DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Priority
The present application, filed August 3, 2023, is a continuation of 16/627578, filed December 30, 2019, now issued as U.S. patent 11,732,254, which is a national stage application of PCT/US2018/040324, filed June 29, 2018, and claims the benefit of U.S. provisional application 62/527659, filed June 30, 2017.
Status of the Application
Applicant’s preliminary amendment, received April 11, 2024, wherein claims 1-16 are canceled and new claims 17-50 are added, is acknowledged.
Claims 17-50 are pending and examined on the merits herein.
Specification
The use of the term Ficoll, which is a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term. The term Ficoll appears on p. 23 in [0068], on p. 27 in [0087], and on p. 29 in [0094].
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Interpretation
Claim 41 depends from claim 33 and requires the aqueous solution comprises an elution buffer. The specification states: “Any elution solution can be used which effects desorption of the bound nucleic acid from the nanomembrane. Classical elution solutions known to effectively elute nucleic acid from a silica surface include but are not limited to water, elution buffers such as TE-buffer, low EDT A TE buffers, and low-salt solutions which have a salt content of 150 mM or less to about 10 mM or are salt-free.” (p. 28, [0089]).
However, claim 33 does not require the nucleic acids as adsorbed to a nanomembrane. Therefore, claim 41 is interpreted as satisfied by a method that comprises resuspending the nucleic acid pellet in buffer that could serve as an elution buffer, even if that buffer is not used for eluting the nucleic acid from a nanomembrane. This interpretation is consistent with exemplary embodiments in the specification, wherein a nucleic acid pellet, after being washed with alcohol, is resuspended in elution buffer (for example, see p. 30, first paragraph, lines 4-6).
Claim Objections
Claims 28 and 43 recite the phrase: “from 1000 base pairs to 10 kilobases.” To improve the clarity of the claims, please amend claims 28 and 43 to express ranges with consistent units, such as base pairs or bases/kilobases. The examiner notes that claim 49 recites a range of 1000 bp to 10000 bp, which is an example of a range with consistent units.
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 50 is 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 50 recites the trademark/trade name Ficoll. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe a highly branched, primarily neutral polysaccharide, and, accordingly, the identification/description is indefinite.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 17-19, 23-29, 31-35, 39, 41-44, and 46-49 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Schmitz (Schmitz, A.; Riesner, D. Analytical Biochemistry 2006, vol. 354, pp. 311-313; cited in PTO-892).
Schmitz teaches purification of nucleic acids by selective precipitation with polyethylene glycol 6000 (p. 311, Title).
Schmitz teaches that for applications in molecular biology, the nucleic acids of interest are needed in a highly purified form, and that nucleoside triphosphates, oligonucleotides, or degradation products frequently have to be removed as they may interfere with downstream procedures. Schmitz teaches that commercially available chromatographic tips are commonly employed for this purpose (p. 311, left column, lines 1-7).
Schmitz teaches that in most cases, comparable results can be achieved by selective precipitation of the product with polyethylene glycol 6000 (PEG6000), and that this process offers the opportunity to fractionate product mixtures, as low percentages of PEG6000 precipitate only nucleic acids of high molecular weight (p. 311, left column, lines 7-13) (emphasis added).
Schmitz teaches examples in which plasmid DNA and PCR products, among others, are purified by precipitation with PEG. For plasmid DNA, Schmitz teaches the method is preceded by an alkaline lysis method, and after removing cellular precipitate, plasmid DNA is directly precipitated from 900 μL supernatant by the addition of 166 μL of 50% PEG6000 and 118 μL of 5M NaCl and extensive mixing by inversion of the tube (p. 311, left column, third paragraph, line 1 to right column, line 12). Schmitz then teaches centrifugation at 16000g and room temperature for 10 min to sediment the DNA, immediate removal of the supernatant, addition of 500 μL of 70% ethanol to the pellet, and additional centrifugation as before. After complete removal of the ethanol, Schmitz teaches the DNA pellet is solubilized in a small volume of buffer A (p. 311, right column, lines 12-17). Buffer A is 5 mM Tris/HCl, pH 8.0, which is interpreted herein as an aqueous solution (p. 311, left column, second paragraph, line 3). In addition, buffer A is interpreted having the properties of an elution buffer, absent a showing that buffer A of Schmitz cannot function as an elution buffer.
For purification of PCR products, Schmitz teaches that to a 50 μL PCR-reaction, 1.4 μL of 500 mM EDTA, 12 μL of 50% PEG6000, and 7 μL of 5M NaCl is added if the expected product is larger than 900 bp, 1.6 μL of 500 mM EDTA, 21 μL of 50% PEG6000, and
8.1 μL of 5M NaCl for product lengths of 400–900 bp, or 1.9 μL of 500mM EDTA, 34 μL of 50% PEG6000, and 9.6 μL of 5M NaCl for product lengths of 120–400 bp. Schmitz teaches that mixing is performed by extensively and repeatedly flicking the tube, followed by incubation at room temperature for 10min. The DNA is sedimented by centrifugation, washed and solubilized as described above using 125 μL of 70% ethanol (p. 311, right column, second paragraph). In each of these examples, Schmitz does not expressly teach the supernatant as nucleic acids remaining in solution, because Schmitz teaches low percentages of PEG6000 precipitate only nucleic acids of high molecular weight, the remaining nucleic acids must remain in solution, absent evidence to the contrary.
Schmitz teaches the efficiency of isolating supercoiled plasmid DNA of length 4701 bp with 7% PEG6000, which satisfies the selected sizes of the nucleic acids and size cutoff requirement of claim 28, 43, and 49 (p. 312, Figure 1, see caption).
Therefore, the methods of purifying plasmid DNA and PCR products of Schmitz satisfy all limitations of present claims 17-19, 23-28, 33-35, 39, 41-43, and 48-49.
Regarding the method as performed separate from a nanomembrane purification method as recited in claims 29 and 44, Schmitz does not teach a nanomembrane purification method, and thus the method of Schmitz, wherein purification of nucleic acids is performed separate from a nanomembrane purification method, satisfies the limitations of claims 29 and 44.
Regarding the method lacking a separate pulsed field gel electrophoresis (PFGE) purification step as recited in claims 31 and 46, Schmitz does not teach a PFGE purification step, and thus the method of Schmitz, wherein the purification of nucleic acid is performed separate from a PFGE purification step, satisfies the limitations of claims 31 and 46.
Regarding the requirement of further comprising processing one or more of the nucleic acids prior to or after size selecting the nucleic acids by way of one or more enzymatic reactions recited in claims 32 and 47, because Schmitz teaches isolation of PCR products, which were processed by an enzymatic reaction (i.e., PCR, which requires a polymerase enzyme) prior to the process of size-selecting as taught by Schmitz, Schmitz satisfies the requirements of claims 32 and 47.
Regarding the lack of separate magnetic bead purification step, because Schmitz does not teach a separate magnetic bead purification step, this limitation in claims 17, 33, and 48 is satisfied by Schmitz.
Thus Schmitz anticipates claims 17-19, 23-29, 31-35, 39, 41-44, and 46-49.
Claims 17-19, 23-25, 27-31, 33-35, 40, 42-46, and 48-49 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Lis (Lis, J. T.; Scleif, R. Nucleic Acids Research 1975, vol. 2, pp. 383-390; cited in PTO-892), as evidenced by the PubChem database entry for polyethylene glycol 6000 (cited in PTO-892).
Lis teaches a method in which DNA molecules of differing molecular mass are separable
by selective precipitation with polyethylene glycol (PEG). Lis teaches higher molecular mass DNA precipitates at lower PEG concentrations than lower molecular mass DNA (p. 383, Abstract, lines 1-4).
Lis teaches PEG precipitation experiments were performed in either Solution A or Solution B. Lis teaches solution A consisted of 0.55 M NaCl, 0.01 M Tris HC1, pH 7.5, 2mM EDTA and contained a mixture of lightly and heavily sonicated λparaB107 DNA at 50 or 100 μg/ml and whole length λparaB107 at 1.2 or 2.4 μg/ml respectively. Lis teaches solution A was used for studies on the effect of PEG concentration, stepwise precipitation, and pH (p. 384, Materials section, second paragraph, lines 1-6).
Lis teaches in their method, solid PEG was added to a 2 mL DNA solution, the mixture was chilled at 0°, and the precipitated DNA was collected by a 10 min centrifugation at 8,000
x g. Lis teaches the precipitate was resuspended in 0.2 ml of 0.01 M Tris borate pH 8.3, 0.1
mM EDTA, 5% glycerol, and 0.02-0.1% bromophenol blue, and analyzed by gel electrophoresis (p. 384, The Standard Assay section, lines 1-4). This method, when practiced with solution A above, anticipates claims 17 and 25.
Lis teaches in experiments designed to test the effect of PEG concentration, as stated above, solution A was used (p. 384, Materials section, second paragraph, lines 1-6). Relating to the experiments presented in Figure 2, Lis teaches PEG was added to 5% and, after centrifugation, the supernatant was poured off and additional PEG added to the supernatant to give a final concentration of 6%. After a second centrifugation the supernatant was again poured off and to it was added PEG to 6.5%, and the procedure repeated at each of the PEG concentrations indicated in Figure 2 (p. 385 last paragraph, line 1 to p. 386, line 3; data shown on p. 386, Figure 2). Lis teaches that the sizes of DNA precipitated (as shown in Figure 2) at each increase in PEG concentration, and using this method, DNA of λ length is separable from 1,125 base pair DNA, 1,125 from 700, and 700 from 240 base pair DNA (p. 387, lines 1-3). This method of Lis demonstrates that a lower cutoff between 1000 and 10,000 bp, as recited in claim 28, may be achieved.
Lis teaches the PEG used in their experiments is sold under the trade name Carbowax 6000. As evidenced by the PubChem entry for polyethylene glycol 6000 (p. 2, Synonyms section), Carbowax 6000 is a synonym of PEG 6000, thus Carbowax 6000 is interpreted as equivalent to PEG 6000 recited in claim 27.
Lis teaches that upon addition of PEG to a DNA solution containing a range of DNA sizes, from 46,500-100 base pairs, we find the sizes of DNA molecules collected by low speed centrifugation is strikingly dependent on the amount of PEG added (p. 385, Effect of PEG concentration section, lines 1-3). These data show that the size of nucleic acid isolated can be determined by the concentration of PEG used during precipitation (p. 386, Figures 1 and 2).
The method above, wherein the amount of PEG may be used to affect the size of DNA isolated, is interpreted as satisfying the PEG concentration of claim 18, wherein the precipitated nucleic acids comprise all sizes above a cutoff value as recited in claim 19, and wherein the precipitated nucleic acids comprise nucleic acids of a desired size range as recited in claim 23. In addition, the method of Lis satisfies the limitations of claims 24 and 25.
Regarding claim 29, Lis does not teach a nanomembrane purification method, and thus the method of Lis in which the steps a)-c) are performed separate from a nanomembrane purification method satisfies claim 29.
Lis further teaches that the sizes of the DNA molecules precipitated with 7.5% and 11% PEG were relatively independent of DNA concentration in the range of 10-1000 μg/mL, but that below 50 μg/mL the efficiency of precipitation begins to decrease from 100% (p. 387, Effect of DNA concentration section, lines 1-4). A concentration of 50 ng/μL is the same concentration as 50 μg/mL. Therefore, because Lis teaches practicing their method with concentrations greater than 50 μg/mL, Lis satisfies the limitations of claim 30.
In addition, the method of Lis described above, specifically in experiments relating to Figure 2 that disclose removing the supernatant, satisfies the method of claim 33, wherein a) a precipitation solution comprising water, salt, and PEG is added to a sample of DNA, b) the sample undergoes centrifugation to produce a nucleic acid pellet comprising nucleic acid sizes the precipitate by PEG and wherein the supernatant comprises nucleic acids in solution, c) the supernatant is removed, and d) the nucleic acid pellet is resuspended in an aqueous solution. In addition, this method of Lis satisfies dependent claims 34, 35, 40, 42, 43, 44, 45, and 46.
Finally, the method of Lis above satisfies the limitations of claims 48-49, wherein a) a precipitation solution comprising water, salt, and polyethylene glycol (PEG) is added to a nucleic acid-containing sample to produce a sample-solution, wherein the PEG has a molecular weight from 1,000 to 20,000 and wherein a concentration of the PEG in the precipitation solution is from 0.1 % to 40%; b) nucleic acids of one or more selected sizes in the nucleic acid-containing sample are allowed to precipitate driven by the PEG to produce precipitated nucleic acids; and, c) the precipitated nucleic acids are separated from the nucleic acid remaining in solution.
Regarding the lack of separate magnetic bead purification step, because Lis does not teach a separate magnetic bead purification step, this limitation in claims 17, 33, and 48 are satisfied by Lis.
Thus Lis anticipates claims 17-19, 23-25, 27-31, 33-35, 40, 42-46, and 48-49.
Claims 17-19, 23-24, 27, 29, 31, and 48 are rejected under 35 U.S.C. 102(a)(1) and 35 U.S.C. 102(a)(2) as being anticipated by O’Neil (Publication No. WO 2016193490 A1; cited in IDS received 08/03/2023).
O’Neil teaches an example in which a precipitation buffer of 22% Peg 8000, 2 M NaCl, 20 mM MgCl2, 200 mM Tris pH 8.88 was added to a sample of sheared human DNA, so end concentrations of 9%, 8%, and 7% PEG 8000 were achieved. O’Neil teaches the sheared DNA was precipitated onto MinElute spin columns which were in advance pre-incubated with a buffer
containing 2 M NaCl, 20 mM MgCl2, 200 mM Tris, pH 8.89. The precipitated DNA that was
bound to the contained silica membrane was washed twice with 80% ethanol and eluted in
elution buffer. Elution in elution buffer is interpreted as equivalent to resuspending the nucleic acids, as required by claim 24.O’Neil teaches that as shown in Figure 3, a polyethylene glycol concentration dependent relocation of the cut-off value is achieved, and that recovery of DNA fragments was high (p. 37, Example 3, lines 10-23). This method satisfies the limitations of claims 17-19, 23-24, 27, and 48.
Regarding claim 29, because O’Neil does not teach the method of Example 3 as performed with a nanomembrane purification method, claim 29 is satisfied by O’Neil.
Regarding claim 31, because O’Neil does not teach the method of Example 3 as performed with a pulsed field gel electrophoresis purification step, claim 31 is satisfied by O’Neil.
Regarding the lack of separate magnetic bead purification step, because this example of O’Neil does not teach a separate magnetic bead purification step, this limitation in claim 17 is satisfied by O’Neil.
Thus O’Neil anticipates claims 17-19, 23-24, 27, 29, 31, and 48.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35
U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 17, 30, 33, 45, and 49 are rejected under 35 U.S.C. 103 as being unpatentable over Schmitz (Schmitz, A.; Riesner, D. Analytical Biochemistry 2006, vol. 354, pp. 311-313; cited in PTO-892) in view of Lis (Lis, J. T.; Scleif, R. Nucleic Acids Research 1975, vol. 2, pp. 383-390; cited in PTO-892).
Independent claims 17 and 33 are anticipated by Schmitz, as described in the above rejection under 35 U.S.C. § 102. Claims 17 and 33 are included in this rejection because claims 30 and 45 depend from claims 17 and 33.
In addition, the examiner believes that claim 49 is anticipated by Schmitz, as described in the above rejection under 35 U.S.C. § 102. However, for the sake of argument, if Schmitz does not anticipate claim 49 because Schmitz does not expressly teach the precipitated nucleic acids comprise a size cutoff value of from 1000 bp to 10000 bp, then claim 49 would have been obvious over Schmitz in view of Lis.
Schmitz teaches as described in the above rejection under 35 U.S.C. § 102.
Schmitz does not teach size selecting the nucleic acids at a nucleic acid concentration greater than 50 ng/μL in the sample-solution, as required by claims 30 and 45. In addition, Schmitz does not expressly teach the precipitated nucleic acids comprise a size cutoff value of from 1000 bp to 10000 bp, as recited in claim 49.
Lis teaches as described in the above rejection under 35 U.S.C. § 102.
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the present application to practice the method of Schmitz on a sample with nucleic acid concentration greater than 50 ng/μL in the sample-solution. One of ordinary skill in the art would have been motivated to practice the method of Schmitz on a sample with nucleic acid concentration greater than 50 ng/μL in the sample-solution because Schmitz teaches a method of nucleic acid fractionation by precipitation with PEG, and because Lis teaches a similar method of DNA fractionation by precipitation with PEG, and expressly teaches that their method may be practiced on samples with a nucleic acid concentration greater than 50 ng/μL. Accordingly, one of ordinary skill in the art would have reasonably contemplated practicing the method of Schmitz on a sample with a nucleic acid concentration greater than 50 ng/μL.
Moreover, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to apply the method of Schmitz for size selecting nucleic acids comprising a size cutoff value of from 1000 bp to 10000 bp, because Schmitz teaches low percentages of PEG6000 precipitate only nucleic acids of high molecular weight and provides embodiments for selecting different sized PCR products with different PEG concentrations, and because Lis teaches the effect of PEG concentration for size selecting nucleic acids, including between 1000 bp and 10000 bp. Accordingly, one of ordinary skill in the art would have reasonably modified the method of Schmitz by adjusting the PEG concentration to select nucleic acids between 1000 bp and 10000 bp.
Therefore the invention taken as a whole is prima facie obvious.
Claims 17-19, 23-27, 29, 31-35, 39-42, 44, and 46-48 are rejected under 35 U.S.C. 103 as being unpatentable over O’Neil (Publication No. WO 2016193490 A1; cited in IDS received 08/03/2023).
Claims 17-19, 23-24, 27, 29, 31, and 48 are rejected under 35 U.S.C. § 102 as anticipated by O’Neil, as described above.
Claim 17 is included in this rejection because claims 25-26 and 32 depend from claim 17 are rejected here. In addition, claims 17-19, 23-27, 29, 31-35, 39-42, 44, and 46-48 would have been obvious over O’Neil with the rationale described below, wherein Example 2 of O’Neil is modified to include a centrifugation step in place of a magnetic bead purification step.
O’Neil teaches as described in the above rejection under 35 U.S.C. § 102, specifically the method of Example 3 (p. 37, lines 10-23).
In addition, O’Neil teaches a poly(alkylene oxide) polymer-based size-selective DNA isolation method for isolating DNA molecules having a size above a certain cut-off value from a DNA-containing sample (cover page, Abstract, lines 1-4). O’Neil teaches that as part of Example 2, the size cut-off value correlates with the polyethylene glycol concentration, wherein higher concentrations of polyethylene glycol led to the recovery of smaller DNA fragments (p. 36, lines 36-39).
In Example 2, O’Neil teaches a binding/precipitation buffer stock solution comprising 22% PEG 8000, 2 M NaCl, 20 mM MgCl2, and 200 mM Tris pH 8.88 was added to the DNA containing sample in an amount so that the end concentrations of PEG 8000 were 14%, 12%, 10% and 8% (p. 36, lines 22-28). O’Neil teaches that sheared human DNA was precipitated onto MagAttract suspension G magnetic silica particles which were preincubated with a buffer containing 2 M NaCl, 20 mM MgC12, 200 mM Tris, pH 8.89 in order to rebuffer the silica particles. O’Neil teaches the beads with the bound DNA were washed twice with 80% ethanol and eluted with elution buffer (p. 36, lines 30-34). Elution with an elution buffer is interpreted as equivalent to resuspending the nucleic acids, as recited in claims 24 and 33. Based on this experiment, O’Neil teaches that when reducing the concentration of polyethylene glycol in the binding mixture, the cut-off value increased in a concentration dependent matter (p. 36, lines 36-39).
The precipitation buffer of Example 2 includes Tris, which is a buffer as required by claim 40. The elution buffer and PEG 8000 of Example 2 satisfy the limitations of claims 27 and 41-42. The nucleic acids that were precipitated comprise all sizes above a cutoff value, as recited in claims 19 and 35, and comprise nucleic acids of a desired size, as recited in claim 23.
O’Neil further teaches that when using a particulate solid phase such as, e.g., silica particles, to bind the precipitated DNA, the particles can be collected by sedimentation which can be assisted by centrifugation or magnetic separation if magnetic particles are used and the supernatant is separated off (e.g. decanted or aspirated or the particles are taken out of the liquid) (p. 21, lines 26-29) (emphasis added). This product of sedimentation by centrifugation taught by O’Neil is interpreted as a pellet comprising the bound precipitated nucleic acid.
O’Neil teaches that binding is in particular achieved by adsorption, and preferably, the solid phase provides a siliceous surface such as a silica surface (p. 18, lines 40-41). O’Neil teaches that silica particles having an unmodified silica surface are used that may have the form of beads (p. 19, lines 22-23).
O’Neil teaches that the bound DNA may be washed (p. 21, line 38), and recites that suitable alcohols for washing include methanol, ethanol, propanol, isopropanol and butanol, and that preferably, isopropanol and/or ethanol are used in the washing solution (p. 22, lines 6-8). In one embodiment, after performing a wash step, O’Neil teaches that the wash buffer is removed from silica particles that include bound DNA (p. 38, lines 10-11).
O’Neil teaches the DNA may be eluted, and recites water and TE buffer as exemplary elution solutions (p. 22, lines 35-38).
O’Neil does not teach their method as including a nanomembrane purification method, and thus the method above taught by O’Neil is considered as separate from a nanomembrane purification method, as required by claims 29 and 44.
O’Neil does not teach their method as including a PFGE purification step, and thus the method above taught by O’Neil is considered as separate from a nanomembrane purification method, as required by claims 31 and 46.
Finally, O’Neil teaches their size selective separation method is particularly suitable for applications such as library preparation for next generation sequencing, where unwanted, small DNA fragments have to be removed while library DNA has to be retained as efficiently as possible (p. 36, line 45 to p. 37, line 3). O’Neil further teaches an example showing cleanup and size selection for preparation of a next-generation sequencing library (p. 40, Example 5, lines 7-10). This is taken as teaching that the products isolated from the methods of O’Neil are intended to be sequenced and to produce sequencing reads, which comprise processing by way of one or more enzymatic reactions as recited in claims 32 and 47.
O’Neil does not teach an embodiment in which a sample of precipitated nucleic acids undergo centrifugation to produce a nucleic acid pellet in the tube, wherein the nucleic acid pellet comprises nucleic acids of one or more selected sizes that precipitate driven by the PEG and wherein a supernatant comprises nucleic acids remaining in solution, as required by claim 33.
It would have been prima facie obvious to modify the method of Example 2 disclosed by O’Neil with a step of sedimentation by centrifugation, in place of magnetic separation. One of ordinary skill in the art would have been motivated to modify the method of Example 2 disclosed by O’Neil with a step of sedimentation by centrifugation, in place of magnetic separation, because O’Neil teaches the embodiment of Example 2, which includes magnetic separation, and further teaches that sedimentation the particles assisted by centrifugation as an alternative to magnetic separation. Accordingly, one of ordinary skill in the art would have reasonably considered practicing the method of sedimentation of silica particles assisted by centrifugation, which would satisfy all limitations of claims 17-19, 23-27, 29, 31-35, 39-42, 44, and 46-48.
Regarding the step of adding alcohol to the nucleic acid pellet, centrifuging the nucleic acid pellet, and removing alcohol supernatant from the nucleic acid pellet as recited in claims 26 and 39, because O’Neil teaches embodiments in which bound DNA is washed and the alcohol supernatant is removed, one of ordinary skill in the art would have considered such a wash step, including sedimentation of the solid support by centrifugation and removal of the alcohol supernatant after centrifugation, when practicing the method of Example 2 with the modification that includes sedimentation of silica particles, as described above.
Therefore the invention taken as a whole is prima facie obvious.
Claims 20-22 and 36-38 are rejected under 35 U.S.C. 103 as being unpatentable over O’Neil (U.S. pre-grant publication no. US 20180291365 A1; cited in IDS received 08/03/2023) as applied to claims 17-19, 23-27, 29, 31-35, 39-42, 44, and 46-48 above, and further in view of Wang (U.S. pre-grant publication no. US 20150037802 A1; cited in IDS received 08/03/2023).
O’Neil teaches as described in the above rejections under 35 U.S.C. § 102 and 35 U.S.C. § 103.
O’Neil does not teach the method of claim 17, comprising performing steps a)-c) prior to, after, or concurrently with performing a nanomembrane purification method, as required by claims 20-22, or the method of claim 33, comprising performing steps a)-d) prior to, after, or concurrently with performing a nanomembrane purification method, as required by claims 36-38.
Wang teaches silica nanomembranes that can be used for solid phase extraction of nucleic acids (cover page, Abstract, lines 5-6). Wang teaches that a fundamental problem in nucleic acid analysis is sample preparation, and that a sample to be investigated usually comprises cells or tissue with partially insoluble constituents which can interfere with the subsequent isolation and analysis (p. 1, [0003], lines 1-5). Wang teaches one benefit of their silica nanomembranes is their extremely high nucleic acid capacity due to its significantly
enlarged specific surface area of silica (cover page, Abstract, lines 10-12).
Wang further teaches a method for extracting nucleic acids from a sample comprising: a) obtaining a sample comprising nucleic acids; b) contacting the sample with a sufficient amount of silica nanomembranes; c) allowing the nucleic acids in the sample to adsorb onto the silica nanomembranes; d) washing the silica nanomembranes to remove any non-nucleic acid components; and e) desorbing the nucleic acids from the silica nanomembranes to obtain the
isolated and purified nucleic acids from the sample (pp. 1-2, [0012], lines 1-10).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the present application to modify the method obvious over O’Neil and replace the solid support with a nanomembrane taught by Wang. One of ordinary skill in the art would have been motivated to modify the method obvious over O’Neil and replace the solid support with a nanomembrane taught by Wang because each of the solid support of O’Neil and nanomembrane of Wang bind to nucleic acids, and because Wang teaches their silica nanomembranes have extremely high nucleic acid capacity due to its significantly enlarged specific surface area. Thus use of the nanomembranes of Wang may improve the yield of nucleic acids isolated using the method obvious over O’Neil. Such a replacement would satisfy the limitations of claims 22 and 38, wherein steps a)-c) or a)-d) are performed concurrently with
a nanomembrane purification method.
Regarding performing steps a)-c) or a)-d) before or after performing a nanomembrane purification method, as required by claims 20-21 and 36-37, because Wang teaches that a fundamental problem in nucleic acid analysis is sample preparation, and that a sample to be investigated usually comprises cells or tissue with partially insoluble constituents which can interfere with the subsequent isolation and analysis, one of ordinary skill in the art would have contemplated performing steps a)-c) or a)-d) either before or after performing the nanomembrane purification taught by Wang, because the method of Wang may remove partially insoluble constituents that may interfere with downstream processes, such as the DNA sequencing taught by Wang. Regarding performing the method of Wang before or after the size-selection method of O’Neil, one of ordinary skill in the art would have considered either option, because performing the method of Wang prior to size selection may remove contaminants that arise from nucleic acid isolation, such as remaining cells or tissue, and performing the method of Wang after size selection may also remove any remaining cells or tissue, in addition to reagents from size selection that may interfere with subsequent analysis.
Therefore the invention taken as a whole is prima facie obvious.
Claim 50 is rejected under 35 U.S.C. 103 as being unpatentable over O’Neil (U.S. pre-grant publication no. US 20180291365 A1; cited in IDS received 08/03/2023) in view of Latham (U.S. pre-grant publication no. US 20050208510 A1; cited in IDS received 08/03/2023).
Present claim 50 recites a method of size selecting nucleic acids comprising steps a)-d) recited in the claim.
O’Neil teaches as described in the above rejections under 35 U.S.C. § 102 and 35 U.S.C. § 103.
O’Neil does not teach adding a precipitation solution comprising water, salt, and polyvinylpyrrolidone (PVP) and/or Ficoll to a nucleic acid-containing sample to produce a sample-solution, as required by claim 50.
Latham teaches methods of precipitating nucleic acids using the reagents polyethylene glycol (PEG), polyvinyl pyrrolidinone (PVP), and Ficoll. In one embodiment, Latham teaches that 1 M salt and PEG enhanced the purification of liver RNA compared to the monomer of polyethylene glycol at final concentrations of 26.6, 13.3, and 6.6% polyethylene glycol using dextran beads (p. 24, [0155], lines 5-10). Latham teaches that after binding to the dextran beads, the beads were placed on a magnetic stand, allowed to collect at the bottom of the well, the supernatant was removed, the beads were washed with 80% ethanol, and the sample was eluted with water (p. 25, left column, lines 1-7).
Latham teaches similar studies using Ficoll of molecular weights 40,000 and 70,000 at concentrations of 26,6, 13.3, and 6.6% (p. 25, left column, [0156], lines 1-5), as well as with PVP of molecular weights 10K, 40K, and 360K at various concentrations between ~5% and ~31% (p. 25, [0158], lines 3-5 and Table 27). For Ficoll, RNA yield was increased compared to the dextran monomer, showing the benefit of Ficoll-mediated RNA co-precipitation (p. 25, [0157], Table 26). PVP was similarly effective in co-precipitating RNA for RNA isolation (p. 25, [0158], Table 27).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the present application to modify the method of O’Neil and substitute Ficoll or PVP in place of PEG. One of ordinary skill in the art would have been motivated to modify the method of O’Neil and substitute Ficoll or PVP in place of PEG because O’Neil teaches a method for isolating DNA above a certain cut-off value by precipitating DNA molecules to a solid phase by modifying the concentration of PEG used for the precipitation, and Latham teaches the use of PEG, PVP, and Ficoll for precipitating nucleic acids to a solid-phase. Therefore, in view of Latham teaching each of PEG, PVP, and Ficoll as precipitants that may be used to precipitate nucleic acids to a solid-phase, and O’Neil teaching that modification of the PEG concentration may impart a size-selection to the precipitation of nucleic acids, one of ordinary skill in the art would have recognized that adjusting the concentration of PVP or Ficoll may enable a similar size-selective precipitation process as observed by O’Neil when using PEG. Moreover, in view of the success of each of the methods of O’Neil and Latham using PEG with silica or dextran beads, and the success of Latham using Ficoll and PVP with dextran beads, one of ordinary skill in the art would have recognized that Ficoll and PVP may be reasonably used to precipitate nucleic acids to other solid surfaces, such as silica beads, which are known to bind precipitated nucleic acids, as shown by O’Neil.
In this instance, the rationale “simple substitution of one known element for another to obtain predictable results” would apply. Because O’Neil teaches a size-selective precipitation method for nucleic acids using PEG, and because Latham teaches precipitation methods for nucleic acids using PEG, PVP, and Ficoll, substitution of PVP or Ficoll for PEG in the method of O’Neil would reasonably be expected to enable size-selective precipitation of nucleic acids.
One of ordinary skill in the art would have had a reasonable expectation of success modifying the method of O’Neil and substituting Ficoll or PVP in place of PEG because Latham teaches each of PEG, PVP, and Ficoll as useful for precipitating nucleic acids, and O’Neil teaches that the size of the nucleic acids precipitated may be adjusted by adjusting the concentration of PEG used during precipitation. Therefore, because Latham teaches each of PEG, PVP, and Ficoll as having similar roles as precipitating agents in their method of isolating nucleic acids, one of ordinary skill in the art would have reasonably expected PVP and Ficoll to exhibit similar size-selective properties as PEG.
Regarding the use of magnetic beads disclosed by O’Neil and Latham, because O’Neil teaches that when using a particulate solid phase such as silica particles to bind the precipitated DNA, the particles can be collected by sedimentation which can be assisted by centrifugation, one of ordinary skill in the art would have considered practicing the method obvious over O’Neil in view of Latham using silica beads that may be sedimented by centrifugation before supernatant is removed. Such a method, when using PVP and/or Ficoll in place of PEG, would satisfy all limitations of present claim 50.
Therefore the invention taken as a whole is prima facie obvious.
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 50 is rejected on the ground of nonstatutory double patenting as being unpatentable over claim 16 of U.S. Patent No. 11,732,254 (reference patent, herein referred to as ‘254) in view of Schmitz (Schmitz, A.; Riesner, D. Analytical Biochemistry 2006, vol. 354, pp. 311-313; cited in PTO-892).
The present application and ‘254 each include Kelvin Jeng-Fang Liu, John Duncan Kilburn, Jeffrey Michael Burke as inventors.
Claim 16 of ‘254 claims a method of size selecting nucleic acids, the method comprising: a) adding a precipitation solution comprising water, salt, and polyvinylpyrrolidone (PVP) and/or Ficoll to a nucleic acid-containing sample in a tube to produce a sample-solution; b) centrifuging the sample-solution to produce a nucleic acid pellet in the tube, wherein the nucleic acid pellet comprises nucleic acids of one or more selected sizes that precipitate driven by the PVP and/or the Ficoll and wherein a supernatant comprises nucleic acids remaining in solution; c) removing the supernatant from the tube; and, d) re-suspending the nucleic acid pellet in an aqueous solution, wherein the method lacks a separate magnetic bead purification step.
Claim 16 of ‘254 satisfies all limitations of present claim 50, except the requirement that the centrifugation occurs at about room temperature.
Schmitz teaches as described in the above rejections under 35 U.S.C. § 102 and 35 U.S.C. § 103. Specifically, Schmitz teaches precipitation of plasmid DNA using PEG, and sedimentation of DNA by centrifugation at 16000g and room temperature for 10 minutes (p. 311, right column, lines 9-13).
It would therefore have been prima facie obvious to one of ordinary skill in the art to separate precipitated DNA by centrifugation at room temperature, in view of ‘254 claiming a method that satisfies all steps of claim 50 except the temperature of centrifugation, and Schmitz teaching separation of precipitated DNA may be achieved by centrifugation at room temperature.
Claims 17-49 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-10, 12-24, and 26-29 of U.S. Patent No. 11,732,254 (reference patent, herein referred to as ‘254) in view of Schmitz (Schmitz, A.; Riesner, D. Analytical Biochemistry 2006, vol. 354, pp. 311-313; cited in PTO-892) and Lis (Lis, J. T.; Scleif, R. Nucleic Acids Research 1975, vol. 2, pp. 383-390; cited in PTO-892).
The present application and ‘254 each include Kelvin Jeng-Fang Liu, John Duncan Kilburn, Jeffrey Michael Burke as inventors.
Claim 1 of ‘254 claims a method of size selecting nucleic acids, the method comprising:
a. adding a precipitation solution comprising water, salt, and polyvinylpyrrolidone (PVP) and/or Ficoll to a nucleic acid-containing sample to produce a sample-solution; b. allowing nucleic acids of one or more selected sizes in the nucleic acid-containing sample to precipitate driven by the PVP and/or the Ficoll to produce precipitated nucleic acids; and, c. size selecting nucleic acids by separating the precipitated nucleic acids from the nucleic acid remaining in solution,
wherein the method lacks a separate magnetic bead purification step.
Claim 2 of ‘254 requires tuning at least one condition of the precipitation solution to determine a selected size cutoff value, wherein the condition is selected from a group that includes, for example, the presence of absence of chaotropic salts, claim 3 requires the precipitated nucleic acids comprise all sizes above a cutoff values, claims 4-6 require performing steps a)-c) prior to, after, or concurrently with performing a nanomembrane purification method, claim 7 requires the precipitated nucleic acids comprise nucleic acids of a desired size range, claim 8 requires re-suspending the pelleting precipitated nucleic acids, claim 9 claims pelleting the nucleic acids in the nucleic acid-containing sample based on the size to produce a nucleic acid pellet, claim 10 claims adding alcohol to the nucleic acid pellet, centrifuging the nucleic acid pellet, and removing alcohol supernatant from the nucleic acid pellet, and claim 12 claims the concentration of the PVP in the sample-solution is such that the one or more selected sizes of the nucleic acids is from 1000 base pairs to 10 kilobases, claim 13 claims steps a)-c) are performed separate from a nanomembrane purification method, claim 14 claims size selecting the nucleic acids at a nucleic acid concentration greater than 50 ng/μL in the sample-solution, and claim 15 claims the method further lacks a separate pulsed field gel electrophoresis (PFGE) purification step.
Claim 16 of ‘254 claims a method of size selecting nucleic acids, the method comprising: a) adding a precipitation solution comprising water, salt, and polyvinylpyrrolidone (PVP) and/or Ficoll to a nucleic acid-containing sample in a tube to produce a sample-solution; b) centrifuging the sample-solution to produce a nucleic acid pellet in the tube, wherein the nucleic acid pellet comprises nucleic acids of one or more selected sizes that precipitate driven by the PVP and/or the Ficoll and wherein a supernatant comprises nucleic acids remaining in solution; c) removing the supernatant from the tube; and, d) re-suspending the nucleic acid pellet in an aqueous solution, wherein the method lacks a separate magnetic bead purification step. Claims 17-24 and 26-29 depend from claim 16 and further limit the method of claim 16 analogous to claims 2-10 and 12-15 further limiting claim 1.
The claims of ‘254 do not claim adding a precipitation solution comprising water, salt, and polyethylene glycol (PEG) to a nucleic acid-containing sample to produce a sample-solution, as required by present claims 17, 33, and 48, or the specific PEG species of claims 27 and 42.
Schmitz and Lis teach as described in the above rejections under 35 U.S.C. § 102 and 35 U.S.C. § 103.
It would therefore have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the present application to substitute the PVP and/or Ficoll in the method claimed by ‘254 with PEG, in view of ‘254 claiming the method of size-selecting nucleic acids recited in claims 1-10 and 12-16, and Schmitz and Lis each teaching a method of size-selecting nucleic acids using PEG as a precipitating agent anticipate or render obvious the above claims. Accordingly, one of ordinary skill in the art would have contemplated practicing the method of ‘254 with PEG in place of PVP and/or Ficoll.
Regarding the present method performed prior to, concurrently with, or after a nanomembrane purification method as recited in claimed 20-22 and 36-38, because the claims of ‘254 claim these limitations, one of ordinary skill in the art would have considered practicing the method obvious over the claims of ‘254 in view of Schmitz and Lis with the required nanomembrane purification methods.
Claim 50 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 3, 13, 15, and 16 of U.S. patent application 17/784474 (reference application, herein referred to as ‘474).
The present application and ‘474 each include Kelvin Jeng-Fang Liu and John Duncan Kilburn as inventors.
The amended claims of ‘474 received September 29, 2025 are cited in this provisional nonstatutory double patenting rejection.
Claim 3 of ‘474 claims a method of purifying a sample containing nucleic acids to
obtain isolated nucleic acids above a tunable cutoff size between 1500 and 3000 bp of a desired
size range, the method comprising: a. combining a nucleic acid-containing sample with a precipitation buffer in a container to provide a precipitation mixture, wherein the precipitation buffer comprises water, a buffer, a salt, and Ficoll and wherein the precipitation mixture comprises a Ficoll concentration of 20%; b. precipitating the nucleic acids in the precipitation mixture to provide a precipitated nucleic acid portion and a remaining sample portion, wherein the precipitated nucleic acid portion predominantly comprises nucleic acid molecules above the tunable cutoff size between 1500 and 3000 bp a selected size cutoff value and wherein the remaining sample portion predominantly comprises nucleic acid molecules below the tunable cutoff size between 1500 and 3000 bp selected size cutoff value; and, c. separating the precipitated nucleic acid portion from the remaining sample portion, thereby obtaining the isolated nucleic acids above the tunable cutoff size between 1500 and 3000 bp.
Claim 13 depends from claim 3 and claims step b) comprises centrifuging the precipitation mixture at 10,000 g for 30 minutes at room temperature (RT).
Claim 15 depends from claim 3 and claims the remaining sample portion comprises supernatant and wherein step c) comprises removing the supernatant from the container.
Claim 16 depends from claim 3 and claims washing the nucleic acid pellet precipitated nucleic acid portion one or more times with an alcohol solution to produce a washed nucleic acid pellet; and, e. resuspending the washed nucleic acid pellet in a resuspension buffer to produce
resuspended nucleic acids.
It would therefore have been prima facie obvious to one of ordinary skill in the art to practice the method claimed by claims 3, 13, 15, and 16 of ‘474 because each of claims 13, 15, and 16 further limit the method of claim 3 with requirements regarding the centrifugation speed and centrifugation temperature, removal of supernatant from the container, and resuspension of the nucleic acid pellet, and accordingly, one ordinary skill in the art would have considered practicing the method of claim 3 of ‘474 with each of the additional requirements recited in claims 13, 15, and 16 of ‘474.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not been patented.
Claims 17-49 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 3, 10-13, 15-16, 18-20, and 22 of U.S. patent application 17/784474 (reference application, herein referred to as ‘474) in view of Schmitz (Schmitz, A.; Riesner, D. Analytical Biochemistry 2006, vol. 354, pp. 311-313; cited in PTO-892) and Lis (Lis, J. T.; Scleif, R. Nucleic Acids Research 1975, vol. 2, pp. 383-390; cited in PTO-892).
Claim 3 of ‘474 claims a method of purifying a sample containing nucleic acids to
obtain isolated nucleic acids above a tunable cutoff size between 1500 and 3000 bp of a desired
size range, the method comprising: a. combining a nucleic acid-containing sample with a precipitation buffer in a container to provide a precipitation mixture, wherein the precipitation buffer comprises water, a buffer, a salt, and Ficoll and wherein the precipitation mixture comprises a Ficoll concentration of 20%; b. precipitating the nucleic acids in the precipitation mixture to provide a precipitated nucleic acid portion and a remaining sample portion, wherein the precipitated nucleic acid portion predominantly comprises nucleic acid molecules above the tunable cutoff size between 1500 and 3000 bp a selected size cutoff value and wherein the remaining sample portion predominantly comprises nucleic acid molecules below the tunable cutoff size between 1500 and 3000 bp selected size cutoff value; and, c. separating the precipitated nucleic acid portion from the remaining sample portion, thereby obtaining the isolated nucleic acids above the tunable cutoff size between 1500 and 3000 bp.
Claim 10 of ‘474 claims the nucleic acid molecules in the nucleic acid-containing sample comprise a concentration range of between about 1-2,000 ng/μL, claim 11 claims tuning at least one condition of the precipitation buffer to determine the tunable cutoff size, claim 12 claims step b) comprises centrifuging the precipitation mixture, claim 13 claims centrifuging the precipitation mixture at 10000g for 30 minutes at room temperature (RT), claim 15 claims the remaining sample portion comprises supernatant and wherein step c) comprises removing the supernatant from the container, claim 16 claims the method further comprises: d. washing the nucleic acid pellet precipitated nucleic acid portion one or more times with an alcohol solution to produce a washed nucleic acid pellet; and, e. resuspending the washed nucleic acid pellet in a resuspension buffer to produce resuspended nucleic acids, and claims 18-20 claim contacting the resuspended nucleic acids with a nanomembrane prior to, after, or concurrently with steps a), b), c), d), or e).
Claim 22 of ‘474 claims further comprising sequencing the isolated nucleic acids of the desired size range after step c) to produce sequencing reads, which is interpreted herein as an enzymatic process as recited in present claims 32 and 47.
The claims of ‘474 do not claim adding a precipitation solution comprising water, salt, and polyethylene glycol (PEG) to a nucleic acid-containing sample to produce a sample-solution, as required by present claims 17, 33, and 48, or the specific PEG species of claims 27 and 42.
Schmitz and Lis teach as described in the above rejection under 35 U.S.C. § 102 and 35 U.S.C. § 103.
It would therefore have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the present application to substitute Ficoll in the method claimed by ‘474 with PEG, in view of ‘474 claiming the method of size-selecting nucleic acids recited in claims 3, 10-13, 15-16, 18-20, and 22, and Schmitz and Lis teaching methods of size-selecting nucleic acids using PEG as a precipitating agent. Accordingly, one of ordinary skill in the art would have contemplated practicing the method of ‘454 with PEG in place of PVP and/or Ficoll.
Regarding the present method performed prior to, concurrently with, or after a nanomembrane purification method as recited in claims 20-22 and 36-38, because the claims of ‘474 claim these limitations, one of ordinary skill in the art would have considered practicing the method obvious over the claims of ‘474 in view of Schmitz and Lis with the required nanomembrane purification methods.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not been patented.
Conclusion
No claims are allowed.
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/B.M.B./ Examiner, Art Unit 1693
/ANDREA OLSON/ Primary Examiner, Art Unit 1693