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 .
Status of the Claims
It is acknowledged that Applicant amended claims 1, 5, 6, 16, and 21 and added new claims 26 and 27 in the reply filed May 18, 2026.
Claims 1-11, 16-19, 21, and 25-27 are pending and herein discussed on their merits.
Priority
It is acknowledged that the instant application is a 371 of international PCT Application No. PCT/GB/2022/051352, filed May 27, 2022, and that it claims benefit of provisional 63/193,649, filed May 27, 2021, and also claims foreign priority to GB2108936.2, filed June 22, 2021. The effective filing date is considered to be May 27, 2021.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-3, 5-11, 16-18, 21, and 25-27 remain/are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The claims are drawn to methods of causing enzymatic digestion of nucleic acids using (reversibly inactivated) nucleases. Claim 1 recites the steps of:
combining reagents, in the presence of a temporarily substantially inactive nuclease, to form in vitro synthesized nucleic acid;
detecting, directly or indirectly, the in vitro synthesized nucleic acid; and
subsequent to the detection, permitting or causing the substantially inactive nuclease to regain substantial nuclease activity, such that the in vitro synthesized nucleic acid is digested by the nuclease.
The claimed nuclease is required to possess certain characteristics in order to perform the method as recited. It must be capable of being rendered substantially inactive and then be able to revert to an active state. It must not interfere substantially with the activity of a polymerase, as it is present in a synthesis reaction, and it must be able to digest the synthesized nucleic acid.
In the instant case, the claims do not set forth the nucleases in terms of sufficient relevant identifying characteristics. The claims encompass the use of nucleases which have only been identified in terms of their function. Only claims 4 and 19 describe specific endonucleases (HL-SAN, HL-dsDNase, Cyanase, Benzonase, Cryonase, and OmniCleave).
The size of the genus is very large, encompassing enzymes with wide variety in structure, function, and mechanism, including enzymes which cause single or double-stranded cleavage, which act on DNA or RNA or both, which have different temperature restrictions, and which result in different oligonucleotide products (Yang W. Nucleases: diversity of structure, function and mechanism. Quarterly Reviews of Biophysics. 2011;44(1):1-93.). Claims which restrict the types of nuclease still encompass a large genus – there are many types of nucleases which act on DNA and which require magnesium or manganese ions for activity, for example.
The specification allows for any type of nuclease (par. 21), but examples are provided only for a subset. While the majority of examples in the instant application feature HL-SAN only, Example 2 (par. 53-68; results in Fig. 2) describes characterization of HL-SAN, HL-dsDNase, Cyanase, Benzonase, Cryonase, and OmniCleave relative to their ability to be reversibly inactivated. All nucleases were inactivated using the same protocol (par. 54): 1mM TCEP and incubation at 60ºC for 30min. After this incubation, the enzymes were equilibrated to room temperature for 40min, and the inactivated enzyme was stored at 40ºC for an hour prior to testing (par. 46). Magnesium was then added or not to the inactivated nuclease mixture at 25ºC and activity was assessed after 10min, 24hr, and 48hr (par. 47-48; Figure 2).
The specification provides written description for the following nucleases that are reversibly inactive and can be used in the claimed methods: HL-SAN, HL-dsDNase, Cyanase, Benzonase, Cryonase, and OmniCleave (par. 21). The specification does not describe any other species within the claimed genus to show possession of those species.
Regarding the genus of nucleases, the specification does not describe any structural features of the disclosed reversibly in-activatable nucleases which would have been expected to be shared by members of the claimed genus. The specification does not describe physical and/or chemical characteristics of the disclosed nucleases that would be shared by members of the claimed genus. All members of the genus have the same function, i.e., they are inactive, do not interfere with nucleic acid synthesis, and can be induced to become active and digest nucleic acids, but no correlation between their structure and the common function is disclosed in the context of any given conditions causing any given nucleases being “temporarily substantially inactive” encompassed by instant claim 1. More elaboration in this regard is provided in the rejection under 112(b) documented below in this Office Action. The level of knowledge and skill in the art does not allow those skilled in the art to structurally envisage or recognize additional members of the claimed genus. Because the structure of the species within the claimed genus is expected to vary unpredictably from the structure of the reversibly in-activatable nucleases disclosed in the specification, the disclosed nucleases are not a “representative number” of species within the claimed genus.
Because the nucleases are not representative of the entire claimed genus, and the specification does not disclose structural features shared by members of the genus, the description of the nucleases would not have put the applicant in possession of common structural attributes or features shared by members of the genus that structurally distinguish the members of the genus from non-members of the genus at the time of filing. Thus, the description of nucleases is not sufficient to describe the claimed genus of reversibly in-activatable nucleases. Accordingly, the specification does not provide a representative number of species or sufficient common structural features to show that the applicant would have been in possession at the claimed genus as a whole at the time of filing.
Regarding the genus of nucleases, the level of knowledge and skill in the art does not allow those skilled in the art to structurally envisage or recognize reversibly in-activatable nucleases, because it is known that enzymes which catalyze DNA and/or RNA cleavage tend to differ unpredictably in terms of their biochemistry (including required cofactors, reaction conditions, substrate and product, and catalytic mechanism). Therefore, those skilled in the art would have recognized that the specification’s disclosure of nucleases: HL-SAN, HL-dsDNase, Cyanase, Benzonase, Cryonase, and OmniCleave would not have put the applicant in possession of any type of nuclease at the time of filing. Thus, the specification does not describe sufficiently detailed, relevant characteristics to show that the applicant was in possession of the claimed genus of any type of nuclease capable of being rendered substantially inactive and able to revert to an active state, which does not interfere substantially with the activity of a polymerase, and is capable of digesting a synthesized nucleic acid.
Claims 2, 3, 5-11, 16-18, 21, and 25-27 depend from claim 1.
Response to Arguments
In the reply filed May 18, 2026, Applicant pointed out that the nucleases recited in claims 4 and 19 were supported by the specification (HL-SAN, HL-dsDNase, Cyanase, Benzonase, Cryonase, and OmniCleave).
This point has been considered and found persuasive. In the rejections under 35 U.S.C. 112(a) set forth above, claims 4 and 19 have been removed.
In the reply, Applicant argued that written description existed for all of the pending claims because a representative number of species falling within the scope of the genus were described, because a person with ordinary skill in the art would possess the ability to identify members of the genus based on their common structural features. Applicant argued that these structural features were sequence and structure shared between members of the genus, such as catalytic domain sequences and/or full-length sequences which can serve as the basis of a search using bioinformatic tools such as BLAST. Applicant argued that a person with ordinary skill in the art would reasonably expect that enzymes having substantially similar sequence to that of any of the provided examples would possess the required functionality, satisfying the requirement for a structure-function correlation based on the provided examples.
These arguments have been considered, and are not found persuasive. MPEP 2163(II)(A)(3)(a)(ii) states that “The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice (see i)(A) above), reduction to drawings (see i)(B) above), or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the inventor was in possession of the claimed genus.”
In this case, the Applicant has provided description sufficient to describe HL-SAN, HL-dsDNase, Cyanase, Benzonase, Cryonase, and OmniCleave. Each of these enzymes is an sequence non-specific endonuclease. Yang (Yang. Q Rev Biophys. 2011 Feb;44(1):1-93) teaches that there is a lack of correlation in structure, mechanism, and biological function for enzymes generally. Yang also teaches that even the specific subgenus of sequence-specific restriction endonucleases encompasses at least five structural families and employs at a minimum four different catalytic mechanisms (pg. 5, Section 3.1). Therefore, it is not considered that the Applicant has provided sufficient description of a representative number of species of the claimed genus of nucleases because the Applicant has not provided disclosure of either: i) structure or other physical and/or chemical properties of the claimed nucleases or ii) disclosure of functional characteristics coupled with a known or disclosed correlation between function and structure.
Even if the instant specification were considered to have fulfilled the written description requirement for sequence non-specific endonucleases, there are no representative examples of the substantial variety of other types of nucleases encompassed by the claims, including: exonucleases, Cas-type nucleases, nicking nucleases, flap endonucleases, etc. A person with ordinary skill in the art would not be able to predict the operability in the invention of any species other than the ones disclosed. Therefore, the rejection is maintained.
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 1-11, 16-19, 21, and 25-27 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.
Claims 1-11, 16-19, 21, and 25-27 are rejected as indefinite over the recitation of the term “temporarily” in claims 1, 7, 9, and 16. Although the specification provides examples of “temporarily” inactivating the nuclease in paragraph 19, it not clear whether the definition of the term is limited to those examples. For example, it is not clear whether inactivating a nuclease which subsequently regains activity before an hour or after 48 hours would be considered temporarily inactivated. Therefore, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter so as to avoid infringement.
Claims 1-11, 16-19, 21, and 25-27 are rejected as indefinite over the recitation of the term “substantially”/”substantial” in claims 1, 7, 10, 16, and 25. Although the specification provides examples of “substantially inactive” nucleases in paragraph 11 and “substantially inactive” nucleases in paragraph 12, the claims are considered indefinite because it is not clear whether “substantially”/”substantial” is limited to those examples. The amended limitations of claim 1 do not provide sufficient clarity, as they are themselves indefinite. Therefore, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter so as to avoid infringement.
Claims 1-11, 16-19, 21, and 25-27 are rejected as indefinite over the recitation of “wherein the substantially inactive nuclease is a nuclease having up to 10% specific activity compared to its maximum specific activity and wherein substantial nuclease activity comprises a specific activity that is at least 80% of the nuclease’s maximum specific activity” in claim 1. Here, it is not clear how specific activity is being defined or measured. The specific activity of an enzyme is defined as enzyme units or the total rate of substrate conversion per unit time per unit of protein mass (such as U/mg). However, the activity or lack of activity of the nuclease of the instant specification are defined by an assay which measures relative end-point fluorescence of the substrate at particular timepoints (Fig. 1). Given that the specification does not provide a clear, limiting definition of the term ‘specific activity,’ and the usage of the term in the specification does not match the term as used in the art, it is unclear how the activity of the enzyme is meant to be measured. It is also unclear what the ‘maximum’ specific activity of the enzyme would be, and under what conditions it would be assessed. Furthermore, the claim recites that “substantial nuclease activity comprises a specific activity that is at least 80% of the nuclease’s maximum specific activity.” The term ‘comprises’ is open-ended, meaning that substantial nuclease activity is not limited to ‘at least 80%’ of the nuclease’s maximum specific activity. Therefore, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter so as to avoid infringement.
Claim 25 is rejected as indefinite over the recitation of the term “sufficient.” The term is considered indefinite because an amount of magnesium or manganese sufficient to cause the nuclease to regain activity is not clearly defined in the specification. Examples of concentrations of Mg2+ and Mn2+ which lead to inactivity are provided (par. 29), but it is not clear whether “sufficient” amounts for regaining activity are limited to concentrations above those examples. Therefore, one of skill in the art would not be able to determine the metes and bounds of the claimed subject matter so as to avoid infringement.
Response to Arguments
In the reply, Applicant traversed the rejections under 35 U.S.C. 112(b) and amended the claims. Those arguments and amendments applicable to the rejections over the terms “"non-thermal cycling DNA amplification reaction," "the temporarily substantially reversibly inactivated nuclease,” and "the solid support,“ have been fully considered and found persuasive. The applicable rejections have been withdrawn. The other rejections under 35 U.S.C. 112(b) are discussed in more detail below.
Regarding the rejection over the recitation of "substantially"/"substantial" in claims 1, 7, 10, 16, and 25 and the recitation of "substantial nuclease activity" in claims 1, 10, and 25, Applicant argued that amendments to the claims provided objective definitions and clear metes and bounds for the terms “substantially inactive nuclease” and “substantial nuclease activity” in claim 1. Regarding the rejection over the recitation of the terms: "temporarily" in claims 1, 7, 9, and 16, Applicant argued that the terminology is not indefinite, but broad – and given clear metes and bounds in view of the fact that the nuclease must regain activity by the end of step (c) in claim 1. These arguments have been fully and carefully considered, but are not found to be fully persuasive.
MPEP 2173.02(II) states that: “Definiteness of claim language must be analyzed, not in a vacuum, but in light of: (A) The content of the particular application disclosure; (B) The teachings of the prior art; and (C) The claim interpretation that would be given by one possessing the ordinary level of skill in the pertinent art at the time the invention was made. In reviewing a claim for compliance with 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph, the examiner must consider the claim as a whole to determine whether the claim apprises one of ordinary skill in the art of its scope and, therefore, serves the notice function required by 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph, by providing clear warning to others as to what constitutes infringement of the patent.”
The term “temporarily” may mean either ‘for a limited time’ or ‘not permanently.’ As discussed in pg. 9-10 of the office action mailed February 17, 2026, nucleases which require the continued presence of an inactivator for inactivity may be considered ‘irreversibly’ (i.e. permanently) by some ordinary artisans (in this case by Lanes: par. 55). However, the same nucleases would be considered to other artisans as temporarily inactivated (that is, capable of regaining activity under the proper conditions), given the plain meaning of the term ‘temporarily.’ Thus, the maximum and minimum bounds of the term ‘temporarily’ remain unclear. As further example, is a nuclease in solution ‘temporarily’ inactive in the fraction of a second after a substrate has been released and before another takes its place? Is it considered ‘temporarily substantially inactive’ when added to solution (under no special conditions) before the addition of required cofactors and/or substrate? The amended claim language requiring particular percent ‘specific activity’ compared to ‘maximum specific activity’ is also indefinite (and thus does not provide sufficient context to render the rest of the claims clear in scope). The amended claim language is further discussed in the modified rejections set forth above. Thus, the claims as a whole do not provide one of ordinary skill in the art of the scope of the invention. The rejections are maintained.
Regarding the rejection over the recitation of "digest"/"digestion" in claim 1, the argument that the limitation is merely broad and not indefinite has been considered and is found persuasive. In light of this argument, ‘digest’/’digestion’ is considered to include all forms of nuclease activity, including activity which may be considered partial digestion (such as the activity of nicking endonucleases).
Regarding the rejection over the recitation of “sufficient,” Applicant argued that the amendments to claim 1 clarify parameters for determining when the substantially inactive nuclease has regained substantial nuclease activity and therefore a person with ordinary skill in the art may reasonably ascertain the scope of claim 25 to identify the amount of magnesium and/or manganese required. This argument has been considered, but in light of the indefiniteness of the amended claim language, as discussed in the modified/new 35 U.S.C. 112(b) rejections, it is not considered persuasive. The rejection is maintained.
Claim Rejections – 35 USC § 103
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 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.
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 1-11, 16-19, 21, and 25 are rejected under 35 U.S.C. 103 as being unpatentable over Tabor et al. (published Nov. 21, 2002; Patent Application No. US 2002/0172972) in view of Lanes et al. (published December 18, 2014; Patent Publication No. 2014/0370514) and Columbia University (published November 11, 2020; ‘Columbia’; accessed from https://web.archive.org/web/20201118222547/https://research.columbia. edu/ehs-covid-19-guidance).
Regarding claim 1, Tabor teaches a method of causing enzymatic digestion of in vitro synthesized nucleic acid (par. 12), comprising the steps:
combining reagents in the presence of a temporarily substantially inactive nuclease to form the in vitro synthesized nucleic acid (par. 15)
detecting, directly or indirectly, the in vitro synthesized nucleic acid (par. 76)
permitting or causing the substantially inactive nuclease to regain substantial nuclease activity such that nucleic acid is digested by the nuclease (par. 8)
This new grounds of rejection under 35 U.S.C. 103 is necessitated by claim amendments filed on 05/18/2026.
For clarity, regarding two wherein clauses recited in lines 9-12 of amended claim 1 filed on 05/18/2026, Tabor teaches the addition of a nuclease to a solution, which is then activated (permitted or caused to regain substantial activity) for the purpose of digesting contaminating nucleic acids. The nuclease is then (temporarily) inactivated, for example with an inhibitor, and reagents are combined to synthesize nucleic acids, which are then detected. Tabor teaches that the substantially inactive nuclease is a nuclease having <1% digestion of nucleic (par. 39) compared to its maximum specific activity of 99.9% degradation of nucleic acid (par. 35). These fall within with the claimed intervals (wherein substantially inactive nucleases have up to 10% specific activity and substantial nuclease activity comprises a specific activity that is at least 80% of the maximum specific activity) with sufficient specificity that the limitation is considered to have been met.
Regarding claim 1, Tabor does not explicitly teach that the nucleic acid digested by the nuclease is the same as the in vitro synthesized nucleic acid. Tabor does not teach that permitting or causing the substantially inactive nuclease to regain substantial nuclease activity occurs subsequent to the detection step. However, Tabor does teach that nucleic acids may be digested in a manner to prevent their reactivity in subsequent assays (par. 13) and for the purposes of removing contaminants (par. 4). Tabor teaches that methods of removing contaminating nucleic acids include those directed to sterilizing equipment and tools or degrading PCR products themselves (par. 5).
The courts have haled that rearrangement of steps is obvious in the absence of unexpected results. Ex parte Rubin, 128 USPQ 440 (Bd. App. 1959) (Prior art reference disclosing a process of making a laminated sheet wherein a base sheet is first coated with a metallic film and thereafter impregnated with a thermosetting material was held to render prima facie obvious claims directed to a process of making a laminated sheet by reversing the order of the prior art process steps.). See also In re Burhans, 154 F.2d 690, 69 USPQ 330 (CCPA 1946) (selection of any order of performing process steps is prima facie obvious in the absence of new or unexpected results); In re Gibson, 39 F.2d 975, 5 USPQ 230 (CCPA 1930) (Selection of any order of mixing ingredients is prima facie obvious).
While Tabor describes the digestion of nucleic acid prior to synthesis, it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to try including this step after synthesis of the nucleic acid. The artisan would have a reasonable expectation of success as the artisan is rearranging known steps. One would be motivated to do so in order to reduce the risk of environmental nucleic acid contamination (Columbia: pg. 3, last paragraph; Tabor: par. 5). One would have had reasonable expectation of success because methods involving steps of digesting in vitro synthesized nucleic acids after synthesis are known (Tabor: par. 5) and because both Columbia and Tabor contemplate contamination on surfaces and equipment, not just in reagent solutions (Tabor: par. 63).
Regarding claims 2 and 18, Tabor teaches an endonuclease (micrococcal nuclease) which acts on DNA substrates (par. 40).
Regarding claim 3, Tabor teaches nucleases which require aqueous magnesium for nuclease activity (par. 40).
Regarding claims 4 and 19, Tabor does not explicitly teach nucleases selected from the group consisting of HL-SAN, HL-dsDNase, Cyanase nuclease, Benzonase nuclease, Cryonase cold-active nuclease, and OmniCleave nuclease.
Lanes teaches endonucleases which are useful for removing contaminating nucleic acids from a sample (Abstract), including HL-SAN, Benzonase, OmniCleave (par. 3). Here, HL-SAN is termed VsEndA_S44E (par. 104; Fig. 16)
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to use HL-SAN, Benzonase, or OmniCleave as the nuclease of Tabor’s invention because the nucleases are used for the same purpose (i.e. they are all nucleases useful for removing contaminating nucleic acids) and therefore they may be considered functional equivalents. One would have had reasonable expectation of success because Lanes explains that activating molecules (par. 35) and inhibitors for such enzymes are known (par. 3, 36). A person with ordinary skill in the art would understand the modulation of conditions required to obtain reversible inactivation (Lanes: par. 31-39; Tabor: par. 14, 30), as required by the instant invention.
Regarding claims 5 and 6, Tabor teaches the use of DNA amplification reactions, including isothermal techniques (par. 24)
Regarding claims 7-9, Tabor does not explicitly teach substantial inactivation by a process comprising contacting the nuclease with a reducing agent comprising DTT or TCEP, wherein the nuclease is heat-labile and the method comprises temporarily inactivating the nuclease by a process comprising incubating the nuclease at a temperature in the range 25-60ºC for at least 15 minutes.
Regarding claims 7-9, Lanes teaches substantial inactivation with reducing agents including DTT and TCEP (par. 56), wherein the nuclease is heat-labile and inactivation is accomplished through incubation between 25-60 ºC for at least 15 minutes (par. 39, 124; Fig. 6). For clarity, Lanes teaches that inactivation with temperature and/or DTT or TCEP can be reversible (par. 127; Figures 8a-d). Figures 8a-d show that significant activity in nucleases is retained after treatment with reducing agents DTT and TCEP and/or temperature inactivation followed by storage on ice (par. 124, 128). In particular, while Figure 6a/b shows almost complete loss of activity in nucleases treated with 1 mM DTT at 40 or 50 ºC for 5-40 minutes, Figure 8a/b show that nucleases inactivated under similar conditions regain their ability to cleave target nucleic acids (par. 127). Lanes discusses factors which affect the ability of nucleases to remain inactive or regain activity in the absence of inactivators (par. 57-58). HL-SAN itself is only taught to be inactivated even in the absence of inactivation agent (i.e. irreversibly) under the following conditions: 10nM TCEP with a 60min incubation at 50ºC followed by removal of TCEP only after storage at room temperature for 2 days (par. 59); 1mM TCEP with a 60min incubation at 50ºC followed by removal of TCEP only after storage at 37ºC for 2 days (par. 60); or 10mM TCEP at 37ºC for 1 day or room temperature for 4 days (par. 61).
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to use the reducing agent and heat combination of Lanes in place of the inhibitor/EGTA of Tabor because the methods are used for the same purpose (i.e. they are both methods of inactivated a nuclease; Tabor: par. 67; Lanes: par. 39) and therefore may be considered functional equivalents. One would have had reasonable expectation of success because Lanes thoroughly describes conditions under which nucleases may be rendered reversibly or irreversibly inactive (see paragraph above).
Regarding claims 10, 11, and 25, Tabor teaches a specific nuclease which requires ions for activity (par. 40: calcium ions) and a step of permitting or causing the nuclease to regain substantial nuclease activity which comprises contacting the nuclease with calcium ions (par. 46).
Regarding claims 10, 11, and 25, Tabor does not explicitly teach that the step of permitting or causing the nuclease to regain substantial nuclease activity comprises contacting the nuclease with aqueous magnesium and/or manganese ions in the concentration range of 10mM to 100mM.
Lanes teaches contacting the nuclease with magnesium or manganese ions at between 10-100 mM concentrations for activity (par. 35).
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to use the magnesium/manganese of Lanes in place of the calcium of Tabor because the ions are used for the same purpose (i.e. they are requirements for the activity of the nuclease) and therefore may be considered functional equivalents. One would have had reasonable expectation of success because both Tabor and Lanes teach that the use and optimization of magnesium and other ions for activation of enzymes/nucleases is known (Tabor: par. 40, 56; Lanes: par. 35).
Regarding claims 16 and 17, Tabor teaches that the method is performed in or on a test device, the test device comprising the reagents, and the reagents comprising a DNA polymerase, a plurality of NTPs comprising one or more of dATP, dCTP, dGTP, and dTTP, and the nuclease in reactivatable form (par. 23, 63, 70). Here, the device is a test tube.
Regarding claim 21, Lanes teaches the reagents provided as a liquid (par. 29).
Claims 26 and 27 are rejected under 35 U.S.C. 103 as being unpatentable over Tabor et al. (published Nov. 21, 2002; Patent Application No. US 2002/0172972) in view of Lanes et al. (published December 18, 2014; Patent Publication No. 2014/0370514) and Columbia University (published November 11, 2020; ‘Columbia’; accessed from https://web.archive.org/web/20201118222547/https://research.columbia.edu/ehs-covid-19-guidance), as applied to claims 1, 5, and 16 above, and further in view of Provins et al. (published July 25, 2019; Patent Publication No. US20190226015).
Tabor, Lanes, and Columbia University teach the limitations of claims 1, 5, and 16, as discussed above.
Regarding claim 26, Tabor, Lanes, and Columbia University do not explicitly teach DNA amplification with is non-isothermal and not a PCR reaction.
Provins teaches a method of performing a non-isothermal nucleic acid amplification reaction (Abstract).
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to combine the teachings of Tabor, Lanes, and Columbia University with the teachings of Provins. One would have been motivated to do so in order to utilize an improved nucleic acid amplification technique (Provins: par. 15). One would have had reasonable expectation of success because Provins demonstrates the non-isothermal method shares many features with the PCR and isothermal methods of Tabor and Lanes (Provins: par. 116).
Regarding claim 27, Tabor, Lanes, and Columbia University do not explicitly teach test devices which are a lateral flow or microfluidic test device.
Provins teaches microfluidic and lateral flow devices for nucleic acid amplification (par. 57-58).
It would have been obvious to a person with ordinary skill in the art before the effective filing date of the instant invention to substitute the devices of Tabor or Lanes (test tubes) with the lateral flow device of Provins because the devices are used for the same purpose (i.e. as reaction vessels) and therefore may be considered functional equivalents. One would have had reasonable expectation of success because Provins explains that lateral flow devices for nucleic acid detection are well known (par. 55).
Response to Arguments
In the reply filed May 18, 2026, Applicant argued that the previous Office Action failed to establish that the Columbia PDF was available as a printed publication prior to the effective filing date of the present application because the Examiner did not prove that the date provided in the document was a ‘publication date.’
This argument has been considered and is not found persuasive. The Examiner met the initial burden of proof by indicating the version date of a document intended for public dissemination as guidance to laboratory personnel. MPEP 2128 states that “When a document is cited in a rejection of a claim in an examination of a patent application or during an reexamination proceeding, an applicant or patent owner may challenge its public availability and/or the date it became publicly accessible, even when the document itself contains a publication date, by filing a proper affidavit or declaration under 37 CFR 1.132 that includes facts and evidence to support the applicant or patent owner's position.” The Applicant has not provided any facts or evidence to support that the date of the provided document is not a publication date.
However, to provide clarity, a copy of the webpage hosting the Columbia PDF document from November 18, 2020 was obtained from the Wayback Machine. This snapshot is included as ‘Columbia EHS’ with this Office Action and was accessed from: https://web.archive.org/web/20201118222547/https://research.columbia.edu/ehs-covid-19-guidance). Columbia EHS is a snapshot of a publicly accessible webpage which contained a link to the Columbia PDF (indicated with a box, sharing the same title and the same date as the Columbia PDF). This provides further evidence that, at least as of November 18, 2020, the version of the document provided in the previous Office Action was distributed to the public before the effective filing date of the instant invention.
In the reply, Applicant argued that Lanes failed to teach the steps (a)-(c) of the claimed method, and therefore the obviousness of rearrangement of steps is irrelevant. As a result of amendments to the claims, the rejections under 35 U.S.C. 103 have been modified and now rely on a new combination of references. Although the rejections have been modified to include a different primary reference, Lanes and Columbia are still relied upon. Those arguments which are still pertinent to the modified rejections are discussed in this section.
In the reply, Applicant argued that a person with ordinary skill in the art wouldn’t have compelling motivation to modify the method of Lanes in view of Columbia PDF because Columbia PDF describes a protocol for cleaning environmental areas of a lab (and there are more routine methods of decontaminating those surfaces).
This argument has been considered but is not found persuasive. The modified rejections set forth above use Columbia PDF as part of motivation to rearrange certain steps of Tabor. To summarize here, Tabor and Columbia in combination teach that digestion of synthesized nucleic acids (such as PCR products) after amplification is a well-known technique for managing nucleic acid contamination in laboratory processing spaces which may have detrimental impact on subsequent nucleic acid amplification assays (Columbia: pg. 3, last paragraph; Tabor: par. 5). Thus, there is ample benefit provided by rearranging steps such as those set forth in either Tabor or Lanes.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/C.M.J./Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
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