherently falling within the range recited in claim 22.
Moreover, this argument is further supported by best estimates of the volume of a bacterial pellet. Volkmer (Volkmer, B.; et al. PLoS One 2011, vol. 6, e23126; cited in previous office action) teaches the density and volume of E. coli in culture. Volkmer teaches that total cell volume in a sample correlates with culture OD (p. 3, right column, first full paragraph, see header). Volkmer teaches that independent of the condition or growth rate, the OD-dependent total volume of the cells is an almost constant number, with the highest and lowest values differing only by a factor of two, which can be considered marginal given the higher condition-dependent variation in cell volumes and OD-specific cell concentrations. Volkmer teaches that that the total cell volume per OD is basically constant for a wide range of different cultivation conditions, and that OD measurements can in fact be used to estimate the total cell volume in a sample (p. 3, right column, second full paragraph, lines 1-9). Volkmer teaches that with the spectrophotometer they used in their study, one mL of culture at OD 1 would correspond to a total cell volume of approximately 3.6 μL (p. 3, right column, second full paragraph, lines 9-11). Volkmer further teaches that for E. coli strain BW25113 grown in LB media, one mL of culture at OD 1 would have a volume of 3.4 μL, and for E. coli strain MG1655, one mL of culture at OD 1 would have a volume of 2.9 μL (p. 2, Table 1). Volkmer further states that comparison experiments using the MG1655 strain show that these results are generally valid for E. coli, suggesting that they are reasonably applied to the strain of E. coli used by Chen.
Chen teaches a 20 L culture of E. coli. Taking Volkmer’s measurement that one mL of culture at OD 1 would correspond to a total cell volume of approximately 3.6 μL, a 20 L solution would have a cell volume of 72 mL (3.6 μL/mL * 20,000 mL). Culture at an OD of 10 would give a total volume of cells of approximately 720 mL.
As taught by Sezenov (Sezenov, G.; et al. Journal of Bacteriology 2007, vol. 189, pp. 8746-8749; cited in previous office action), Luria-Bertani broth supports Escherichia coli growth to an optical density at 600 nm (OD600) of 7 (p. 8746, Abstract, line 1). Although Chen does not disclose the specific type of media used to grow their cultures, an OD of 10 may be a higher concentration of cells present in the experiment of Chen.
Chen teaches the cells were isolated by filtration with 20 g of Celpure® filter aid. As taught by Advanced Minerals (Advanced Minerals Corporation, “Comparing Conventional Diatomite and Celpure® Filter Aid”, 2002; cited in previous office action), the wet density of Celpure® 300 is approximately 0.25 g/cm3 (p. 2, left column, Density section, lines 1-3), and thus 20 g would give a volume of approximately 80 cm3, which is equivalent to 80 mL.
Therefore, assuming an E. coli/Celpure® filter cake volume of 800 mL (720 mL + 80 mL; derived from a culture of OD 10), the concentration of SDS after addition Sol. I and Sol. II would be 0.357%, and the concentration of potassium salt after adding Sol. III would be approximately 159 mM, assuming all volumes are additive. These concentrations fall withing the range of claims 22-23.
Furthermore, even if the volume of the E. coli/Celpure® filter cake were much larger, for example, 1.5 L, the concentrations of SDS after adding Sol. I and Sol II would be approximately 0.286%, and the concentration of potassium salt after adding Sol. III would be approximately 133 mM, each of which are still well within the claimed range. Even if the volume of bacterial pellet and filter cake were 20 L, the volume of the original culture, the concentrations of SDS after adding Sol. I and Sol II would be approximately 0.022%, and the concentration of potassium salt after adding Sol. III would be approximately 23 mM, each within the claimed range.
Therefore, even when accounting for a volume of the cell pellet present in the experiment of Chen discussed above, the concentrations of SDS and potassium salt required by claim 22 fall within the range recited in claim 22.
MPEP 2112.01 (especially at I) citing In re Best, 562 F.2d 1252, 195 USPQ 430 (C.C.P.A. 1977) and In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990) discusses the support of rejections wherein the prior art discloses subject matter in which there is reason to believe inherently includes functions or characteristics that are newly recited or identical to an invention as instantly claimed. In such a situation the burden is shifted to the applicants to show the invention of the applicant and the prior art are not the same or that the invention of the prior art products does not necessarily possess the characteristics of the claimed invention. As stated above, the Office has not identified conditions in which the conditions of Example 8 would not have a potassium concentration within the claimed range, and Applicant has not provided a persuasive to rebut the potassium concentration present in Example 8 of Chen.
Therefore, for the reasons described above, the present rejection is maintained.
The following rejection is modified from the previous Office action as it applies to claims 22-23, necessitated by Applicant’s amendment narrowing the final concentration of require the final concentration of potassium salt ranges from about 8 mM to about 190 mM. In addition, this rejection is modified to include new claims 32, 34, and 36.
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.
The factual inquiries for establishing a background for determining obviousness under 35
U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 16-23, 32, 34, and 36 are rejected under 35 U.S.C. 103 as being unpatentable over Chen (U.S. pre-grant publication no. US 20090227011 A1; of record).
Chen teaches as described in the above rejection under 35 U.S.C. § 102. In addition, Chen teaches methods to purify plasmid DNA from host cells (cover page, Abstract, lines 1-2), specifically teaching kits as part of their invention. Chen teaches kits for the purification of plasmid DNA comprising a Solution A that comprises Tris-HCl, EDTA, NaOH, and SDS and a Solution B that comprises acetic acid, potassium acetate, and manganese chloride (p. 4, [0032], lines 1-5). In one embodiment, Chen teaches that Solution A comprises 50 mM Tris-HCl, 10 mM EDTA, 0.2 N NaOH and 1 % SDS, and that Solution B comprises 2.0 M acetic acid, 0.6 M potassium acetate, 0.4 M calcium chloride, and 0.4 M manganese chloride (p. 4, [0032], lines 7-11).
Chen teaches that the concentration of the acetic acid and acetate salt, such as potassium acetate, in the neutralization buffer can vary over a wide range (p. 4, [0036], lines 6-8). Chen teaches that acetic salt can be used to provide the at least one monovalent cation, and in an embodiment, the concentration of acetate salt is about 0.05 M to about 6 M (p. 4, [0037], lines 1-3).
Chen further teaches that the divalent ions can be provided by adding a variety of divalent cation salts, including ZnCl2, CuSO4, NiSO4, CaCl2, or MnCl2, and that these salts can be present in a concentration of about 0.05 M to about 4 M (p. 4, [0038], lines 1-8).
Chen teaches that for obtaining clarified lysate via filtration, the transferring
adaptor can be used to combine centrifugation with filtration, and that in this circumstance, the pore size of the filter membrane should be smaller, e.g., not larger than about 20 microns, preferably not larger than 10 microns, and preferably about 5 microns (p. 7, [0073], lines 1-6). Furthermore, Chen teaches an example wherein cell lysate is filtered through a 5 micron membrane after addition of the addition of solution comprising potassium acetate and MnCl2 (p. 8, [0100]-[0101]).
Chen does not teach a specific kit that satisfies all limitations of present claims 16-20, or a method for extracting nucleic acids contained in a complex sample, comprising extracting the nucleic acid using the kit according to claim 16. In addition, Chen does not teach a specific embodiment that satisfies all limitations of claims 32, 34, and 36.
It would have been prima facie obvious to one of ordinary skill in the art to prepare a kit that satisfies all limitations of present claims 16-20. One of ordinary skill in the art would have been motivated to prepare a kit that that satisfies all limitations of present claims 16-20 because Chen teaches kits for extraction and purification of plasmid DNA that includes a lysis buffer comprising a concentration of SDS ranging from 1% to 25% and a buffer comprising a concentration of a potassium salt ranging from about 0.1 M to about 5.0 M. Moreover, Chen teaches methods that a buffer with a divalent metal ion, specifically suggesting ZnCl2 and CuSO4 as exemplary divalent metal ions, and Chen teaches methods that utilize filtration to clarify the sample lysate.
Specifically regarding the divalent metal ion, because Chen teaches methods of purifying plasmid DNA that utilize a divalent metal ion, and because Chen teaches these salts can be present in concentrations from about 0.05 M to about 4 M, one of ordinary skill in the art would have contemplated the kit for performing the method of Chen that includes a buffer comprising ZnCl2 and CuSO4 in concentrations from about 0.5 M to about 4 M. Moreover, because Chen teaches embodiments with MnCl2 as the divalent metal ion in a concentration of 0.4 M, one of ordinary skill in the art would have considered a buffer comprising an alternative divalent metal ion, such as ZnCl2 or CuSO4, present in this concentration.
Regarding the kit comprising a filter with a pore diameter ranging from about 1 μm to about 10 μm, because Chen teaches methods of purifying plasmid DNA that utilize a filter for clarifying the sample, one of ordinary skill in the art would have contemplated including a filter in the kit taught by Chen, because the filter may be used for the purposes of clarifying lysate when practicing the method taught by Chen. Moreover, because Chen teaches a preferable pore size of about 5 microns and teaches an example in which a 5 micron pore size filter is used to clarify a lysate, one of ordinary skill in the art would have contemplated a filter with a pore size of 5 microns to be included in the kit suggested by Chen.
Regarding the method for extracting nucleic acids contained in a complex sample comprising extracting the nucleic acid using the kit according to claim 16, as recited in claim 21, because Chen further teaches methods of extracting plasmid DNA using components of said kit, such as a lysis buffer comprising a concentration of SDS ranging from about 1 % to about 25% and a buffer comprising a concentration of a potassium salt ranging from about 0.1 M to about 5.0 M, the method of claim 21 would also have been obvious over Chen. Moreover, claim 21 requires a method of isolating nucleic acid using the kit of claim 16. Claim 21 does not specifically require use of each and every reagent in the kit of claim 16, and thus even the use of one of the kit components, such as the lysis buffer comprising SDS, when isolating nucleic acids contained in a complex sample would satisfy the limitations of claim 21.
Regarding claim 32, Example 8 of Chen discussed above would lead one of ordinary skill in the art to contemplate final potassium salt concentrations of approximately 200 mM. Moreover, Chen suggests that the concentration of potassium salt may be higher or lower when practicing their method, and accordingly, one of ordinary skill in the art would have reasonably considered a potassium concentration of 190 mM.
Regarding the method of claims 34 and 36, It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the present application to modify the method taught by Chen by adding a solution comprising ZnCl2 or CuSO4 to facilitate precipitation of host cell impurities from the lysate, as suggested by Chen. One of ordinary skill in the art would have been motivated to modify the method of Chen by adding a solution comprising ZnCl2 or CuSO4 to facilitate precipitation of host cell impurities from the because Chen teaches addition of a divalent cation, such as ZnCl2 or CuSO4, with a monovalent ion such as potassium to precipitate host cell impurities in the lysate. Therefore, one of ordinary skill in the art, in view of Chen, would have considered adding an additional divalent ion, such as zinc or copper, to the monovalent potassium ion taught by Chen, because addition of a divalent metal ion such as ZnCl2 or CuSO4 may improve precipitation of host cell impurities in the lysate.
Regarding the concentration of the ZnCl2 or CuSO4 stock, Chen teaches in an embodiment a solution that comprises 0.4 M manganese chloride, which is present in a final concentration of approximately 133 mM (p. 6, [0055]-[0059]). Because Chen also teaches ZnCl2 or CuSO4 as alternatives to MnCl2, one of ordinary skill in the art would have reasonably considered the same final concentration of ZnCl2 or CuSO4 as MnCl2. With respect to the concentration of the stock solution, Chen teaches additional concentrations up to about 4 M, and because Chen teaches that the divalent metal ion may be present in a concentration as low as 0.05 M (p. 4, [0038], lines 6-8), one of ordinary skill in the art would have reasonably considered stock solutions that have higher concentrations of ZnCl2 or CuSO4, absent a showing of the criticality of a stock concentration of 0.5 M, and similarly would have reasonably considered final concentrations down to 0.05 M, as suggested by Chen.
Regarding the timing of the addition of the buffer comprising a concentration of a zinc and/or copper salt, Chen teaches addition of both the divalent metal ion (such as zinc or copper) and monovalent metal ion (such as potassium) simultaneously. However, one of ordinary skill in the art would have recognized that the method of Chen would not have been affected by addition of the buffer comprising the zinc and/or copper salt followed immediately by the buffer comprising a concentration of potassium salt, absent evidence to the contrary. Because Chen teaches the role of these metal ions is to facilitate precipitation of cell debris, one of ordinary skill in the art would have expected that each metal ion being present together in solution would be sufficient to precipitate the cell debris, regardless of which metal ion was added first.
Therefore the invention taken as a whole is prima facie obvious.
Response to Applicant’s arguments: With respect to the previous rejection of claims 16-23 under 35 U.S.C. 103 as unpatentable over Chen, Applicant presents the following arguments:
Regarding the isolation and amplification of nucleic acids in the present specification, Applicant argues that Tables 1 and 2 present binary results: presence or absence of the gene of interest after extraction. The nucleic acid amplification step employed ("isothermal amplification at 65°C for 30 min") in those comparative examples is known to such one with ordinary skill in the art and includes the use of controls to monitor the amplification curve of reference genes. Tables 1 and 2 therefore do not show an increase in the quantity of amplified nucleic acid but rather the presence or absence in the amplified sample of the gene of interest ND5S for Table 1 and the gene B2M for Table 2. Overall, Table 1 shows that a final concentration of KHCO3 at 265 mM leads to positive amplification even in a complex sample such as feces, whereas no amplification is observed at 533 mM.
With respect to the putative presence of iron contaminants in the experimental section,
pages 19-20 of the specification as filed explicitly rule out the presence of contaminants, wherein the filter is more particularly intended to retain the precipitate which contains the SDS,
the potassium salt, and possibly the insoluble cellular debris and intended to allow the
passing through of the nucleic acids contained in the sample. Applicant argues there is no evidence on record pointing at the iron contamination with the experimental results and the PCR amplification, so that all the results determining the effective concentrations of these components are reliable.
Finally, Applicant argues that claim 21 depends from claim 16, and thus is used for extracting nucleic acids.
Applicants arguments have been fully considered. Regarding Applicant’s claim of unexpected results, these are persuasive for zinc and copper at 8 mM to 33 mM and potassium at 8 mM to 133 mM, as discussed in the Allowable Subject Matter section below. However, as stated, following the guidance of Example 8 of Chen would lead one of ordinary skill in the art to practice the method of Chen with a final concentration of approximately 200 mM potassium salt, which falls within the claimed range. Accordingly, Applicant’s unexpected results, in which a specific range of potassium salt concentrations provides superior extraction results, does not establish a nexus between the range recited in claim 22 and the prior art (Chen).
Regarding the concentration of potassium salt ranging from about 8 mM to 190 mM recited in claim 32, as stated, one of ordinary skill in the art, in view of Chen, would have reasonably contemplated potassium concentrations both higher and lower than the 200 mM concentration taught in Example 8 of Chen. Although Applicant has demonstrated that the concentration of potassium has an effect on the isolation of nucleic acids, Applicant has not demonstrated criticality of a concentration of 190 mM potassium compared with the 200 mM potassium taught by Chen. Instead, Applicant has shown that an increase in potassium concentration from 133 mM to 267 mM results in a decrease in nucleic acid isolated (p. 31, Table 1). Because Chen embodies a concentration of potassium salt of 200 mM and suggests this concentration of potassium salt may be both higher and lower than 200 mM, one of ordinary skill in the art would have considered both higher and lower concentrations of potassium salt, including a concentration of 190 mM.
Regarding claims 16-20, these claims are drawn to a kit comprising the components listed. These are examined as product claims, and as stated above, these kits are obvious over Chen. Moreover, claim 21 merely requires extracting a nucleic acid with the kit of claim 16. The use of a single component of the kit of claim 16 for isolating a nucleic acid from a complex sample would reasonably constitute using the kit of claim 16. Therefore, claims 16-21 are also obvious over Chen.
Regarding the concentration of zinc and/or copper from about 8 mM to about 70 mM of claims 34 and 36, because Chen suggests concentrations of zinc and copper down to 50 mM (0.05M), one of ordinary skill in the art would have contemplated the addition of 50 mM zinc or copper. Applicant has demonstrated superior nucleic acid isolation with a concentration of zinc up to 33 mM, and thus Applicant’s superior results are not commensurate with the scope of the claim.
Accordingly, for the reasons described above, the present rejection is maintained.
Allowable Subject Matter
Claims 24-31, 33, 35, and 37-38 are objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
The closest prior art to the present claims is considered Chen, who teaches as described in the above rejections under 35 U.S.C. § 102 and 35 U.S.C. § 103. However, Chen teaches their method is for purifying plasmid DNA, and embodies isolation of plasmid DNA from E. coli. Chen does not teach or suggest their method applied to other complex samples, such as a blood sample, feces sample, saliva sample, a product of respiratory lavage sample, and a nasopharyngeal secretion sample, as required by claims 24-30, or for extracting genomic nucleic acids, as required by claim 31. Accordingly, one of ordinary skill in the art would not have considered the method of Chen for isolating nucleic acids from other complex samples or for isolating genomic nucleic acids.
In addition, the combination of Arad (Arad, U. Biotechniques 1998, vol. 24, pp. 760-762; of record) and Kemp (U.S. pre-grant publication no. US 20150225713 A1; cited in IDS received December 14, 2022) was previously used to render the method of claims 24-31 obvious. However, each of Arad and Kemp teach specific examples with higher concentrations of potassium salt than about 190 mM, and Kemp suggests a very broad range of potassium salt concentrations useful for their methods of nucleic acid isolation. Accordingly, in view of Arad and Kemp, one of ordinary skill in the art would have considered the higher concentrations of potassium salts for nucleic acid isolation. Furthermore, even if one of ordinary skill in the art would have considered a broader range of potassium concentrations suggested by Kemp, one would not have recognized the benefit of the specific potassium salt concentration required in claims 24-31, 33, 35, and 37-38, as discussed below.
Applicant has pointed to persuasive evidence of non-obviousness regarding the isolation of nucleic acids from complex samples using the claimed methods. Table 1 of the instant specification discloses that lower concentrations of KHCO3 are more effective for isolation and amplification of nucleic acids. Table 1 shows that effective isolation and amplification of nucleic acids occurs at concentrations of 67 and 133 mM (wherein 2/2 and 5/5 samples show amplification), and at 267 mM (wherein 2/5 samples show amplification), but not at 533 mM (wherein a single sample is not amplified). The prior art of record above does not teach or suggest that concentrations of potassium salt up to 133 mM are more effective for nucleic acid isolation than are higher concentrations of potassium.
Similarly, Tables 2 and 3 of the specification disclose the concentration-dependence of nucleic acid isolation in the presence of ZnSO4, showing effective isolation and amplification of nucleic acids at 25 and 33 mM, but no isolation and/or amplification at concentrations greater than 33 mM (specification, pp. 33-34). This concentration dependence of the divalent metal ion is neither anticipated nor obvious over the prior art of record.
Conclusion
Claims 16-23, 32, 34, and 36 are rejected.
Claims 24-31, 33, 35, and 37-38 are objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/B.M.B./ Examiner, Art Unit 1693
/ANDREA OLSON/ Primary Examiner, Art Unit 1693
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