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 .
Amendments
In the reply filed 1/07/2026, Applicant has made no amendments.
Claims 102-115 are under consideration.
Maintained 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 of this title, 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 set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied 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 102-107, 109-115 are rejected under 35 U.S.C. 103 as being unpatentable over Singer et al., (US2008/0113348, see IDS filed 5/06/2023), in view of Lander et al. (US 6,797,476, see IDS filed 5/06/2023), and DeVocht et al., (US 8,470,585, see IDS filed 5/06/2023), as evidenced by QIAGEN (QIAprep Miniprep Handbook, 2nd Ed., June 2005, pgs. 1-52)
Singer teaches a method for isolating plasmid DNA using quaternary ammonium-based cationic detergents (Abstract, [0063].
In regard to claim 102, Singer teaches the steps of alkaline lysis comprising
Step (a) obtaining a sample of plasmid DNA comprising resuspending bacterial cells comprising plasmid DNA is a first aqueous solution [0043, 0089], lysing the sample with a second alkaline lysis solution [0044, 0052, 0057, 0090], and neutralizing the sample [0044, 0053, 0057, 0091];
Step (b) capturing phase separated plasmid DNA on a silica-based mineral matrix with a phase separation salt solution comprising a quaternary ammonium-based cationic surfactant [0045, 0047, 0054, 0094]. For example, Singer reduces to practice the taught method with the cationic surfactant dodecyltrimethylammonium bromide (CTAB) in the presence of NaCl (Example 1, [0103]) in order to precipitate the plasmid DNA before adding the mixture to a silica column matrix (see steps 5-7 of protocol 1).
In regard to the conditions that allow for selective capture of plasmid DNA versus RNA, Singer teaches in step (a) that the lysis step is conducted in such a manner so as to prevent contamination of the plasmid with RNA [0037]. Thus, Singer teaches conditions that would allow for selective capture of plasmid DNA vs RNA. Furthermore, when the DNA sample captured on the matrix, Singer teaches step (c), see below, that uses a salt solution in combination with the cationic surfactant for removing RNA contamination bonded to the column matrix. Since the “conditions” for step (b) are not set forth in the claim with structural limitations that affect the method in a physical or tangible way, and Singer establishes conditions in the method before step (b) and in step (c) for enhancing retention of plasmid DNA over RNA contamination, the end result of the method of Singer appears to be the same and/or obvious over the claimed “conditions”. It has been held that to be entitled to patentable weight in method claims, the recited structure limitations of a step (i.e., the “conditions”) therein must affect the method in a manipulative sense. Ex parte Pfeiffer, 1962 C.D. 408 (1961);
Step (c) treating the mineral matrix and captured plasmid DNA with salt solutions for removing RNA contamination ([0055, 0059, 0098, 0111, 0113-0115, 0117], Example 3), In regard to the salt solution, enhancing the retention of the capture DNA, salts remove water molecules from the binding interface between the DNA and mineral matrix of silica glass fibers [0041];
Step (d) washing the mineral matrix and captured plasmid DNA with an organic wash solution (e.g. Qiagen PE buffer [0099]); and
Step (e) eluting the plasmid DNA from the mineral matrix, thereby isolating the plasmid DNA [0056, 0102].
However in regard to claim 102, step (b), although Singer discloses a genus of substituted quaternary ammonium-based cationic surfactants such as the C16 substituted CTAB (as stated supra) and the C12 substituted dodecyltrimethylammonium bromide (DoTAB) [0070], and clearly suggest that the R1 group from the quaternary amine comprise a phenylalkyl group, while the R2 represents the higher alky with 12 carbons, and R3 & R4 represent methyl groups [Abstract, 0003, 0006, 0018], they are silent with respect to a phenoxyethyl R1 group such as domiphen bromide (alias dodecyldimethyl(2-phenoxyethyl)ammonium bromide) wherein the R2 represents the higher alky with 12 carbons, and R3 & R4 represent methyl groups.
Lander teaches a method of isolating plasmid DNA by alkaline lysis and selective precipitation (col 8, col 14, see Fig. 1). Specifically, Lander teaches the step of selective precipitation of plasmid DNA onto a silica mineral matrix (i.e., diatomaceous earth) in the presence of a quaternary ammonium cationic detergent to generate a filter cake containing the plasmid DNA (col 19, 2nd para. see lines 30-40, see also Example 1, Purification of Plasmid DNA). In regard to claim 102 step (b), Lander teaches the quaternary ammonium cationic detergent is domiphen bromide (alias dodecyldimethyl-2-phenoxyethylammonium bromide, col 16, line 19).
Accordingly, it would have been obvious to one of ordinary skill in the art at the time of filing to practice the method of plasmid DNA purification on a mineral matrix as taught by Singer and substitute the cationic detergent domiphen bromide as taught by Lander with a reasonable expectation of success. The ordinary skilled artisan would have been motivated to do so for several reasons. First, as stated supra, Singer teaches a genus of cationic detergents having a phenylalkyl R1 group, C12 R2 group, and methyl R3/R4 groups, while Lander teaches domiphen bromide was an obvious member of this genus with the phenoxyethyl R1 group, C12 R2 group, and methyl R3/R4 groups. Furthermore, related art of DeVocht et al., (2013) teaches that domiphen bromide is useful in precipitating DNA and domiphen bromide is particularly preferred to use in purification methods because of its availability as a GMP grade material for use in products intended for human use (col 5-6).
In regard to claim 103, as stated supra, Singer teaches salt solution comprising a quaternary ammonium-based cationic surfactant in the presence of NaCl (Example 1, [0103]).
In regard to claims 104 and 105, as stated supra, Singer teaches washing the mineral matrix and captured plasmid DNA with an organic wash solution of Qiagen PE buffer [0099], which were well known to comprises about 80% ethanol (as evidenced by QIAGEN, 2005, p. 16, line 2). Furthermore, Singer teaches the wash buffer should have about 80% ethanol [0060].
In regard to claims 106 and 107, Singer teaches 1% of the cationic detergent CTAB in the presence of 0.8 M NaCl is used in the capture buffer [0111], which would have been an obvious starting point for the % of the cationic detergent DB to be used, since it has been held that where the general conditions of a claim are disclosed in the prior art, discovering the optimum or workable ranges involves only routine skill in the art. In re Aller, 105 USPQ 233.
In regard to claim 109, as stated supra, Singer teaches the sample is obtained by alkaline lysis of bacterial cells.
In regard to claim 110, as stated supra, Singer teaches the alkaline lysis of bacterial cells comprises a first cell lysis solution, and a second neutralizing solution that precipitates the genomic DNA and cellular proteins (as evidenced by QIAGEN, 2005, p. 12, 1st para., p. 15, Buffer notes, p. 22, step 3).
In regard to claim 111, Singer teaches the lysate is cleared by filtration after the neutralization step [0045].
In regard to claim 112, Singer teaches the second lysis solution comprises NaOH and SDS [0044, 0057].
In regard to claims 113 and 114, Singer teaches the neutralization buffer comprises 3 M potassium acetate [0044, 0057] and discloses the use of RNAse A in the resuspension solution [0043], which would carry over to the neutralization buffer. Furthermore, it would be obvious to include RNAase A in said buffers so as to degrade contaminating RNA away from the plasmid DNA to be purified.
In regard to claim 115, Singer teaches the purified DNA is essentially endotoxin free (Example 4).
Hence, the claimed invention as a whole was prima facie obvious in the absence of evidence to the contrary.
Claims 107 and 108 are rejected under 35 U.S.C. 103 as being unpatentable over Singer et al., (US2008/0113348, see IDS filed 5/06/2023), in view of Lander et al. (US 6,797,476, see IDS filed 5/06/2023), DeVocht et al., (US 8,470,585, see IDS filed 5/06/2023), as applied to claim 102, in further view of Bair et al. (US2005/0032105, see IDS filed 5/06/2023)
As stated supra, Singer et al. suggest a method for isolating a plasmid DNA comprising treating the mineral matrix and captured DNA with a cationic detergent and salt solution.
In regard to claim 107, Singer teaches 1% of the cationic detergent CTAB in the presence of 0.8 M NaCl is used in the capture buffer [0111], which would have been an obvious starting point for the % of the cationic detergent DB to be used, since it has been held that where the general conditions of a claim are disclosed in the prior art, discovering the optimum or workable ranges involves only routine skill in the art. In re Aller, 105 USPQ 233.
In regard to claim 108, Singer teaches the resuspension buffer comprises 50 mM Tris-HCl buffer [0043], which is mixed with the lysis and neutralization buffers. Thus, the phase separation buffer of step (b) would still have some Tris-HCl, albeit diluted.
However in regard to claims 107 and 108, although Singer teaches that the capturing of the plasmid DNA to the mineral matrix of step (b) is in the presence of sodium chloride, they are silent with respect to about 1 M lithium chloride as the salt capture the nucleic acid/detergent complex to the mineral matrix.
Bair teaches a method of isolating DNA by alkaline lysis using a mineral matrix Abstract, [0015, 0018, 0044]. Specifically in regard to claim 102 step (b), Bair teaches the DNA is first combined in a buffer comprising a surfactant and about 1 M lithium salt [0010-0013, 0016], wherein the lithium salt is lithium chloride [0016, 0045-0047].
Accordingly, it would have been obvious to one of ordinary skill in the art at the time of filing to practice the method of plasmid DNA purification on a mineral matrix in the presence of about 1% of the cationic detergent DM and about 1 M NaCl as suggested by Singer et al., and substitute about 1 M LiCl as taught by Bair with a reasonable expectation of success. The ordinary skilled artisan would have been motivated to do so as taught by Bair because the lithium salt causes improved adsorption of DNA to the solid phase matrix by making the DNA/matrix interaction more energetically favorable [0050]. In regard to the rational to substitute sodium for lithium, Bair teaches that the lithium ion is unique in that is has a smaller radius that sodium, and this allows it surface charge density to be larger than the other monovalent cations in this group [0046]. In regard to choosing about 1 M LiCl, clearly Singer establishes salt concentration as a results effective variable for plasmid DNA bonding with the cationic deteregent to the mineral matrix (Example 2), thus it would have been obvious to one having ordinary skill in the art at the time the invention was made to at least start optimizing DNA binding in about 1 M LiCl, since it has been held that discovering an optimum value of a result effective variable involves only routine skill in the art. In re Boesch, 617 F.2d 272, 205 USPQ 215 (CCPA 1980).
. Hence, the claimed invention as a whole was prima facie obvious in the absence of evidence to the contrary.
RESPONSE TO ARGUMENTS
Applicant's arguments filed on 1/07/2026 are acknowledged.
First, Applicant argues that the cited prior art does not teach or suggest a salt wash step in combination with the cationic detergent domiphen bromide (DB), nor do they teach the enhanced retention of the captured plasmid DNA. Specifically, Applicant argues that Singer teaches away from Claim 1, step (c) directed to treating the mineral matrix and bound DNA with a salt solution because Fig. 1 of Singer demonstrates that the salt washes of mineral matrix with the bound DNA reduced DNA yield. Thus, a skilled artisan would not have been motivated to include step (c), much less the substitution of CTAB for DB.
Second, Applicant argues that combining DB with a salt wash yielded unexpected results. Specifically, Applicant argues that Fig. 5A of instant specification demonstrates that the claimed method provided an unexpected improvement of selective DNA purification over RNA when DB was combined with the salt wash. Continuing, Applicant argues that Fig. 6E of instant specification demonstrates that the claimed method provided an unexpected improvement of selective DNA purification over RNA when DB was combined with a lithium chloride salt wash. Applicant argues, as little as 0.1 M LiCl substantially boost DNA plasmid recovery. In Fig. 5B, Applicant argues that both NaCl and LiCl increased the amount of pDNA recovered in a concentration dependent manner. In Figs. 7A & B, Applicant argues that MgCl increased the amount of pDNA recovered over RNA. In Fig. 7D, Applicant argues that sodium formate selectively purified pDNA over RNA. In Figs. 7E & F, Applicant argues that potassium chloride and sodium acetate were able to purify pDNA over RNA. Overall, Applicant argues that they have demonstrated unexpected results in selective pDNA purification over RNA when DB is combined with a salt wash, and that this unexpected results extends to a genus of salts including sodium chloride, lithium chloride, magnesium chloride, sodium formate, potassium chloride, and sodium acetate.
Applicant's arguments have been fully considered but they are not persuasive
In regard to Applicant’s first arguments that Singer allegedly teaches away from this step (c), contrary to Applicant’s assertion, Singer does NOT teach away from including salts in the wash buffer. Singer explicitly states that between a 300 to 1000 mM concentration “common salt solution is used as a wash buffer” [0059], and recites step 10, comprising washing the bound DNA “by adding 750 L salt buffer” [0098]. Specifically in regard to Example 3, and Fig. 1 of Singer, although Applicant is correct in that total nucleic acid binding (i.e., both DNA and RNA) is decreased as the salt solution increases (as measured by a decrease in total OD260), the relative amount of plasmid DNA is actually increased (as measured by the gel values). In other words, Singer demonstrates that salt in the wash buffer preferentially purifies plasmid DNA away from total nucleic acids as measured by the OD/GEL ratio. Thus, Singer provides both the motivation and a reasonable expectation of success in including a salt in the wash buffer for purifying plasmid DNA. Furthermore, in response to Applicant's arguments that Singer does not teach that the wash step “enhances the retention of the captured DNA”, MPEP 2144 (IV) states that the reason or motivation to modify a reference may often suggest what the inventor has done, but for a different purpose or to solve a different problem. It is not necessary that the prior art suggest the combination to achieve the same advantage or result discovered by Applicant. See, e.g., In re Kahn, 441 F.3d 977, 987, 78 USPQ2d 1329, 1336 (Fed. Cir. 2006). In instant case, the prior art of Singer teaches to include a salt wash step to enhance the retention of the DNA relative to the total nucleic acids. The fact that Applicant might have recognized another advantage which would flow naturally from following the suggestion of the prior art cannot be the basis for patentability when the differences would otherwise be obvious. See Ex parte Obiaya, 227 USPQ 58, 60 (Bd. Pat. App. & Inter. 1985).
Second, in regard to the purported unexpected results in Figures 5, 6 and 7, Applicant’s unexpected results are not commensurate in scope with the claimed method, because the salts are added in the binding buffer comprising the DB of step (b), not in the wash buffer of step (c).
Specifically, in regard to Fig. 5 A-E, Applicant demonstrates a range of 0 M to 3M NaCl or 0.25 M to 3.75 M LiCl added to the binding buffer comprising DB, which is subsequently loaded onto the glass fiber matrix (Example 5, p. 50, [00130] of Applicant’s disclosure). Applicant’s Fig. 5 appears to demonstrate that between 0.75 M to 3 M NaCl or 0.75 M to 2.75 M LiCl added to the binding buffer improved plasmid DNA purification. Thus, the purported unexpected results are not commensurate with claimed invention as far as the step at which the salt is added and the range of NaCl LiCl used. Furthermore, in regard to Fig. 5, Applicant’s specification appears to suggests that the indicated concentrations of salts in the binding buffer are not the final concentration, but are in fact the undiluted amount of P4 buffer added 1:4 to the DNA mixture prior to loading the solution onto the glass fiber matrix [0129]. Thus, Applicant must make clear and properly claim what is the final concentration of salt in the binding buffer of step (b) before any secondary considerations can be made by the Examiner.
Similarly, in regard to Fig. 6A-D, Applicant demonstrates a range of 1M to 2.75 M LiCl added to the binding buffer comprising DB, which is subsequently loaded onto the glass fiber matrix (Example 5, p. 51 of Applicant’s disclosure). Applicant’s Fig. 6A-D appear to demonstrate that between 1 M to 1.75 M LiCl added to the binding buffer improved plasmid DNA purification. However, in regard to Fig. 6E, the Examiner agrees that the Applicant has surprisingly demonstrated a range of 0.1 M to 0.7 M LiCl added to the treatment solution appears to improve plasmid DNA purification. Thus, again the purported unexpected results are not commensurate with claimed invention as far as the range of LiCl used in rejected claims 107 and 108. Furthermore, in regard to Fig. 6, again Applicant’s specification appears to suggests that the indicated concentrations of LiCl in the buffer are not the final concentration, but are in fact the undiluted amount of P4 buffer added 1:4 to the DNA mixture prior to loading the solution onto the glass fiber matrix [0132, 0135]. Thus, again Applicant must make clear and properly claim what is the final concentration of LiCl in the buffer before any secondary considerations can be made by the Examiner.
Finally, in regard to Fig. 7 A-F, Applicant demonstrates different ranges of MgCl, LiAc, K and Na salts added to the capture/binding buffers comprising DB that are subsequently loaded onto the glass fiber matrix (Example 6, p. 54 of Applicant’s disclosure). Again, these results are not commensurate in scope with the claimed method and as they occur in step (b), not step (c). Furthermore, in regard to the limited concentration ranges where the salts have an effect, Applicant is reminded that MPEP 716.02 (d), II, states that in order to establish unexpected results over a claimed range, Applicants should compare a sufficient number of tests both inside and outside the claimed range to show the criticality of the claimed range. In re Hill, 284 F.2d 955, 128 USPQ 197 (CCPA 1960).
Terminal Disclaimer
The terminal disclaimer filed on 1/07/2026 disclaiming the terminal portion of any patent granted on this application which would extend beyond the expiration date of US Patent 11,236,325 has been reviewed and is accepted. The terminal disclaimer has been recorded.
Withdrawn Double Patenting
The prior rejection of Claims 102-115 on the grounds of nonstatutory double patenting over claims 1-20 of U.S. Patent No. 11,236,325 (Kemp et al., Patented 2/1/2022) is withdrawn in light of the terminal disclaimer filed.
Conclusion
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 extension fee 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 date of this final action.
No claims are allowed.
Examiner Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ARTHUR S LEONARD whose telephone number is (571)270-3073. The examiner can normally be reached on Mon-Fri 9am-5pm.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, James Doug Schultz can be reached on 571-272-0763. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/ARTHUR S LEONARD/Examiner, Art Unit 1631
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