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 .
The amendment filed on 07/03/2026 has been entered.
Claims 4-6, 8, 10-16, 19-33, 37-41, 48-51, 54-56 and 58 were amended in the claim set filed on 07/03/2026. No new matter was added.
Claims 1-58 are pending.
Applicant’s election without traverse of Invention I (claims 1-51), drawn to a method for isolating target nucleic acids below a target size from a sample comprising nucleic acid components in the reply filed on 03/04/2026 is acknowledged.
Claims 52-58 are withdrawn drawn to a nonelected Group II.
Claims 1-51 in the claim set filed on 07/03/2026 are currently under examination.
Response to the Arguments
Objections to the claims 5-23 and 25-51 in the previously mailed non-final have been withdrawn in light of applicants claim amendments.
As necessitated by amendment, new grounds of rejection under 35 U.S.C. 112 rejections of claim(s) 23-43 are made, as documented below in the 35 U.S.C. 112 rejection in this office action on Pg. 4-5.
Applicant’s arguments regarding previous rejection(s) of claim(s) 1-4 and 24 under 35 U.S.C. 103 have been fully considered but are not persuasive. The 35 U.S.C. 103 rejections documented in the previously mailed non-final have been maintained and revised in light of applicants arguments on Pg. 13-16, as documented below in the 35 U.S.C. 103 rejection in this office action on Pg. 5-29.
As necessitated by amendment, new grounds of rejection under 35 U.S.C. 103 rejections of claim(s) 5-24 and 44-51 are made, as documented below in the 35 U.S.C. 103 rejections in this office action on Pg. 5-29.
Applicant’s arguments, filed 07/03/2026, on Pg. 16, with respect to previous Nonstatutory Double Patenting (NSDP) rejections of claim 1, state that “A terminal disclaimer in compliance with 37 CFR 1.32l(c) or 37 CFR 1.32l(d) is filed with this response. Applicant respectfully submits that the rejections on claim 1 are moot”, have been fully considered and are partially persuasive. The signed terminal disclaimer was filed 07/03/2026. The NSDP rejections of claim 1 over claims 1, 15 and 18 of U.S. Patent No. US 12129511 B2, claims 1, 4 and 8 of U.S. Patent No. US 12442034 B2, and claims 1, 6 and 9 of U.S. Patent No. US 12258616 B2 have been withdrawn, accordingly. However, the provisional rejection of co-pending U.S. Patent App. No. 19/262133 remains rejected as documented below in the NSDP rejections in this office action on Pg. 30-33.
The revised or newly added rejections for claims 1-51 are documented below in this Final Office Action are necessitated by claim amendments filed on 07/03/2026.
Priority
This application claims priority to, and the benefits of, U.S. Provisional Application having Serial No. 63/381,933 filed on November 2, 2022. The priority date of claim set filed on March 4, 2026, is determined to be November 2, 2022.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 06/02/2026 was filed after the mailing date of the Non-final office action mailed on 04/06/2026. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 23-43 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 23 is indefinite over the limitation “ATPS components are selected from the group consisting of a polymer, salt, surfactant, and combinations thereof” (ln 4-5). It is unclear if the ATPS components comprise a polymer. It is unclear if the ATPS components comprise a salt. It is unclear if the ATPS components comprise a surfactant. It is unclear if the ATPS components comprise any combination of polymer, salt and/or surfactant. Thus, it is unclear as to what the metes and bounds of the ATPS component(s) comprise. Claims 25-43
depend on claim 23.
Claim 24 is indefinite over the limitation “ATPS components are selected from the group consisting of a polymer, salt, surfactant, and combinations thereof” (ln 4-5). It is unclear if the ATPS components comprise a polymer. It is unclear if the ATPS components comprise a salt. It is unclear if the ATPS components comprise a surfactant. It is unclear if the ATPS components comprise any combination of polymer, salt and/or surfactant. Thus, it is unclear as to what the metes and bounds of the ATPS component(s) comprise. Claims 25-43
depend on claim 24.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 1-2, 23 and 48-49 are rejected under 35 U.S.C. 103 as being unpatentable over Johnson-Buck et al. (“Johnson-Buck”; Patent App. Pub. WO 2019118705 A1, Jun. 20, 2019 ).
Claim interpretation: Regarding claim 1, the sample solution of (a) reads on any solution comprising a sample and the fractionation buffer of (c) reads on any buffer. The beads read on any beads that can bind an analyte. Regarding claim 23, the limitation reciting “selected from the group” is interpreted as at least one of following is included. Thus, rendering the polymer, salt, surfactant, or combinations thereof as possibly optional, if not selected. Dependent claims of claim 23 are rendered optional. Claims 25-43 optionally depend on claim 23.
Johnson-Buck discloses “technology relating to detection of analytes and particularly, but not exclusively, to compositions, methods, and systems for concentrating an analyte at a surface, e.g., for imaging and detection of low-abundance analytes.” (Abstract).
Regarding claim 1, Johnson-Buck teaches a method comprising “providing a sample comprising an analyte” (Pg. 9 ln 1) and “analytes (e.g., biomolecules (e.g., nucleic acids” (Pg. 2 ln 21-22). Johnson-Buck teaches a method comprising “the method comprises providing an aqueous two-phase system (ATPS) comprising an analyte; concentrating the analyte into a first phase of the ATPS; and contacting said first phase to a substrate.” (Pg. 4 ln 19-21). Johnson-Buck teaches a method comprising “In some embodiments, methods comprise immobilizing an analyte to a solid support. In some embodiments, the solid support is a surface (e.g., a substantially planar surface, a rounded surface), e.g., a surface in contact with a bulk solution, e.g., a bulk solution comprising analyte. In some embodiments, the solid support is a freely diffusible solid support (e.g., a bead” (Pg 59 ln 4-8) and “In some embodiments, the freely diffusing substrate comprises and/or is made of, e.g., .. gold”(Pg 41 ln 4-5). Johnson-Buck teaches a method comprising “Dynabead (~1 um) capture and magnetic deposition” (Pg. 98 Table 2). Johnson-Buck teaches a method comprising “In some embodiments related to ATPS technologies, the ATPS further comprises… a chaotropic agent” (Pg. 5 ln 29-30). Johnson-Buck teaches a method comprising “adding an analyte containing composition (e.g., a biofluid or sample) to an aqueous two-phase system (ATPS) (e.g., a mixture of materials that forms an aqueous two-phase system upon mixing). In some embodiments, the ATPS is a solid-phase ATPS.” (Pg. 61 ln 30-35). Johnson-Buck also teaches a method wherein “In some embodiments, the technology provides for the size selection of analytes, e.g., to provide a defined size range of molecules including the target analytes” (Pg. 87 ln 5-6). “the technology provides for the size selection of analytes, e.g., to provide a defined size range of molecules including the target analytes” reads on the specific isolation, capture and release of target nucleic acids below a target size. It would have been obvious to one of ordinary skill in the art that the beads-analyte complex would be immobilized or collected in a manner to where they are no longer mobile to allow for separation of the beads-analyte complex from unbound/released impurities, solution exchange(wash/elution), released analytes and further analysis. Furthermore, it would be obvious to the ordinary artisan performing size selection of analytes to selectively release and isolate the target nucleic acids below the target size. Thus, Johnson-Buck suggests a method for isolating target nucleic acids below a target size from a sample comprising nucleic acid components; comprising the steps of:(a) preparing a sample solution from the sample; (b) contacting a plurality of beads with the sample solution, wherein the nucleic acid components bind to the plurality of beads to form a beads-analyte complex; (c) mixing the beads-analyte complex with a fractionation buffer comprising at least one chaotropic agent to form a bulk fractionation solution, wherein the target nucleic acids below the target size are released from the beads-analyte complex into the bulk fractionation solution; (d) immobilizing the beads-analyte complex; and (e) separating the bulk fractionation solution comprising the isolated target nucleic acids below the target size from the immobilized beads-analyte complex.
Johnson-Buck also teaches that “Various modifications and variations of the described compositions, methods, and uses of the technology will be apparent to those skilled in the art without departing from the scope and spirit of the technology as described. Although the technology has been described in connection with specific exemplary embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments.” (Pg. 103 ln 5-10). Therefore, the invention as recited in claim 1 is prima facie obvious over the prior art Johnson-Buck et al. One of ordinary skill in the art would have had a reasonable expectation of success given the obviousness of claim 1 in view of Johnson-Buck. These claim elements were known in the art and one of skill in the art could have combined these elements by known methods with no change in their respective functions. Thus, it would have been obvious to provide a method for isolating target nucleic acids below a target size from a sample comprising nucleic acid components according to the limitations of the instant application claim 1 based on Johnson-Buck et al. (Patent App. No. WO 2019118705 A1).
Furthermore, Johnson-Buck teaches the limitations of dependent claims 2 and 48-49 depend on claim 1, and claim 23, which depends on claim 2, which depends on claim 1.
Regarding claim 2, Johnson-Buck teaches a method comprising “the method comprises providing an aqueous two-phase system (ATPS) comprising an analyte; concentrating the analyte into a first phase of the ATPS” (Pg. 4 ln 19-21). Johnson-Buck teaches a method wherein “contact is maintained between the analyte rich phase and the surface by contacting the surface with the ATPS while a force is applied to the ATPS to separate the phases such that the analyte rich phase is produced (e.g., and separated from the analyte poor phase) and contacts the surface. That is, in some embodiments the surface contacts the ATPS (e.g., contacts the analyte rich phase of the ATPS)” (Pg. 62 ln 26-31.). Johnson-Buck teaches a method comprising “the methods further comprise separating said first phase from a second phase” (Pg. 4 ln 22-23). Thus, Johnson-Buck suggests a method wherein the step (a) further comprises (a1) adding the sample to a first aqueous two-phase system (ATPS) to form a mixture that partitions into a first target-rich phase and a first target-poor phase, wherein the nucleic acid components are concentrated in the first target-rich phase; and (a2) isolating the first target-rich phase containing the concentrated nucleic acid components, resulting in the sample solution.
Regarding claim 23, Johnson-Buck teaches a method wherein “An aqueous two-phase system ATPS… arises when two water-soluble components - e.g., two polymers or a polymer and a salt - exceed a threshold concentration and separate into two aqueous phases with distinct compositions. Several types of ATPS selectively partition biomolecules, including DNA … into one of the two phases” (Para. 48; Figure 1 elements 22, 24 and 26). Thus, Johnson-Buck suggests a method wherein the first ATPS comprises first ATPS components capable of forming the first target-rich phase and the first target-poor phase when the first ATPS components are dissolved in an aqueous solution, wherein the first ATPS components are selected from the group consisting of a polymer, salt, surfactant, and combinations thereof.
Regarding claim 48, Johnson-Buck teaches a method wherein “Analytes can be obtained directly from an organism or from a biological sample obtained from an organism, e.g., from blood, urine, cerebrospinal fluid, seminal fluid, saliva, sputum, stool, hair, sweat, tears, … Exemplary samples include, but are not limited to, whole blood, lymphatic fluid, serum, plasma… sweat, tears, saliva, sputum … cerebrospinal fluid (CSF)… vaginal excretions… and swabs …washes (e.g., oral, nasopharyngeal, bronchial, bronchialalveolar, optic, rectal, intestinal, vaginal, epidermal, etc.)” (Pg. 86 ln 17-26 ). Thus, Johnson-Buck and Mather suggest a method wherein the sample is blood, plasma, urine, saliva, stool, cerebrospinal fluid (CSF), lymph, serum, sputum, peritoneal fluid, sweat, tears, nasal swab, vaginal swab, endocervical swab, semen, or breast milk.
Regarding claim 49, Johnson-Buck teaches a method wherein “A sample can also be … a cDNA library” (Pg. 86 ln 33-35) and “Analytes (e.g., nucleic acid molecules…) can be obtained, e.g., by extraction from a biological sample, e.g., by a variety of techniques.” (Pg. 87 ln 1-2). Thus, Johnson-Buck suggests a method wherein the step (a) comprises the step of preparing a DNA library from the sample, resulting in the sample solution.
Response to Arguments
Applicant's arguments filed 07/03/2026 (Pg. 13-16) with respect to claims 1-2 have been fully considered but they are not persuasive. To clarify some instances argued in the response filed 07/03/2026 see responses to each argument made by Applicant below:
Applicants’ argument: “Johnson-Buck does not teach or suggest at least features (b)-(e) recited in claim 1” (Pg. 13)
Response: Applicant’s arguments have been fully considered and found unpersuasive because as cited on Pg. 4-6 of the final office action above, in brief, “Johnson-Buck teaches a method comprising “In some embodiments, methods comprise immobilizing an analyte to a solid support. In some embodiments, the solid support is a surface (e.g., a substantially planar surface, a rounded surface), e.g., a surface in contact with a bulk solution, e.g., a bulk solution comprising analyte. In some embodiments, the solid support is a freely diffusible solid support (e.g., a bead” (Pg 59 ln 4-8).” relates to step b. “Johnson-Buck teaches a method comprising “adding an analyte containing composition (e.g., a biofluid or sample) to an aqueous two-phase system (ATPS) (e.g., a mixture of materials that forms an aqueous two-phase system upon mixing). In some embodiments, the ATPS is a solid-phase ATPS.” (Pg. 61 ln 30-35).”; “Johnson-Buck teaches a method comprising “the method comprises providing an aqueous two-phase system (ATPS) comprising an analyte; concentrating the analyte into a first phase of the ATPS” (Pg. 4 ln 19-21).”; and Johnson-Buck teaches a method comprising “In some embodiments related to ATPS technologies, the ATPS further comprises… a chaotropic agent” (Pg. 5 ln 29-30) relates to steps c-e.. “Johnson-Buck teaches a method wherein “In some embodiments, the technology provides for the size selection of analytes, e.g., to provide a defined size range of molecules including the target analytes” (Pg. 87 ln 5-6)” relates to steps c-e.
Applicants’ argument: “Johnson-Buck in fact teaches away from using Dynabead or any solid support” (Pg. 13)
Response: Applicant’s arguments have been fully considered and found unpersuasive because as recited on Pg. 3-6 of the Non-final office action filed on 04/06/2026 “Johnson-Buck teaches a method comprising “In some embodiments, methods comprise immobilizing an analyte to a solid support. In some embodiments, the solid support is a surface (e.g., a substantially planar surface, a rounded surface), e.g., a surface in contact with a bulk solution, e.g., a bulk solution comprising analyte. In some embodiments, the solid support is a freely diffusible solid support (e.g., a bead” (Pg 59 ln 4-8) and “In some embodiments, the freely diffusing substrate comprises and/or is made of, e.g., .. gold”(Pg 41 ln 4-5)”; and “In some embodiments, the ATPS is a solid-phase ATPS.” (Pg. 61 ln 30-35)”. The “solid-phase ATPS” reads on solid surface such as magnetic beads and liquid phase separation. While Table 2 of Johnson-Buck does suggest lower relative sensitivity using 1 um Dynabead, although it does not appear to be in the context of ATPS or any of the other strategies that it is compared to. So along with the other teaching of John-Buck stated in this response, one of skill in the art would be motivated to use ATPS in combination with a solid support such as a bead. Thus, Johnson-Buck does suggest using Dynabead or any solid support.
Applicants’ argument: “As a side note, the Examiner has cited Gironella et al. (AU 2015201072 A1) in the Office Action. Based on the Applicant's review, this appears to be a typographical or citation error, as the referenced document does not appear to be relevant to the subject matter of the present application. Accordingly, the Applicant's analysis and response will focus on addressing Johnson-Buck as the relevant reference. Applicant respectfully requests clarification from the Examiner regarding this citation” (Pg. 14).
Response: Applicant’s arguments have been fully considered and found unpersuasive because Gironella et al. accidently stated in the previous office action the intent was to address Johnson-Buck as recited in the Final office action above, “Johnson-Buck also teaches that “Various modifications and variations of the described compositions, methods, and uses of the technology will be apparent to those skilled in the art without departing from the scope and spirit of the technology as described. Although the technology has been described in connection with specific exemplary embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments.” (Pg. 103 ln 5-10). Therefore, the invention as recited in claim 1 is prima facie obvious over the prior art Johnson-Buck et al. One of ordinary skill in the art would have had a reasonable expectation of success given the obviousness of claim 1 in view of Johnson-Buck. These claim elements were known in the art and one of skill in the art could have combined these elements by known methods with no change in their respective functions. Thus, it would have been obvious to provide a method for isolating target nucleic acids below a target size from a sample comprising nucleic acid components according to the limitations of the instant application claim 1 based on Johnson-Buck et al. (Patent App. No. WO 2019118705 A1).”
Claims 3 and 24 remain rejected under 35 U.S.C. 103 as being unpatentable over Johnson-Buck et al. (“Johnson-Buck”; Patent App. Pub. WO 2019118705 A1, Jun. 20, 2019) in view of Chiu et al. (“Chiu”; Patent App. Pub. WO 2021037075 A1, Mar. 4, 2021).
Claim interpretations: Regarding claim 24, the limitation reciting “selected from the group” is interpreted as at least one of. Thus, rendering the polymer, salt, surfactant, or combinations thereof as possibly optional if not selected. Dependent claims of claim 24 are rendered optional. Claims 25-43 optionally depend on claim 24.
The teachings of Johnson-Buck are documented above in the rejection of claims 1-2, 23 and 48-49 under 35 U.S.C. 103. Claim 3 depends on claim 2, which depends on claim 1. Claim 24 depends on claim 3, which depends on claim 2, which depends on claim 1.
Regarding claim 3, Johnson-Buck teaches a method comprising “the method comprises providing an aqueous two-phase system (ATPS) comprising an analyte; concentrating the analyte into a first phase of the ATPS; and contacting said first phase to a substrate” (Pg. 4 ln 19-21). However, Johnson-Buck does not explicitly teach the limitations of claim 3 and 24.
Chiu discloses “Provided is a method for isolating and concentrating nucleic acids of selected target sizes (e.g., in increments less than 1000 base pairs) from a biological fluid mixture comprising combining the biological fluid mixture and a first aqueous two-phase system (ATPS) formed from a first phase forming polymer or surfactant component dissolved in a first phase solution, and a second phase solution, such that target nucleic acid fragments below a desired target size partition to said second phase solution and contaminants partition to the first phase solution, extracting and mixing the second phase solution with a second ATPS formed from a second phase forming polymer or surfactant component dissolved in a third phase solution and a fourth phase solution, such that the target nucleic acid fragments partition to and concentrate in the third phase solution, and recovering the concentrated target nucleic acid fragments from the third phase solution. A composition and kit for isolating and concentrating nucleic acids of selected target sizes as described above are also provided.” (Abstract).
Regarding claim 3, Chiu teaches a method wherein “In some embodiments of concentrating step 30, the second phase solution 24 containing target nucleic acid fragments 26 may be extracted from vessel 14 and mixed with concentration components 31 in a second vessel 32, with or without centrifugation, in order to form a second ATPS 34.” (Para. 51; Figure 1 see below). Furthermore, Chiu teaches a method further comprising “the target nucleic acid fragments 26 partition into and concentrate in the third phase solution 36 ( e.g., a polymer-rich upper phase)” (Para. 51) and “the concentrated target nucleic acid fragments 26 may be
recovered from the third phase solution 36. Fig. 1 illustrates one optional method (steps 40a
PNG
media_image1.png
784
1419
media_image1.png
Greyscale
through 40c) for recovering the fragments 26” (Para. 61). Thus, Johnson-Buck and Chiu suggest a method wherein the step (a) further comprises the following steps after step (a2):(a3) adding the sample solution in step (a2) to a second ATPS to form a second mixture that partitions into a second target-rich phase and a second target-poor phase, wherein the nucleic acid components are concentrated in the second target-rich phase and (a4) isolating the second target-rich phase containing the concentrated nucleic acid components to form the sample solution in step (a).
Johnson-Buck and Chiu are both considered to be analogous to the claimed invention because they are in the same field separation and concentration of target nucleic acids from biological samples. Therefore, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method for isolating target nucleic acids below a target size from a sample comprising nucleic acid components as taught by Johnson-Buck to incorporate the method wherein the step (a) comprises adding the isolated target rich phase from the first ATPS to a second ATPS and further isolating the second target-rich phase as taught by Chiu and provide a method for isolating target nucleic acids from a sample comprising nucleic acid components. These claim elements were known in the art and one of skill in the art could have combined these elements by known methods with no change in their respective functions, and the combination would have yielded the predictable outcome according to the limitations of claim 3. Doing so would allow for increased target nucleic acid yield from the isolation process of a sample.
Regarding claim 24, Chiu teaches a method wherein “a second ATPS 34… The concentration components 31 may comprise a second phase forming polymer or surfactant component dissolved in a third phase solution 36 (e.g., a top phase) and a fourth phase solution 38 (e.g., a bottom phase), such that the target nucleic acid fragments 26 partition into and concentrate in the third phase solution 36 (e.g., a polymer-rich upper phase), while salt and other contaminants partition to the fourth phase solution 38 (e.g., a salt-rich bottom phase)” (Para. 51; Figure 1 elements 26, 36 and 38). Thus, Johnson-Buck and Chiu suggest a method wherein the second ATPS comprises second ATPS components capable of forming the second target-rich phase and the second target-poor phase when the second ATPS components are dissolved in an aqueous solution, wherein the second ATPS components are selected from the group consisting of a polymer, salt, surfactant, and combinations thereof.
Response to Arguments
Applicant's arguments filed 07/03/2026 (Pg. 15-16) with respect to claims 1-3 and 24 have been fully considered but they are not persuasive as discussed above. Furthermore, to clarify some instances argued in the response filed 07/03/2026 see responses to each argument made by Applicant above in addition to below:
Applicants' argument: “Chiu does not teach or suggest any of the steps involving solid phase media as recited in claim 1 ”(Pg. 15).
Response: In response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986).
Claim 4-17, 19-22, 44-47 and 50-51 are rejected under 35 U.S.C. 103 as being unpatentable over Johnson-Buck et al. (“Johnson-Buck”; Patent App. Pub. WO 2019118705 A1, Jun. 20, 2019) in view of Mather et al. (“Mather”; Patent App. Pub. WO 2009020609 A2, Feb. 12, 2009).
The teachings of Johnson-Buck are documented above in the rejection of claims 1-2, 23 and 48-49 under 35 U.S.C. 103. However, Johnson-Buck does not explicitly teach the limitations of claim 4. Claim 4-6, 10-13, 16, 20-21, 50-51 depends on claim 1. Claims 44-45 depend on claim 4, which depends on claim 1. Claims 7, 9 and 46-47 depend on claim 5, which depends on claim 1. Claims 8 depends on claim 6, which depends on claim 1. Claim 15 depends on claim 14, which depend on claim 13, which depends on claim 1. Claims 17 and 19 depend on claim 16, which depends on claim 1. Claim 22 depends on claim 21, which depends on claim 1.
Mather discloses “Provided are solid supports that contain at least one hydrophilic ligand; and at least one hydrophobic ligand, where amount of the at least one hydrophobic ligand on the solid support relative to the amount of the at least one hydrophilic ligand on the solid support is adjusted for binding target nucleic acid(s) from a sample onto the solid support and/or for eluting the bound target nucleic acid(s) from the solid support, so that the amount of target nucleic acid(s) bound to the solid support and/or recovered after elution from the solid support is about 5% to about 500% greater than the amount of target nucleic acid(s) bound to the solid support and/or recovered from the solid support in the absence of either the at least one hydrophobic ligand or the at least one hydrophilic ligand or both. The solid supports with ligands are used for isolation of nucleic acid molecules from samples.” (Abstract).
Regarding claim 4, Mather teaches a method wherein “A combination for isolating nucleic acids using a solid support can contain a modified solid support as provided herein and further contain one or more reagents including a chaotropic substance, a binding buffer, an elution buffer, or reagents to make the modified solid support and/or the reagents” (Pg. 17 ln 7-11). Mather teaches a method wherein “Prior to the use of the amine-coupled carboxylated paramagnetic beads, or other appropriate solid support, in the isolation of nucleic acids molecules, the beads are typically washed in a buffer” (Pg. 52 ln 8-10). Mather teaches a method wherein “A non-limiting example of a suitable lysis buffer is one that contains 2.5 M guanidinium thiocyanate, 50% isopropyl alcohol, 0.5% lauroylsarcosine, 0.05 M Tris HCl, pH 7.0. Other chaotropic agents can be used, including, but not limited to, guanidinium chloride, and sodium chloride, at varying concentrations” (Pg. 52 ln 24-28). “a buffer” reads on reads on any buffer including that of a sample lysis buffer. Thus, Johnson-Buck and Mather suggest a method wherein the plurality of beads and the sample solution of step (a) are mixed with a binding buffer prior to the step (b), wherein the binding buffer comprises at least one chaotropic agent.
Johnson-Buck and Mather are considered to be analogous to the claimed invention because they are in the same field of method for extracting or separating nucleic acids from biological samples by means of a solid support carrier, e.g. particles, polymers. Therefore, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method for isolating target nucleic acids below a target size from a sample comprising nucleic acid components as taught by Johnson-Buck to incorporate the method wherein the plurality of beads and the sample solution of step (a) are mixed with a binding buffer prior to the step (b), wherein the binding buffer comprises at least one chaotropic agent as taught by Mather and provide a method for isolating target nucleic acids from a sample comprising nucleic acid components. These claim elements were known in the art and one of skill in the art could have combined these elements by known methods with no change in their respective functions, and the combination would have yielded the predictable outcome according to the limitations of claim 4. Doing so would allow for preparation of the beads to increase target nucleic acid yield and facilitate adsorption to the beads (Pg. 40 ln 5-6-Mather).
Regarding claim 5, Johnson-Buck teaches a method comprising “adding an analyte containing composition (e.g., a biofluid or sample) to an aqueous two-phase system (ATPS) (e.g., a mixture of materials that forms an aqueous two-phase system upon mixing). In some embodiments, the ATPS is a solid-phase ATPS” (Pg. 61 ln 30-35). Johnson-Buck teaches a method comprising “the method comprises providing an aqueous two-phase system (ATPS) comprising an analyte; concentrating the analyte into a first phase of the ATPS” (Pg. 4 ln 19-21). Johnson-Buck teaches a method comprising “In some embodiments related to ATPS technologies, the ATPS further comprises… a chaotropic agent” (Pg. 5 ln 29-30). “Johnson-Buck teaches a method wherein “In some embodiments, the technology provides for the size selection of analytes, e.g., to provide a defined size range of molecules including the target analytes” (Pg. 87 ln 5-6)”.
Regarding claim 5, Mather teaches a method comprising “methods for isolating nucleic acid molecules by contacting any of the supports with linked or coupled ligands provided herein with a sample containing a nucleic acid molecule, such as DNA, RNA and mixtures thereof whereby the nucleic acid molecule is captured by the support. Any method for eluting or removing captured nucleic acid molecules can be used” (Pg. 7, ln 7-11) and “mixing the components of the previous step in a solution comprising a chaotropic buffer and alcohol, where the amounts of the chaotropic substance and alcohol are adjusted for binding or capturing the nucleic acid molecules onto the solid support” (Pg. 7, ln 14-17). Mather teaches a method wherein “The sample also can be a semi-pure preparation obtained by other nucleic acid recovery processes” (Pg. 38 ln 3-5). Mather teaches a method wherein “The solid supports can be in any form, such as in the form of beads” (Pg. 4 ln 15). Mather teaches a method wherein “Modifications can be made to a basic isolation protocol that enables the user to separate various nucleic acid species on a solid support. Separation can be based on the type of nucleic acid e.g. DNA versus RNA, or the molecular size of the nucleic acid molecule e.g. 100 nt versus 1000 nt. Separation can be effected by altering the properties of the solid support, the binding conditions, wash conditions, elution conditions, or any combination thereof” (Pg. 45 ln 26-31). Mather further teaches a method wherein “The methods can be for separating target nucleic acid molecules from each other according to type, length or sequence. The amount or concentration of the chaotropic substance and/or the alcohol and/or the elution buffer is adjusted so that the target nucleic acid molecules are eluted sequentially according to type, length or sequence” (Pg. 8 ln 11-15). Hence, one of skill in the art would be motivated to use a second plurality of beads and conditions to further isolate target nucleic acids below a target size from a partially purified nucleic acids. Thus, Johnson-Buck and Mather suggest a method wherein the step (e) further comprises the steps of:(e1) mixing the bulk fractionation solution with a target binding buffer and a plurality of second beads, such that the plurality of second beads bind the target nucleic acids below the target size to form a second beads-analyte complex, wherein the target binding buffer comprises at least one chaotropic agent; and (e2) recovering the target nucleic acids below the target size from the second beads-analyte complex.
Regarding claims 6-7, Mather teaches a method wherein “The solid supports can be magnetic or paramagnetic, such magnetic or paramagnetic beads” (Pg. 4 ln 15-16); “Examples of bead materials include, but are not limited to, silica …”(Pg. 21 4-5); “Carboxylated paramagnetic beads” (Pg. 50 ln 11); “The carboxylated paramagnetic beads are coupled to an amine ligand” (Pg. 50 ln 16); “The underlying principles of many nucleic acid and protein purification techniques are based upon hydrophobic interactions. A protein or nucleic acid with hydrophobic groups on its surface can be purified based on hydrophobic interactions
with an insoluble hydrophobic group immobilized on a solid support… The hydrophobic ligand also can contain one or more functional groups, such as for example, an amine, hydroxyl… carboxylate” (Pg. 26 ln 21-23) Thus, Johnson-Buck and Mather suggest a method wherein the plurality of beads is magnetic beads, silica-based beads, carboxyl beads, hydroxyl beads, amine-coated beads, or any combination thereof; and wherein the plurality of second beads is magnetic beads, silica-based beads, carboxyl beads, hydroxyl beads, amine-coated beads, or any combination thereof.
Regarding claim 8, Mather teaches a method wherein “The paramagnetic beads are attracted to the magnet and concentrated, facilitating removal by, for example, pipetting or vacuum suction, of any solution from the tube and the beads. The magnet is then removed from the vicinity to remove the magnetic force, and the beads fall to the bottom of the tube.” (Pg. 43 ln 4-7). Thus, Johnson-Buck and Mather suggest a method wherein the plurality of beads is magnetic beads, and the step (b) further comprises the steps of:(b1) immobilizing the beads-analyte complex by applying a magnetic field to separate the beads-analyte complex from a blk supernatant;(b2) removing the bulk supernatant; and (b3) removing the magnetic field and proceeding to step (c).
Regarding claim 9, Mather teaches a method wherein “The solid supports can be magnetic or paramagnetic, such magnetic or paramagnetic beads” (Pg. 4 ln 15-16).. Mather teaches a method wherein “For example, provided is a method for isolating nucleic acid molecules, by: contacting a solid support with a sample that contains or is suspected of containing nucleic acid molecules, including target nucleic acid molecules; mixing the components of the previous step in a solution comprising a chaotropic buffer and alcohol, where the amounts of the chaotropic substance and alcohol are adjusted for binding or capturing the nucleic acid molecules onto the solid support; separating the solid support containing the bound target nucleic acid molecules from the solution; washing the solid support containing bound or captured nucleic acid molecules; and combining the resulting washed solid support with a second solution for eluting the bound target nucleic acids, whereby the target nucleic acid molecules are purified from the sample. The methods can be for purifying target nucleic acid molecules from a sample. Any of the solid supports provided herein can be used in such methods” (Pg. 11 ln 11-23). Furthermore, Mather teaches a method wherein “The paramagnetic beads are attracted to the magnet and concentrated, facilitating removal by, for example, pipetting or vacuum suction, of any solution from the tube and the beads. The magnet is then removed from the vicinity to remove the magnetic force, and the beads fall to the bottom of the tube.” (Pg. 43 ln 4-7). Thus, Johnson-Buck and Mather suggest a method wherein the plurality of second beads is magnetic beads, and the target nucleic acids recovery of step (e2) further comprises steps of: (i) immobilizing the second beads-analyte complex by applying a first magnetic field to separate the second beads-analyte complex from a first supernatant; (ii) removing the first supernatant; (iii) washing the immobilized second beads-analyte complex with a washing buffer;(iv) discarding the washing buffer; (v) removing the first magnetic field; (vi) mixing the second beads-analyte complex with an elution buffer to form a bulk elution solution, wherein the target nucleic acids below the target size are separated from the magnetic beads in the second beads-analyte complex and released into the bulk elution solution; (vii) immobilizing the magnetic beads by applying a second magnetic field; (viii) collecting the bulk elution solution comprising the isolated target nucleic acids below the target size.
Regarding claim 10, Mather teaches a method wherein “The isolation of nucleic acids is a necessary step for a multitude of applications in the fields of, for example, molecular biology, biotechnology and medicine, and is required for both diagnostic, therapeutic and research purposes. In most instances, the purity and quality of the isolated nucleic acid, the recovery
efficiency, and the ease with which the nucleic acid is isolated, are all equally important.” (Pg. 38 ln 18-23). Thus, Johnson-Buck and Mather suggest a method further comprising the step of: (f) subjecting the isolated target nucleic acids to a diagnostic assay for detection, quantification, characterization, or combinations thereof, of the target nucleic acids.
Regarding claims 11-12, Mather teaches a method wherein “The amount or concentration of the chaotropic substance and/or the alcohol and/or the elution buffer is adjusted so that the target nucleic acid molecules are eluted sequentially according to type, length or sequence” (Pg. 8 ln 11-15). Mather teaches “As used herein, a "chaotropic substance" refers to any substance capable of altering the secondary, tertiary and/or quaternary structure of nucleic acids or proteins, while leaving at least the primary structure intact. Examples of chaotropic substances include, but are not limited to, guanidinium isothiocyanate, guanidine hydrochloride, sodium iodide, potassium iodide, sodium isothiocyanate, urea, or combinations thereof” (Pg. 17 ln 12-17). Thus, Johnson-Buck and Mather suggest a method wherein the at least one chaotropic agent of the fractionation buffer is selected from the group consisting of thiocyanate, isothiocyanate, perchlorate, acetate, trichloroacetate, trifluoroacetate, chloride, and iodide; and wherein the at least one chaotropic agent of the fractionation buffer is selected from the group consisting of guanidinium hydrochloride (GHCI), guanidinium thiocyanate, guanidinium isothiocyanate (GITC), sodium thiocyanate, sodium iodide, sodium perchlorate, sodium trichloroacetate, sodium trifluroacetate, lithium perchlorate, lithium acetate, magnesium chloride, phenol, 2-propanol,thiourea, and urea.
Regarding claim 13, Mather teaches a method wherein “chaotropic compounds useful for precipitating nucleic acid… High concentrations typically are required for efficient nucleic acid precipitation, such as for example, 1 M, 2 M, 3 M and 4 M guanidinium thiocyanate.” (Pg. 40 ln 6-10). Mather also teaches a method wherein “a suitable chaotropic lysis buffer for adsorbing nucleic acids from complex starting materials… is one that contains 8 M guanidinium isothiocyanate… The guanidinium isothiocyanate can be substituted with another chaotropic substance, such as potassium iodide (3M), sodium iodide (3 M), sodium thiocyanate (3 M), or any of these in combination with 8M urea” (Pg. 41 ln 6-11). Of note, the MPEP states "Where the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation." (MPEP 2144.05). Thus, Johnson-Buck and Mather suggest a method wherein the at least one chaotropic agent has a concentration of around 1.5-8M in the fractionation buffer.
Regarding claims 14-15, Mather teaches a method wherein “chaotropic compounds useful for precipitating nucleic acid… High concentrations typically are required for efficient nucleic acid precipitation, such as for example, IM, 2M, 3M and 4M guanidinium thiocyanate.” (Pg. 40 ln 6-10). Of note, the MPEP states "Where the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation." (MPEP 2144.05). Thus, Johnson-Buck and Mather suggest a method wherein the at least one chaotropic agent is present at a concentration of around 1.8-3.9M in the fractionation buffer; and wherein the at least one chaotropic agent is present at a concentration of around 1.8-3.0M in the fractionation buffer.
Regarding claim 16, Mather teaches a method wherein “Such conditions are achieved by the use of appropriate buffers, which are modified by, for example, altering pH or salt concentrations, and including variously functional agents, to alter the adsorption characteristics. … A sufficient quantity of a nucleic acid precipitation agent is required to adsorb the nucleic acid onto the suspended beads. Precipitation and binding of nucleic acid to solid supports can be effected by an agent such as, for example, a polyalcohol including polyethylene glycol (PEG)” (Pg. 39 ln 4-12). Mather also teaches a method wherein “using carboxyl-coated magnetic microparticles, DNA fragments of different sizes can be separated by adjusting the ionic strength or PEG concentration of the elution buffer. Smaller fragments can be eluted from the column with buffers of higher ionic strength or PEG concentration than larger nucleic acid fragments” (Pg. 49 ln 28-30 – Pg. 50 ln 1-2). Thus, Johnson-Buck and Mather suggest a method wherein the fractionation buffer further comprises at least one polymer selected from the group consisting of polyvinyl alcohol, polyethylene glycol, polypropylene glycol, dextran, poly(ethylene glycol-ran- propylene glycol), pluronics, polyvinylpyrolidone, and polyacrylate.
Regarding claim 17, Mather teaches a method wherein “PEG 8000 concentrations ranging from 11% to 40% can be used in conjunction with variable concentrations of salt {e.g.
0.6 M to 3.3 M NaCl, or 20 mM MgC12) to precipitate different sized DNA molecules onto paramagnetic microparticles (US 6,534,262)” (Pg. 39 ln 21-24). “PEG 8000 concentrations ranging from 11% to 40%... to precipitate different sized DNA molecules onto paramagnetic microparticles” reads on at least one polymer is present at a concentration of around 11-15% (w/w) in the fractionation buffer since depending on the size some DNA will be capable of binding the beads and some DNA molecules will not precipitate thus, some DNA molecules will be capable of release into the fractionation buffer at the various polymer concentrations around 11-15%. Of note, the MPEP states "Where the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation." (MPEP 2144.05). Thus, Johnson-Buck and Mather suggest a method wherein the at least one polymer is present at a concentration of around 0.1-15% (w/w) in the fractionation buffer.
Regarding claim 19, Mather teaches a method wherein “The molecular weight of the PEG can range from about 6,000 to about 10,000, from about 6,000 to about 8,000, from about 7,000 to about 9,000, from about 8,000 to about 10,000” (Pg. 39 ln 12-15). Thus, Johnson-Buck and Mather suggest a method wherein the at least one polymer has an average molecular weight range from 100 to 35,000 Da.
Regarding claim 20, Mather teaches a method wherein “Aqueous elution buffers suitable for the dissociation of nucleic acid molecules from solid supports are known. These, include, but are not limited to, TE buffer (typically 10 mM Tris, 1 mM EDTA pH 7.5 to 8.0” (Pg 45 ln 3-6). “EDTA” reads on metal chelator. Thus, Johnson-Buck and Mather suggest a method wherein the fractionation buffer further comprises one or more of a pH buffer, metal chelator, or combination thereof.
Regarding claims 21-22, Mather teaches a method wherein “nucleic acid molecule, such as DNA, RNA and mixtures thereof” (Pg. 7 ln 9). Mather also teaches a method wherein “Naturally-occurring RNA molecules include, but are not limited to, transfer RNA (tRNA; generally smaller molecules of approximately 75 nucleotides), ribosomal RNA (rRNA; ranging from approximately 100 to 3000 nucleotides)…, but are not limited to, small interfering RNA (siRNA; typically 100 nucleotides or fewer) and microRNA (miRNA).” (Pg. 35 ln 29-31- Pg. 36 ln 1-4). Furthermore, Mather teaches a method wherein “Solid phase isolation of nucleic acids can be applied to nucleic acids of essentially any length. Short fragments, such as for example, oligonucleotides of between 5 and 50 nucleotides in length, are routinely isolated using solid supports. Equally so are larger nucleic acid molecules, such as those that make up plasmids and generally range from 1 to over 400 kilobases (kb)” (Pg. 35 ln 13-18). Thus, Johnson-Buck and Mather suggest a method wherein the nucleic acid components and/or the target nucleic acids are DNA, RNA or combinations thereof; and wherein the nucleic acid components and/or the target nucleic acids are cDNA, plasmid DNA, cell-free DNA (cfDNA), circulating tumor DNA (ctDNA), circulating fetal DNA, micro RNA (miRNA), messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), or combinations thereof.
Regarding claims 44-47, Mather teaches a method wherein “Chaotropic agents, which are those that alter the secondary, tertiary, and/or quaternary structure of proteins and nucleic acids, but leave the primary structure intact, also can be used in buffers to precipitate the nucleic acid and facilitate adsorption to the beads. Non-limiting examples of chaotropic compounds useful for precipitating nucleic acid are guanidinium chloride, guanidinium thiocyanate, guanidinium isothiocyanate, sodium thiocyanate, sodium iodide, potassium iodide and urea” (Pg. 40 ln 3-9).Thus, Johnson-Buck and Mather suggest a method wherein the at least one chaotropic agent of the binding buffer comprises an anion selected from the group consisting of thiocyanate, isothiocyanate, perchlorate, acetate, trichloroacetate, trifluoroacetate, chloride, and iodide; wherein the at least one chaotropic agent of the binding buffer is selected from the group consisting of guanidinium hydrochloride (GHCl), guanidinium thiocyanate, guanidinium isothiocyanate (GITC), sodium thiocyanate, sodium iodide, sodium perchlorate, sodium trichloroacetate, sodium trifluroacetate, lithium perchlorate, lithium acetate, magnesium chloride, phenol, 2-propanol, thiourea, and urea; wherein the at least one chaotropic agent of the target binding buffer comprises an anion selected from the group consisting of thiocyanate, isothiocyanate, perchlorate, acetate, trichloroacetate, trifluoroacetate, chloride, and iodide; and wherein the at least one chaotropic agent of the target binding buffer is selected from the group consisting of guanidinium hydrochloride (GHCl), guanidinium thiocyanate, guanidinium isothiocyanate (GITC), sodium thiocyanate, sodium iodide, sodium perchlorate, sodium trichloroacetate, sodium trifluroacetate, lithium perchlorate, lithium acetate, magnesium chloride, phenol, 2-propanol, thiourea, and urea.
Regarding claims 50, Johnson-Buck teaches a method wherein “Analytes can be obtained … from a biological sample obtained from an organism” and “Exemplary samples include… plasma” (Pg. 86 ln 17-18 and 20). Johnson-Buck teaches a method wherein “The present technology contemplates any deoxyribonucleotide, ribonucleotide, or peptide nucleic acid component, and any chemical variants thereof, such as methylated, hydroxymethylated, or glycosylated forms of these bases, and the like” (Pg. 32 ln 17-20). Johnson-Buck teaches a method wherein “During the development of embodiments of the technology described herein, experiments using ATPS indicated that embodiments of the technology provided greater than an 80-fold increase in the surface density of captured tumor DNA sequences… The increase in the surface density of captured analyte resulted in greater than an 80-fold increase in the sensitivity of subsequent detection” (Pg. 2 ln 32-34 and Pg. 3 ln 1-2). Furthermore, Mather teaches a method wherein “loss of heterozygosity in tumors… allelic loss analysis” (Pg. 61 ln 25-26). Thus, Johnson-Buck and Mather suggest a method wherein the target nucleic acids are cell-free DNA and circulating tumor DNA, whereby the method increases a ratio of circulating tumor DNA: cell- free DNA, and/or variant allele frequency (VAF) in the sample for cancer diagnostic assay.
Regarding claims 51, Johnson-Buck teaches a method wherein “Analytes can be obtained … from a biological sample obtained from an organism” and “Exemplary samples include… plasma” (Pg. 86 ln 17-18 and 20). Johnson-Buck teaches a method wherein “The present technology contemplates any deoxyribonucleotide, ribonucleotide, or peptide nucleic acid component, and any chemical variants thereof, such as methylated, hydroxymethylated, or glycosylated forms of these bases, and the like” (Pg. 32 ln 17-20). Furthermore, Mather teaches a method wherein “parentage testing” (Pg. 61 ln 24). Thus, Johnson-Buck and Mather suggest a method wherein the target nucleic acids are circulating fetal DNA, whereby the method enriches fetal fraction in the sample for non-invasive prenatal testing.
Response to Arguments
Applicant's arguments filed 07/03/2026 (Pg. 15-16) with respect to claims 1 and 4 have been fully considered but they are not persuasive as discussed above. Applicant's arguments filed 07/03/2026 (Pg. 15-16) with respect to claims 5-17, 19, 22, 44-47 and 50-51 have been fully considered but do not apply to the new grounds of rejection. Furthermore, to clarify some instances argued in the response filed 07/03/2026 see responses to each argument made by Applicant above in addition to arguments below:
Applicants' argument: “There is no teaching or suggestion in Mather to use a fractionation buffer that enables size selective release of target nucleic acids below a target size from a beads-analyte complex. Mather's elution step releases majority bound nucleic acids in the elution (page 54, lines 25-28), not selectively released nucleic acids below a target size” (Pg. 15).
Response: In response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). Additionally, the MPEP states that "Where the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation." (MPEP 2144.05).
Claim 18 is rejected under 35 U.S.C. 103 as being unpatentable over Johnson-Buck et al. (“Johnson-Buck”; Patent App. Pub. WO 2019118705 A1, Jun. 20, 2019) in view of Mather et al. (“Mather”; Patent App. Pub. WO 2009020609 A2, Feb. 12, 2009) as applied to claim 16 and further in view of Chiu et al. (“Chiu”; Patent App. Pub. WO 2021037075 A1, Mar. 4, 2021).
The teachings of Johnson-Buck as applied to claim 1 and Johnson-Buck and Mather are documented above in the rejection of claims 1, 4-17, 19-22, 44-47 and 50-51 under 35 U.S.C. 103. Claim 18 depends on claim 16, which depends on claim 1. However, Johnson-Buck and Mather does not explicitly teach the limitations of claim 18.
Chiu discloses “Provided is a method for isolating and concentrating nucleic acids of selected target sizes (e.g., in increments less than 1000 base pairs) from a biological fluid mixture comprising combining the biological fluid mixture and a first aqueous two-phase system (ATPS) formed from a first phase forming polymer or surfactant component dissolved in a first phase solution, and a second phase solution, such that target nucleic acid fragments below a desired target size partition to said second phase solution and contaminants partition to the first phase solution, extracting and mixing the second phase solution with a second ATPS formed from a second phase forming polymer or surfactant component dissolved in a third phase solution and a fourth phase solution, such that the target nucleic acid fragments partition to and concentrate in the third phase solution, and recovering the concentrated target nucleic acid fragments from the third phase solution. A composition and kit for isolating and concentrating nucleic acids of selected target sizes as described above are also provided.” (Abstract).
Regarding claim 18, Chiu teaches a method wherein “selected from polymer … solution that is about 1 % w/w, about 2% w/w, about 3% w/w, about 4% w/w, about 5% w/w” (Para. 12; Fig. 2, lane 3) Of note, the MPEP states "Where the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation." (MPEP 2144.05). Thus, Johnson-Buck, Mather and Chiu suggest a method wherein the at least one polymer is present at a concentration of around 1.0-5.0% (w/w) in the fractionation buffer.
Johnson-Buck, Mather and Chiu are considered to be analogous to the claimed invention because they are in the same field of method for extracting or separating nucleic acids from biological samples by means of a solid support carrier, e.g. particles, polymers. Therefore, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method for isolating target nucleic acids below a target size from a sample comprising nucleic acid components wherein the fractionation buffer further comprises at least one polymer as taught by Johnson-Buck and Mather to incorporate the polymer present at a concentration of 1.0-5.0% (w/w) in the fractionation buffer as suggested by Chiu and provide a method for isolating target nucleic acids from a sample comprising nucleic acid components. These claim elements were known in the art and one of skill in the art could have combined these elements by known methods with no change in their respective functions, and the combination would have yielded the predictable outcome according to the limitations of claim 18. Doing so would allow for further separation of target nucleic acid below a target size cut off from other nucleic acid fragments above the target size cut off. (Fig. 2 lane 3-Chiu).
Response to Arguments
Applicant's arguments filed 07/03/2026 (Pg. 15-16) with respect to claim 18 have been fully considered but they do not apply to the new grounds of rejection. Furthermore, to clarify some instances argued in the response filed 07/03/2026 see responses to each argument made by Applicant above in addition to arguments below:
Applicants' argument: “Even if one of ordinary skill in the art were to combine the teachings of Johnson-Buck, Chiu and Mather, the combination would not include a reverse fractionation method comprising a bead analyte complex that selectively releases nucleic acids below a target size” (Pg. 15).
Response: In response to applicant's argument that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (i.e., reverse fractionation method) are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993). Furthermore, in response to applicant's argument stated above, the test for obviousness is not whether the features of a secondary reference may be bodily incorporated into the structure of the primary reference; nor is it that the claimed invention must be expressly suggested in any one or all of the references. Rather, the test is what the combined teachings of the references would have suggested to those of ordinary skill in the art. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981).
Additionally, the MPEP states that, "Where the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation." (MPEP 2144.05).
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.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claim 1 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 4 and 7 of copending U.S. Patent App. No. 19/262133). Although the claims at issue are not identical, they are not patentably distinct from each other because the instantly claimed invention is made obvious over claims 1, 4 and 7 of copending U.S. Patent App. No. 19/262133.
Claims 1, 4 and 7 of copending U.S. Patent App. No. 19/262133 is drawn to:
“1. A method for concentrating and purifying at least one target analyte from a clinical biological sample, comprising the steps of (a) combining the clinical biological sample with a first aqueous two-phase system (ATPS) composition comprising a polymer, a salt component comprising at least one salt, a surfactant, or any combination thereof dissolved in an aqueous solution to form a target-rich phase solution and a target-poor phase solution, such that the target analyte is concentrated in the target-rich phase solution;(b) collecting the target-rich phase solution;(c) optionally adding the target-rich phase solution to a second ATPS composition comprising a polymer, a salt component comprising at least one salt, a surfactant, or any combination thereof dissolved in an aqueous solution to form a second target-rich phase solution and a second target-poor phase solution, such that the target analyte is concentrated in the second target-rich phase solution, and collecting the second target-rich phase solution;(d) optionally mixing the target-rich phase solution from step (b) or the second target- rich phase solution from step (c) with a binding buffer to form a mixed solution;(e) contacting the target-rich phase solution from step (b), the second target-rich phase solution from step (c) or the mixed solution from step (d) with a solid phase medium configured to selectively bind the target analyte such that the solid phase medium binds to the target analyte; and(f) eluting and collecting the target analyte from the solid phase medium with an eluting solution, resulting in a final solution containing the concentrated and purified target analyte; wherein the clinical biological sample is urine; and wherein the target analyte is cell-free DNA (cfDNA) or circulating fetal DNA.
4. The method of claim 1, wherein the binding buffer comprises a chaotropic agent comprising an anion selected from the group consisting of thiocyanate, isothiocyanate, perchlorate, acetate, trichloroacetate, trifluoroacetate, chloride, and iodide.+
7. The method of claim 6, wherein the solid phase medium is a plurality of beads, wherein the beads are selected from the group consisting of magnetic beads, silica- based beads, carboxyl beads, hydroxyl beads, and amine-coated beads; the solid phase extraction complex is a beads-analyte complex; perturbing is spinning; and the flowthrough is the supernatant.
Therefore, the invention as recited in claims 1 is prima facie obvious over the claims 1, 4 and 7 of copending U.S. Patent App. No. 19/262133. One of ordinary skill in the art would have had a reasonable expectation of success given the obviousness of claim 1 over copending U.S. Patent App. No. 19/262133. It would have been obvious to provide a method for isolating target nucleic acids below a target size from a sample according to the limitations of the instant application based on claims 1, 4 and 7 of copending U.S. Patent App. No. 19/262133.
This is a provisional nonstatutory double patenting rejection.
Response to Arguments
Applicant's arguments filed 07/03/2026 (Pg. 15-16) with respect to claim 1 have been fully considered and are partially persuasive. To clarify some instances argued in the response filed 07/03/2026 see responses to each argument made by Applicant arguments below:
Applicants' argument: “A terminal disclaimer in compliance with 37 CFR 1.32l(c) or 37 CFR 1.32l(d) is filed with this response. Applicant respectfully submits that the rejections on claim 1 are moot” (Pg. 16).
Response: In response to applicant's argument stated above, a signed terminal disclaimer was filed 07/03/2026 by the Applicant. The NSDP rejections of claim 1 over claims 1, 15 and 18 of U.S. Patent No. US 12129511 B2, claims 1, 4 and 8 of U.S. Patent No. US 12442034 B2, and claims 1, 6 and 9 of U.S. Patent No. US 12258616 B2 have been withdrawn, accordingly. However, the provisional rejection of co-pending U.S. Patent App. No. 19/262133 remains rejected, as a notice of abandonment has not been filed in the co-pending cases, thus the provisional rejection of claim 1 under NSDP is maintained.
Conclusion of Response to Arguments
In view of the amendments, revised rejections, new grounds of rejections and above responses to arguments, no claims are in condition for allowance.
Conclusion
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KENDRA R VANN-OJUEKAIYE whose telephone number is (571)270-7529. The examiner can normally be reached M-F 9:00 AM- 5:00 PM.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Winston Shen can be reached at (571) 272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/KENDRA R VANN-OJUEKAIYE/Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
Prosecution Insights