DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Claims 19-38 are pending as amended 9/6/23, and are considered herein.
Formalities:
The drawings of 6/14/23 are accepted.
The specification of 6/14/23 are accepted.
The IDS of 1/29/24 and references therein have been considered, a signed copy of which is provided herein.
The office-recognized priority is a CON to 16/938,222 (US PAT 11,702,696), filed 7/24/20, which is a CON of 15/945,348 (US PAT 10,724,094), filed 4/4/2018, which is a DIV of 14/855,705 (US PAT 9,938,577), filed 9/16/2015), which is a CON of 13/763,066 (US PAT 9,139,667), filed 2/8/2013, which claims priority to 61/597,064, filed 2/9/2012.
Claim Objections
Claim 22 objected to because of the following informalities:
Claim 22 recites several instances of “…amonium,”. Proper spelling is “…ammonium”.
Appropriate correction is required.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
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Claims 19-33 and 35-36 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-18 of U.S. Patent No. 9,139,667 in view of Halpin, et al. (2004) “DNA Display I. Sequence-Encoded Routing of DNA Populations”, PLoS Biology, 2(7): 1015-21.
Claim 19: Claim 1 teaches the steps of exchanging a positive ion associated with a negatively charged group on a biomolecule, with a positively-charged counterion having 2-4 hydrocarbon groups, forming the complex, which is then dispersed in a nonaqueous solvent and coupled to a substrate. Claim 2 teaches the biomolecule may be a polynucleotide. Claim 16 teaches the substrate may be a polymeric particle. Also, Claim 18 parallels Claim 16, but requires the biomolecule to be a polynucleotide, the exchange being between a metal counter ion, and the amphiphile having a non-metal counter ion, along with the polymeric particle having a electrophilic or nucleophilic group which interacts with the opposite, thereby linking the polymeric particle to the polynucleotide.
Claim 20: Claim 3 teaches the same lipophilic ions.
Claim 21: Claim 4 teaches the same lipophilic ammonium ions.
Claim 22: Claim 5 teaches same ammonium ions, and alkyl and aryl mixtures.
Claim 23: Claim 6 teaches tetraphenylphosphonium.
Claim 24: Claim 7 teaches the same arsonium ions.
Claim 25: Claim 8 teaches tetraphenylarsonium.
Claim 26: Claim 9 teaches trialkylsulfonium.
Claim 27: Claim 10 teaches the nonsqueous solvent is nonreactive with coupling groups on the substrate and biomolecule.
Claims 28-29: Claim 11 teaches several nonaqueous solvents that are polar, amounting to all the described embodiments of polar solvent.
Claim 30: Claim 12 teaches the same amides and ureas.
Claim 31: Claim 13 teaches the same carbonates.
Claim 32: Claim 14 teaches tetrahydrofuran.
Claim 33: Claim 15 teaches the same sulfoxides and sulfones.
Claim 35: Claim 16 teaches the coupling group reactive to a reactive group on the biomolecule.
Claim 36: Claims 17 and 18 teach the nucleophile/electrophile pairings.
However, the claims of the patent do not claim the further binding of the probe to a target polynucleotide, washing of it, and release of the target polynucleotide into a second solution.
On the other hand, the Artisan, interested in using substrate-linked oligonucleotides, would be aware of Halpin. Halpin teaches the manufacture of column matrix, linked to DNAs which are used to bind and isolate binding nucleic acids, which are then eluted. See Figure 3 and its legend. In the process, the binding nucleotides bind the substrate-bound nucleic acid, which is then eluted from the column, using a salt gradient, further releasing the bound nucleic acids, which are then in a second solution, as the buffer changes during elution.
Therefore, at the time of invention, it would have been obvious to add to the claimed methods of the patent, with the isolation and elution of binding nucleic acids. The Artisan would do so to isolate the same. The Artisan would expect success, as it is claimed subject matter, and/or utilized for art-recognized purposes.
Claims 19-36 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-18 of U.S. Patent No. 9,139,667 in view of Halpin, et al. (2004) “DNA Display I. Sequence-Encoded Routing of DNA Populations”, PLoS Biology, 2(7): 1015-21 and Lee, et al. (2008) “Efficiency of bulky protic solvent for SN2 reaction”, Organic Letters, 10(1): 61-4.
As shown above, the base claims are obvious over the patent and Halpin, however, the aspect of utilizing tert-butyl alcohol as the nonaqueous polar solvent is not taught.
On the other hand, the Artisan, interested in SN2 reactions to link the nucleic acid and the substrate, would be aware of Lee, for its teaching that tert-butyl alcohol is efficient as a solvent in such reactions (e.g., ABSTRACT).
Thus, at the time of invention, it would have been obvious to modify the patent and Halpin, to further utilize the tert-butyl alcohol as taught by Lee. The Artisan would do so, for linkings that utilize SN2 reactions. The Artisan would expect success, as the components are utilized for art-recognized purposes.
Claims 19-33 and 35-36 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-19 of U.S. Patent No. 9,938,577 in view of Halpin, et al. (2004) “DNA Display I. Sequence-Encoded Routing of DNA Populations”, PLoS Biology, 2(7): 1015-21.
Claim 19: Claim 1 teaches conjugating a substrate, comprising an exchange of a counter ion with a lipophilic counterion on a biomolecule. (The biomolecule may be a polynucleotide, in Claim 2.) Subsequently, the dispersing the biomolecule in a nonaqueous solvent, and coupling it to a substrate in the nonaqueous solvent. (The substrate may be polymeric particle in Claim 16.) Claim 17 is parallel, but requires the biomolecule to a nucleic acid, and the substrate is required to be a polymeric particle.
Claim 20: Claim 3 teaches same lipophilic counter ion generas.
Claim 21: Claim 4 teaches the same lipophilic ammonium ion generas.
Claim 22: Claim 5 teaches the same lipophilic ammonium ions.
Claim 23: Claim 6 teaches tetraphenylphosphonium lipophilic ions.
Claim 24: Claim 7 teaches the same lipophilic arsonium ion generas.
Claim 25: Claim 8 teaches tetraphenylphosphonium ion.
Claim 26: Claim 9 teaches trialkylsulfonium ion.
Claim 27: Claims 1-19 teach non-reactive nonaqueous solvents.
Claim 28: Claim 10 teaches polar nonaqueous solvent.
Claim 29: Claim 11 teaches the same nonaqueous solvents.
Claim 30: Claim 12 teaches the same amides and ureas.
Claim 31: Claim 13 teaches the same carbonates.
Claim 32: Claim 14 teaches tetrahydrofuran.
Claim 33: Claim 15 teaches the same sulfoxides and sulfones.
Claim 35: Claims 1 and 17 teach the coupling groups.
Claim 36: Claims 1 and 17 teach the nucleophiles and electrophiles.
However, the claims of the patent do not claim the further binding of the probe to a target polynucleotide, washing of it, and release of the target polynucleotide into a second solution.
On the other hand, the Artisan, interested in using substrate-linked oligonucleotides, would be aware of Halpin. Halpin teaches the manufacture of column matrix, linked to DNAs which are used to bind and isolate binding nucleic acids, which are then eluted. See Figure 3 and its legend. In the process, the binding nucleotides bind the substrate-bound nucleic acid, which is then eluted from the column, using a salt gradient, further releasing the bound nucleic acids, which are then in a second solution, as the buffer changes during elution.
Therefore, at the time of invention, it would have been obvious to add to the claimed methods of the patent, with the isolation and elution of binding nucleic acids. The Artisan would do so to isolate the same. The Artisan would expect success, as it is claimed subject matter, and/or utilized for art-recognized purposes.
Claims 19-36 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-18 of U.S. Patent No. 9,938,577 in view of Halpin, et al. (2004) “DNA Display I. Sequence-Encoded Routing of DNA Populations”, PLoS Biology, 2(7): 1015-21 and Lee, et al. (2008) “Efficiency of bulky protic solvent for SN2 reaction”, Organic Letters, 10(1): 61-4.
As shown above, the base claims are obvious over the patent and Halpin, however, the aspect of utilizing tert-butyl alcohol as the nonaqueous polar solvent is not taught.
On the other hand, the Artisan, interested in SN2 reactions to link the nucleic acid and the substrate, would be aware of Lee, for its teaching that tert-butyl alcohol is efficient as a solvent in such reactions (e.g., ABSTRACT).
Thus, at the time of invention, it would have been obvious to modify the patent and Halpin, to further utilize the tert-butyl alcohol as taught by Lee. The Artisan would do so, for linkings that utilize SN2 reactions. The Artisan would expect success, as the components are utilized for art-recognized purposes.
Claims 19-33 and 35-38 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-17 of U.S. Patent No. 10,724,094 in view of Halpin, et al. (2004) “DNA Display I. Sequence-Encoded Routing of DNA Populations”, PLoS Biology, 2(7): 1015-21.
Claim 19: Claim 1 teaches conjugating a nucleic acid to a polymer, comprising exchanging the counterion with a lipophilic counterion (in Claim 4), dispersing it in a nonaqueous solvent, and coupling it to the oligonucleotide.
Claim 20: Claim 5 teaches the same lipophilic ions.
Claim 21: Claim 6 teaches the same lipophilic ammonium ion generas.
Claim 22: Claim 7 teaches the same lipophilic ammonium ion subgeneras.
Claim 23: Claim 8 teaches tetraphenylphosphonium.
Claim 24: Claim 9 teaches the same lipophilic arsonium ion generas.
Claim 25: Claim 10 teaches tetraphenylarsonium.
Claim 26: Claim 11 teaches trialkylsulfonium.
Claim 27: Claim 1 teaches the solvent is non-reactive with the coupling groups on the substrate and oligonucleotide.
Claim 28: Claim 12 teaches non-polar nonaqueous solvent.
Claim 29: Claim 13 teaches the same non-aqueous solvent characteristics.
Claim 30: Claim 14 teaches the same amide and urea solvent generas.
Claim 31: Claim 15 teaches the same carbonates.
Claim 32: Claim 16 teaches THF.
Claim 33: Claim 17 teaches the same sulfoxide and sulfone Markush.
Claim 35: Claims 1 and 4 teach the coupling groups.
Claim 36: Claim 1 teaches the coupling groups NHS ester and disuccinimidyl carbonate along with an amine terminated oligonucleotide, meeting the requirement for an electrophile and nucleophile.
Claim 37: Claim 1 teaches the amine functionality, the ester or carbonate functionality, and amine terminated oligonucleotice, thus the treatments necessarily occur to link them together.
Claim 38: Claim 2 teaches the same.
However, the claims of the patent do not claim the further binding of the probe to a target polynucleotide, washing of it, and release of the target polynucleotide into a second solution.
On the other hand, the Artisan, interested in using substrate-linked oligonucleotides, would be aware of Halpin. Halpin teaches the manufacture of column matrix, linked to DNAs which are used to bind and isolate binding nucleic acids, which are then eluted. See Figure 3 and its legend. In the process, the binding nucleotides bind the substrate-bound nucleic acid, which is then eluted from the column, using a salt gradient, further releasing the bound nucleic acids, which are then in a second solution, as the buffer changes during elution.
Therefore, at the time of invention, it would have been obvious to add to the claimed methods of the patent, with the isolation and elution of binding nucleic acids. The Artisan would do so to isolate the same. The Artisan would expect success, as it is claimed subject matter, and/or utilized for art-recognized purposes.
Claims 19-38 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-17 of U.S. Patent No. 10,724,094 in view of Halpin, et al. (2004) “DNA Display I. Sequence-Encoded Routing of DNA Populations”, PLoS Biology, 2(7): 1015-21 and Lee, et al. (2008) “Efficiency of bulky protic solvent for SN2 reaction”, Organic Letters, 10(1): 61-4.
As shown above, the base claims are obvious over the patent and Halpin, however, the aspect of utilizing tert-butyl alcohol as the nonaqueous polar solvent is not taught.
On the other hand, the Artisan, interested in SN2 reactions to link the nucleic acid and the substrate, would be aware of Lee, for its teaching that tert-butyl alcohol is efficient as a solvent in such reactions (e.g., ABSTRACT).
Thus, at the time of invention, it would have been obvious to modify the patent and Halpin, to further utilize the tert-butyl alcohol as taught by Lee. The Artisan would do so, for linkings that utilize SN2 reactions. The Artisan would expect success, as the components are utilized for art-recognized purposes.
Claims 19-33 and 35-38 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-17 of U.S. Patent No. 11,702,696 in view of Andreadis, et al. (2000) “Use of immobilized PCR primers to generate covalently immobilized DNAs for in vitro transcription/translation reactions”, 28(2): e5, 8 pages long.
Claim 19: Claim 1 teaches exchanging an oligonucleotide counterion with a lipophilic counterion, dispersing it a non-aqueous solvent, and coupling the complex to a polymeric particle, applying a primer to the complex-polymeric particle. The application of the primer may be considered the binding for isolating.
Claim 20: Claim 2 teaches the same Markush of lipophilic counterions.
Claim 21: Claim 3 teaches the same lipophilic ammonium ions.
Claim 22: Claim 4 teaches the same lipophilic ammonium ions.
Claim 23: Claim 5 teaches tetraphenylphosphonium.
Claim 24: Claim 6 teaches the same lipophilic arsonium ions.
Claim 25: Claim 7 teaches tetraphenylarsonium.
Claim 26: Claim 8 teaches trialkylsulfonium.
Claim 27: Claim 9 teaches non-reactive solvent to the coupling groups.
Claim 28: Claim 10 teaches polar solvent.
Claim 29: Claim 11 teaches the same solvent characteristic Markush.
Claim 30: Claim 12 teaches the same amide/urea Markush.
Claim 31: Claim 13 teaches the carbonates.
Claim 32: Claim 14 teaches tetrahydrofuran.
Claim 33: Claim 15 teaches the same sulfoxide/sulfones.
Claim 34: Claim 16 teaches tert-butyl alcohol.
Claim 35: Claim 17 teaches the coupling group reactive with a group on the biomolecule.
Claim 36: Claim 18 teaches the nucleophile/electrophile reactive groups.
However, the claims do not teach the aspects of washing and releasing the annealed and extended polynucleotide.
On the other hand, the artisan, interested in such extensions, would be aware of Andreadis for its teaching of immobilized PCR primers for generation of DNAs for transcription/translation. Andreadis teaches that it is known to capture nucleic acids via immobilized primers and utilize the same for making attached DNA templates that could be collected and re-used. See ABSTRACT. In the process of collection, the DNA would be isolated and purified from the conjugate-polymer particle.
Thus, in light of Andreadis, the Artisan would modify the methods of the patent, to include the same. The Artisan would do so to isolate the DNA obtained. The Artisan would expect success, as the components are claimed and/or utilized for art-recognized purposes.
Conclusion
No claim is allowed.
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ROBERT M. KELLY
Examiner
Art Unit 1638
/ROBERT M KELLY/Primary Examiner, Art Unit 1638