DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application is being examined under the pre-AIA first to invent provisions.
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 prior art rejection(s) set forth below will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection(s), would be the same under either status.
Status of the Application
2. Applicant’s response filed on October 15, 2025 has been entered.
Claims 42-62 are pending and under examination.
Response to Arguments
3. Applicant’s arguments filed on October 15, 2025 have been fully considered.
Rejection of claims 42-59 and 61 under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Piepenburg 1
Arguments:
Applicant argues that the rejection should be withdrawn because Piepenburg 1 fails to teach or suggest the freeze-dried pellet of independent claim 42, in which Tris buffer is present and potassium acetate is absent (Remarks, pages 6-8). Instead, Applicant argues, “Piepenburg 1 only describes lyophilized pellets that either have both Tris and potassium acetate or exclude both Tris and potassium acetate” (Remarks, page 6). Applicant acknowledges the portions of Piepenburg 1 cited in the Office action and argues that the rejection uses impermissible hindsight as no specific motivation has been provided as to why the ordinary artisan would consider these portions of Piepenburg 1 to suggest freeze-dried pellets “containing Tris and lacking potassium acetate in addition to pellets containing or lacking both reagents” (Remarks, page 7).
Applicant additionally argues that Applicant has recognized advantages associated with the claimed pellets, which are neither taught nor suggested by Piepenburg 1. In particular, Applicant first argues, citing para. 35 of the pre-grant publication of the instant application for support, that “Applicant identified that excluding salt (e.g., Potassium Acetate) from the freeze-dried pellet, while maintaining the Tris-buffer, maximized the stability of the freeze-dried pellet – particularly when stored above 0 ⁰C” (Remarks, page 7). Applicant also argues, citing para. 36 of the pre-grant publication of the instant application for support, that Applicant has “also identified that with the elimination of salt in the lyophilizate, polyethylene glycol is no longer required to stabilize the lyophilizate and can be transferred to the rehydration buffer” (Remarks, pages 7-8).
Lastly, Applicant argues that many reagent combinations are possible, but Piepenburg 1 fails to provide any teaching or motivation that would lead the ordinary artisan to form a freeze-dried pellet containing the particular combination of reagents required by claim 42 (Remarks, page 8).
Response:
These arguments have been fully considered, but they were not persuasive.
In response to Applicant’s arguments concerning improper hindsight reasoning and the failure of Piepenburg 1 to suggest a freeze-dried pellet containing the specific combination of reagents recited in independent claim 42, it must be recognized that any judgment concerning obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971).
In this case, the rejection only uses the teachings of Piepenburg 1 in combination with the knowledge possessed by the ordinary artisan. More specifically, as discussed in the rejection, Piepenburg 1 teaches that any components of a recombinase polymerase amplification (RPA) reaction can be lyophilized to form freeze-dried pellets (pp. 28-30). The reference also discloses an example in which Tris and potassium acetate are excluded from the pellets (see, e.g., p. 182) and additionally teaches that Tris may be included in the pellets (p. 28). These teachings in the reference clearly indicate that many different freeze-dried pellets are possible and that the buffer (Tris) may be included in or omitted from the pellets according to user preference. The ordinary artisan would, therefore, have recognized from the above teachings and also the entirety of Piepenburg 1 that artisans may select which RPA reagents to include in the freeze-dried pellets. Therefore, the rejection is not, in fact, the result of improper hindsight.
In response to Applicant's argument that the inventors discovered that eliminating potassium acetate, but not Tris, from lyophilized pellets produced more stable pellets, particularly when the pellets are stored above 0 ⁰C (Remarks, page 7) and Applicant’s argument that eliminating salt in the lyophilizate allowed PEG to be transferred to the rehydration buffer, the fact that the inventors recognized additional advantages which would flow naturally from following the suggestion of the prior art cannot be the basis for patentability when the differences would otherwise be obvious. See Ex parte Obiaya, 227 USPQ 58, 60 (Bd. Pat. App. & Inter. 1985). In this case, the teachings of Piepenburg 1 suggest pellets with the required components for the reasons set forth above and in the rejection.
It is also noted that Applicant’s argument on pages 7-8 of the Remarks regarding eliminating PEG from the pellets does not apply to all of the claims because PEG is an option for the pellets of claim 43 and a requirement of the pellets of new claim 62.
Lastly, it is noted that no persuasive evidence of unexpected results or secondary considerations has been provided. Paragraphs 35 and 36 of the specification, which are cited in Applicant’s arguments, describe advantages associated with the disclosed freeze-dried pellets, but these statements are not supported by data. Such data would be necessary to establish unexpected results. See also MPEP 2145 I, which notes that arguments cannot replace evidence.
Since Applicant’s arguments were not persuasive, the rejection has been maintained with modifications to address the presence of new claim 62.
Rejection of claim 60 under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Piepenburg 1 in view of Piepenburg 2
Applicant argues that the rejection of this dependent claim should be withdrawn in view of the arguments presented with respect to independent claim 42 (Remarks, page 8). In other words, Piepenburg 2 does not remedy the deficiencies of Piepenburg 1 with respect to independent claim 42 (Remarks, page 8).
This argument was not persuasive because Piepenburg 1 is not deficient for the reasons set forth above. The rejection has been maintained.
Double Patenting
Applicant’s response acknowledges the rejections made on the ground of nonstatutory double patenting citing US Patent Nos. 9,057,097 and 10,329,602 and states that filing a terminal disclaimer will be considered when the double patenting rejections are the only remaining rejections (Remarks, pages 8-9).
It is noted that this is not fully responsive because rejections are not matters of form that can be held in abeyance. See MPEP 714.02 and MPEP 804. The rejections have been maintained with modifications to address the presence of new claim 62 since they remain applicable.
Claim Rejections - 35 USC § 103
4. The following is a quotation of pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negatived by the manner in which the invention was made.
5. This application currently names joint inventors. In considering patentability of the claims under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
6. Claims 42-59, 61, and 62 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Piepenburg et al. (WO 2005/118853 A2; “Piepenburg 1” below).
The instant claims are drawn to a freeze-dried pellet for use in a recombinase polymerase amplification (RPA) process. The pellet does not contain potassium acetate and does contain the following components: (i) a recombinase, (ii) a recombinase loading protein, (iii) a single-stranded DNA binding protein, (iv) a strand-displacing DNA polymerase, (v) trehalose, (vi) a first primer, (vii) a second primer, and (viii) Tris buffer.
Regarding claims 42, 43, 57-59, and 61, Piepenburg 1 teaches a freeze-dried pellet for use in an RPA reaction that comprises trehalose at a concentration of 20 mM to 200 mM (i.e., 0.69% (w/v) to 6.8% (w/v)), preferably between 40 mM and 80 mM (i.e., 1.3% (w/v) to 2.7% (w/v)) (page 29, first full paragraph; see also Example 13 on page 182). These ranges overlap with the trehalose concentration range recited in claim 66. Piepenburg 1 also teaches that the freeze-dried pellets may contain first and second oligonucleotide primers, PEG (i.e., Carbowax 20M), a uvsX recombinase, a uvsY recombinase loading protein, and a single-stranded DNA binding protein (gp32) (see Example 13 on page 182; see also pages 28-31 for a more general description of the freeze-dried pellets). Piepenburg 1 also teaches that Tris buffer may be included in the pellets (page 28, first and second full paragraphs). And, in Example 13 on page 182, Piepenburg 1 teaches that the freeze-dried pellets may lack potassium acetate.
Further regarding claims 42 and 43 as well as claim 46, Piepenburg 1 also teaches that the freeze-dried pellets may also include a DNA polymerase, dNTPs, DTT, and ATP (see Example 13 on page 182; see also pages 28-31). The Bsu DNA polymerase disclosed on page 29, for example, is a strand-displacing DNA polymerase.
Further regarding claim 42 and also claim 47, as noted above, Piepenburg teaches that Tris buffer may be included in the freeze-dried pellets. The reference also teaches that a suitable Tris concentration for RPA is 1-60 mM (see, e.g., page 30). The concentration (25 mM) recited in claim 52 lies within this range.
Regarding claims 44 and 45, Piepenburg 1 teaches practicing RPA in the presence of a nuclease, specifically Nfo (pages 204-207). The reference further teaches that any reagent useful for practicing RPA may be included in the freeze-dried pellets (pages 28-29).
Regarding claim 48, Piepenburg 1 teaches that the dNTP concentration may range from 1-300 micromolar (page 29). This range includes the claimed concentration of 240 micromolar. The reference also teaches a specific concentration of 200 micromolar on page 29, which is a concentration close to the claimed concentration.
Regarding claim 49, Piepenburg 1 teaches that the DTT concentration may range from 1-10 mM (page 29). This range includes the claimed concentration of 5 mM.
Regarding claim 50, Piepenburg 1 teaches that the ATP concentration may range from 1-10 mM (page 29). The reference also teaches a concentration of 3 mM on page 29, which is close to the claimed concentration.
Regarding claim 51, Piepenburg 1 teaches that the pellets may include creatine kinase and phosphocreatine (see, e.g., pages 29-30). The creatine kinase concentration may range from 50 ng/microliter to 200 ng/microliter, and the phosphocreatine concentration may range from 10-40 mM (page 29, last paragraph – page 30). These concentration ranges for creatine kinase and phosphocreatine include the claimed creatine kinase concentration of 100 ng/microliter lie close to the claimed phosphocreatine concentration of 50 mM.
Regarding claims 52-56, Piepenburg 1 teaches that the freeze-dried pellet may be freeze dried on the bottom of a tube or in a well of a multi-well container (see, e.g., page 29, last paragraph – page 30, first paragraph). This portion of the reference also teaches freeze drying “onto a mobile solid support such as a bead or a strip, or a well.”
Regarding claim 62, Piepenburg 1 teaches that the freeze-dried pellet may contain PEG (see, e.g., Example 13 on page 182; see also pages 28-31). Piepenburg 1 further teaches that the freeze-dried pellets “are reconstituted in a buffer solution and with a crowding agent, or simply a buffered solution or water, dependent on the composition of the freeze-dried reagents” (page 28, 2nd full paragraph).
Piepenburg 1 does not teach all of the elements of the claims for the following reasons. First, regarding independent claim 42, Piepenburg 1 is not anticipatory because the reference fails to disclose a specific example of a freeze-dried pellet lacking potassium acetate and containing Tris buffer. The portions of pages 28 and 29 cited above indicate that Tris, like other RPA reagents, may be included or omitted from the freeze-dried pellets, as desired by the practitioner, but these portions of Piepenburg 1 do not directly discuss potassium acetate. As well, Example 13 on page 182 discloses omitting potassium acetate from freeze-dried pellets, but Tris buffer is also omitted from the freeze-dried pellets in this specific example. In addition, regarding claims 44 and 45, although Piepenburg 1 teaches that RPA may be conducted in the presence of the Nfo nuclease, the reference fails to disclose a specific example of a freeze-dried pellet containing this protein. As to claims 47-51 and 61, although Piepenburg 1 discloses concentration ranges that include the claimed concentrations of Tris, dNTPs, ATP, creatine kinase, and phosphocreatine and overlap with the claimed Tris and trehalose concentration ranges, the reference fails to disclose a freeze-dried pellet in which these reagents are present at the required concentrations. Lastly, regarding new claim 62, as noted above Piepenburg 1 teaches that PEG may be present in the freeze-dried pellets (pp. 28-31 and p. 182). The reference also teaches that a crowding agent (e.g., PEG) may be present in the rehydration buffer/solution (p. 28), but it is not clear that Piepenburg clearly teaches freeze-dried pellets containing PEG at an amount such that the rehydration buffer/solution must also contain PEG.
It would have been prima facie obvious, though, for the ordinary artisan to prepare a freeze-dried pellet containing the components listed above (i.e., trehalose, a recombinase, a recombinase loading protein, a strand-displacing DNA polymerase, a single-stranded DNA binding protein, a first primer, a second primer, phosphocreatine, creatine kinase, DTT, dNTPs, and ATP), lacking potassium acetate, and containing Tris buffer. The teachings of Piepenburg 1 provide motivation to do so as well as a reasonable expectation of success for the following reasons. In particular, Piepenburg 1 teaches that “[T]he reagents for RPA, with the possible exception of the crowding agent and buffer may be freeze dried (i.e., lyophilized) before use” (page 28, first full paragraph). The reference goes on to describe reconstitution “in a buffer solution and with a crowding reagent, or simply a buffered solution or water dependent on the composition of the freeze-dried reagents” (page 28, second full paragraph), thereby clearly indicating that the buffer may be included or omitted from the freeze-dried pellet, as desired by the practitioner. Then, since the reference further teaches that the user may select different combinations of reagents for freeze drying according to preference (page 28, last paragraph – page 29, first paragraph) and additionally describes omitting potassium acetate from the freeze-dried pellets (Example 13 on page 182), the ordinary artisan would have concluded that Piepenburg 1 suggests pellets containing Tris and lacking potassium acetate in addition to pellets containing or lacking both reagents. Thus, in the absence of any persuasive evidence of unexpected results, a freeze-dried pellet containing a recombinase, a recombinase loading protein, a first primer, a second primer, trehalose, a single-stranded DNA binding protein, a strand-displacing DNA polymerase, and Tris buffer is prima facie obvious.
Further regarding the specific Tris concentration within this range recited in claim 47, and the specific concentrations for dNTPs, DTT, ATP, phosphocreatine, and creatine kinase recited in claims 48-51, and the trehalose concentration range recited in claim 61, attention is first directed to MPEP 2144.05 I, which states that, in the absence of unexpected results, ranges that overlap with a claimed range or amounts that lie close to a claimed amount are prima facie obvious. Also, as noted in MPEP 2144.05 II, differences in concentration are typically obvious in the absence of unexpected results. In this case, no persuasive evidence of unexpected results has been presented, and Piepenburg 1 discloses overlapping ranges for Tris and trehalose, a concentration range for Tris that includes the claimed concentration, and concentration ranges and/or example concentrations for dNTPs, DTT, ATP, phosphocreatine, and creatine kinase that contain or lie close to the claimed concentrations. This is sufficient to render obvious the claimed concentrations and concentration ranges, and the freeze-dried pellets of claims 42, 43, 46-59, and 61 are prima facie obvious.
Further regarding claims 44 and 45, it also would have been prima facie obvious to further include a nuclease, such as Nfo, in the freeze-dried pellets suggested by Piepenburg 1. First, as noted above, Piepenburg 1 teaches that any reagent useful for practicing RPA may be included in the freeze-dried pellets (pages 28-29). Then, since Piepenburg 1 also described RPA reactions conducted in the presence of Nfo (pages 204-207), the ordinary artisan would have been motivated to include this nuclease in the freeze-dried pellets suggested by Piepenburg 1 with a reasonable expectation of success.
Lastly, further regarding new claim 62, as noted above, Piepenburg 1 clearly teaches that PEG may be present in the freeze-dried pellet (pp. 28-31 and p. 182). The reference goes on to describe reconstitution “in a buffer solution and with a crowding reagent, or simply a buffered solution or water dependent on the composition of the freeze-dried reagents” (page 28, second full paragraph), thereby clearly indicating that PEG may be included or omitted from the freeze-dried pellet, as desired by the practitioner. The ordinary artisan also would have recognized, both from the teachings throughout Piepenburg 1 and from the general knowledge in the art that it is desirable to optimize the concentration of reagents (e.g., PEG) in a freeze-dried pellet, that one could prepare any of the following types of freeze-dried pellet: (1) a freeze-dried pellet containing an amount of PEG sufficient for amplification (i.e., an amount of PEG that does not require the rehydration solution to also contain PEG); (2) a freeze-dried pellet lacking PEG such that the rehydration solution must contain a sufficient amount of PEG for amplification; and (3) an intermediate amount of PEG, such that the rehydration solution must also contain PEG so that the resulting solution will contain enough PEG for amplification. The ordinary artisan would have recognized that each of these options could be suitable, and accordingly, would have been motivated to select any desired option with a reasonable expectation of success given the teachings throughout Piepenburg 1 and also in view of the fact that no evidence of unexpected results has been presented.
In view of the foregoing, the freeze-dried pellets of claims 42-59, 61, and 62 are prima facie obvious.
7. Claim 60 is rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Piepenburg et al. (WO 2005/118853 A2; “Piepenburg 1” below) in view of Piepenburg et al. (WO 2008/035205 A2; “Piepenburg 2” below).
Claim 60 depends from claim 42 and requires the freeze-dried pellet to contain at least one of the following: (i) T6 uvsX H66S recombinase as the recombinase, (ii) Rb69 uvsY as the recombinase loading protein, and (iii) Rb69 gp32 as the single-stranded DNA binding protein.
As discussed above, the teachings of Piepenburg 1 render obvious the freeze-dried pellets of claims 42-59, 61, and 62.
Regarding claim 60, Piepenburg 1 does not teach or suggest freeze-dried pellets with any of the required components.
The teachings of Piepenburg 2, though, remedy this deficiency in Piepenburg 1. In particular, Piepenburg 2 teaches that RPA can be practiced using the T4 or T6 uvsX recombinase (page 8, lines 10-15). The reference also teaches that the T4 and Rb69 gp32 proteins are functional equivalents useful in RPA (page 8, lines 10-20) and that the claimed T6 uvsX recombinase having an H66S mutation is an improvement compared to the wild-type form (see page 9, lines 8-12 and Example 4 on pages 58-59). Piepenburg 2 also teaches that the uvsY recombinase loading protein from Rb69 can be used in RPA mixtures also containing the Rb69 gp32 protein and a T6 uvsX recombinase (see, e.g., page 83, lines 7-21).
It would have been prima facie obvious for one of ordinary skill in the art at the time of the invention to substitute the Rb69 gp32 protein and/or the Rb69 uvsY recombinase loading protein disclosed in Piepenburg 2 for the T4 gp32 protein and T4 uvsY recombinase loading protein contained in the freeze-dried pellets of Piepenburg 1. As discussed in MPEP 2144.06, it is prima facie obvious to substitute art-recognized equivalents known to be useful for the same purpose in the absence of unexpected results. It is also prima facie obvious to select a known material based on its suitability for the intended purpose in the absence of unexpected results (MPEP 2144.07). In this case, the teachings of Piepenburg 2 establish that the gp32 protein and uvsY recombinase loading proteins from bacteriophage T4 disclosed in Piepenburg 1 and the claimed gp32 and uvsY proteins from Rb69 are equivalents useful for the same purpose, and no persuasive evidence of unexpected results has been presented with respect to the inclusion of either of these Rb69 proteins in the claimed freeze-dried pellets. Accordingly, their substitution in the freeze-dried pellets of Piepenburg 1 is prima facie obvious.
It also would have been prima facie obvious to substitute the T6 H66S uvsX recombinase disclosed in Piepenburg 2 for the T4 uvsX recombinase disclosed in Piepenburg 1. Since the teachings of Piepenburg 2 also indicate that the claimed T6 uvsX H66S recombinase is a functional equivalent of the T4 uvsX recombinase used by Piepenburg 1 and no persuasive evidence of unexpected results has been presented concerning the inclusion of this uvsX recombinase in the claimed freeze-dried pellets, this substitution is also prima facie obvious in view of MPEP 2144.06 and 2144.07. Additional motivation is provided by the teaching in Piepenburg 2 that the T6 uvsX H66 recombinase is an improvement relative to the T4 protein used in Piepenburg 1 (Piepenburg 2 at pages 58-59).
Thus, the freeze-dried pellet of claim 60 is prima facie obvious.
Double Patenting
8. 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 USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/process/file/efs/guidance/eTD-info-I.jsp.
9. Claims 42-59, 61, and 62 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-21, 40, and 41 of U.S. Patent No. 9,057,097 B2.
Although the claims at issue are not identical, they are not patentably distinct from each other because claims 1-21, 40, and 41 of the ‘097 patent overlap in scope with the instant claims and teach or suggest all of their limitations.
The instant claims are drawn to a freeze-dried pellet for use in a recombinase polymerase amplification (RPA) process. The pellet does not contain potassium acetate and does contain the following components: (i) a recombinase, (ii) a recombinase loading protein, (iii) a single-stranded DNA binding protein, (iv) a strand-displacing DNA polymerase, (v) trehalose, (vi) a first primer, (vii) a second primer, and (viii) Tris buffer. As well, the pellet cannot contain potassium acetate.
Claim 1 of the ‘097 patent is drawn to a kit comprising freeze-dried pellets. The freeze-dried pellets contain the following components: (i) a recombinase (uvsX), (ii) a single-stranded DNA binding protein (gp32), (iii) a DNA polymerase with strand displacement activity (Sau polymerase), (iv) dNTPs, (v) a reducing agent (DTT), (vi) ATP, (vii) a recombinase loading protein (uvsY), (viii) trehalose, and (ix) Tris buffer. Potassium acetate is not required to be present in the pellets. As well, dependent claim 13 of the ‘097 patent states that the pellets may contain a first and second primer. Thus, the claims of the ‘097 patent overlap in scope with the instant claim 42 and suggest a freeze-dried pellet with all of the required components.
The limitations of the instant claims 43, 46, 57-59, and 61 are recited in claim 1 of the ‘097 patent.
The limitations of the instant claims 44 and 45 are recited in claims 14 and 17-21 of the ‘097 patent.
The limitations of the instant claims 47-51 are recited in claim 2 of the ‘097 patent.
The claims of the ‘097 patent do not state how the freeze-dried pellets are provided in the kit, but providing these pellets on the bottom of a tube, in a well of a multi-well container, or attached to a mobile solid support (e.g., a bead or a strip) as recited in the instant claims 52-56 would have been obvious to the ordinary artisan. More specifically, the ordinary artisan would have recognized that any of these commonly used ways of providing the freeze-dried pellet would have been suitable, and accordingly, would have been provided to so provide the freeze-dried pellets of the ‘097 patent.
Further regarding the instant claim 62, the freeze-dried pellet in the kit recited in claim 1 of the ‘097 patent contains PEG (see part (a)(1)). Claims 5, 6, 40, and 41 of the ‘097 patent state that the kit also contains a rehydration buffer for reconstituting the freeze-dried pellets. This rehydration buffer may also contain PEG. Therefore, the claims of the ‘097 patent clearly teach freeze-dried pellets that contain PEG and also a PEG-containing rehydration buffer. It would have been obvious to the ordinary artisan to optimize the PEG concentration in the freeze-dried pellets and rehydration buffer such that the resulting reconstituted pellets contain a PEG concentration suitable for amplification since this is the intended purpose of the claimed kits (see the preamble of claim 1 of the ‘097 patent).
Thus, the instant claims 42-59, 61, and 62 are not patentably distinct from claims 1-21, 40, and 41 of the ‘097 patent.
10. Claim 60 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-21, 40, and 41 of U.S. Patent No. 9,057,097 B2 in view of Piepenburg et al. (WO 2008/035205 A2; “Piepenburg 2” below).
The instant claim 60 depends from the instant claim 42 and requires the freeze-dried pellet to contain at least one of the following: (i) T6 uvsX H66S recombinase as the recombinase, (ii) Rb69 uvsY as the recombinase loading protein, and (iii) Rb69 gp32 as the single-stranded DNA binding protein.
As discussed above, the instant claims 42-59, 61, and 62 are not patentably distinct from claims 1-21, 40, and 41 of the ‘097 patent.
The claims of the ‘097 patent do not teach or suggest freeze-dried pellets with any of the required components.
The teachings of Piepenburg 2, though, remedy this deficiency. In particular, Piepenburg 2 teaches that RPA can be practiced using the T4 or T6 uvsX recombinase (page 8, lines 10-15). The reference also teaches that the T4 and Rb69 gp32 proteins are functional equivalents useful in RPA (page 8, lines 10-20) and that the claimed T6 uvsX recombinase having an H66S mutation is an improvement compared to the wild-type form (see page 9, lines 8-12 and Example 4 on pages 58-59). Piepenburg 2 also teaches that the uvsY recombinase loading protein from Rb69 can be used in RPA mixtures also containing the Rb69 gp32 protein and a T6 uvsX recombinase (see, e.g., page 83, lines 7-21).
It would have been prima facie obvious for one of ordinary skill in the art at the time of the invention to select the Rb69 gp32 protein and/or the Rb69 uvsY recombinase loading protein disclosed in Piepenburg 2 as the gp32 protein and uvsY recombinase loading protein contained in the freeze-dried pellets of the ‘097 patent. As discussed in MPEP 2144.06, it is prima facie obvious to substitute art-recognized equivalents known to be useful for the same purpose in the absence of unexpected results. It is also prima facie obvious to select a known material based on its suitability for the intended purpose in the absence of unexpected results (MPEP 2144.07). In this case, the teachings of Piepenburg 2 establish that the gp32 protein and uvsY recombinase loading proteins recited in the claims of the ‘097 patent and the claimed gp32 and uvsY proteins from Rb69 are equivalents useful for the same purpose, and no persuasive evidence of unexpected results has been presented with respect to the inclusion of either of these Rb69 proteins in the claimed freeze-dried pellets. Accordingly, their substitution in the freeze-dried pellets of the ‘097 patent is prima facie obvious.
It also would have been prima facie obvious to select the T6 H66S uvsX recombinase disclosed in Piepenburg 2 for as the uvsX recombinase in the freeze-dried pellets of the ‘097 patent. Since the teachings of Piepenburg 2 also indicate that the claimed T6 uvsX H66S recombinase is a functional equivalent of the uvsX recombinase used in the freeze-dried pellets of the ‘097 patent and no persuasive evidence of unexpected results has been presented concerning the inclusion of this uvsX recombinase in the claimed freeze-dried pellets, this substitution is also prima facie obvious in view of MPEP 2144.06 and 2144.07. Additional motivation is provided by the teaching in Piepenburg 2 that the T6 uvsX H66 recombinase is an improvement relative to T4 uvsX recombinase (Piepenburg 2 at pages 58-59).
Thus, the instant claim 60 is not patentably distinct from the claims of the ‘097 patent in view of Piepenburg 2.
11. Claims 42-59, 61, and 62 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-21 of U.S. Patent No. 10,329,602 B2 in view of Piepenburg et al. (WO 2005/118853 A2; “Piepenburg 1” below).
The instant claims are drawn to a freeze-dried pellet for use in a recombinase polymerase amplification (RPA) process. The pellet does not contain potassium acetate and does contain the following components: (i) a recombinase, (ii) a recombinase loading protein, (iii) a single-stranded DNA binding protein, (iv) a strand-displacing DNA polymerase, (v) trehalose, (vi) a first primer, (vii) a second primer, and (viii) Tris buffer. As well, the pellet cannot contain potassium acetate.
Claim 1 of the ‘602 patent is drawn to dried composition that contains the following components: (i) a recombinase, (ii) a polymerase, (iii) trehalose, and (iv) a crowding agent. Potassium acetate is not required to be present in the composition. Dependent claim 2 of the ‘602 patent states that the composition may be provided as a freeze-dried pellet as required by the instant claim 42. As well, the following dependent claims of the ‘602 patent state that the composition may further include the following additional components required by the instant claim 42: (i) a recombinase loading protein (claim 12), (ii) a single-stranded DNA binding protein (claims 8 and 9), (iii) a strand displacing DNA polymerase (claim 6), and (iv) a first primer and a second primer (claim 7).
Thus, the claims of the ‘602 patent overlap in scope with the instant claim 42 and suggest a freeze-dried pellet with all of the required components except for the requirement in the instant claim 42 for the freeze-dried pellet to further include Tris buffer.
Including Tris buffer in the freeze-dried pellets suggested by the claims of the ‘602 patent would have been obvious, though, in view of the teachings of Piepenburg 1. Piepenburg 1 teaches that “[T]he reagents for RPA, with the possible exception of the crowding agent and buffer may be freeze dried (i.e., lyophilized) before use” (page 28, first full paragraph). The reference goes on to describe reconstitution “in a buffer solution and with a crowding reagent, or simply a buffered solution or water dependent on the composition of the freeze-dried reagents” (page 28, second full paragraph), thereby clearly indicating that the buffer may be included or omitted from the freeze-dried pellet, as desired by the practitioner. Then, since the reference further teaches that the user may select different combinations of reagents for freeze drying according to preference (page 28, last paragraph – page 29, first paragraph) and additionally describes omitting potassium acetate from the freeze-dried pellets (Example 13 on page 182), the ordinary artisan would have concluded that Piepenburg 1 suggests pellets containing Tris and lacking potassium acetate in addition to pellets containing or lacking both reagents. Thus, in the absence of any persuasive evidence of unexpected results, a freeze-dried pellet containing a recombinase, a recombinase loading protein, a first primer, a second primer, trehalose, a single-stranded DNA binding protein, a strand-displacing DNA polymerase, and Tris buffer as recited in the instant claim 42 is prima facie obvious over claims 1-21 of the ‘602 patent in view of Piepenburg 1.
The limitations of the instant claim 43 are suggested by claims 10, 11, 14, and 21 of the ‘602 patent.
The claims of the ‘602 patent do not teach or suggest including a nuclease as required by the instant claims 44 and 45, but this would have been obvious in view of Piepenburg 1. Piepenburg 1 provides motivation to do so by teaching that any reagent useful for practicing RPA may be included in the freeze-dried pellets (pages 28-29) and further describing RPA reactions conducted in the presence of a nuclease recited in the instant claim 45 (Nfo) (pages 204-207). Accordingly, the ordinary artisan would have been motivated to include this nuclease in the freeze-dried pellets suggested by the claims of the ‘602 patent in view of Piepenburg 1 with a reasonable expectation of success.
The claims of the ‘602 patent do not state that the strand-displacing DNA polymerase is Bsu polymerase or Sau polymerase as recited in the instant claim 46, but selecting either polymerase would have been obvious since Piepenburg 1 taught that both were strand-displacing DNA polymerases suitable for use in RPA (see, e.g., page 29). See also MPEP 2144.06 and 2144.07.
Regarding the instant claim 47, the claims of the ‘602 patent in view of Piepenburg 1 suggest including Tris buffer in the freeze-dried pellets. The teachings of Piepenburg 1 also suggest the claimed concentration of 25 mM by disclosing an overlapping range and a concentration range that includes the claimed concentration (see, e.g., page 30). Thus, in the absence of unexpected results, the instant claim 47 is not patentably distinct from the claims of the ‘602 patent in view of Piepenburg 1. See also MPEP 2144.05 I.
Regarding the instant claim 48, the claim 20 of the ‘602 patent discloses a range for the dNTP concentration that includes the claimed concentration, and no evidence of unexpected results has been presented. This is sufficient to establish a prima facie case of obviousness. See also MPEP 2144.05 I.
Regarding the instant claims 49-51 and 61, claim 11 of the ‘602 patent states that the composition may include a reducing agent, and claim 14 of the ‘602 patent state that the composition may include ATP. DTT at a concentration of 5 mM is not specified, nor is the required concentration of ATP. As well, the inclusion of the required amounts of phosphocreatine and creatine kinase is not taught, but these differences would have been obvious in view of the teachings of Piepenburg 1. In particular, as discussed in greater detail above in the obviousness rejection, that reference teaches that DTT, ATP, phosphocreatine, and creatine kinase may be included in RPA reactions (see Example 13 on page 182; see also pages 28-31) and also discloses overlapping concentration ranges for these components and/or concentrations that lie close to the claimed concentrations (see, e.g., pages 28-31). The reference also teaches an overlapping trehalose concentration range (page 29 and Example 13 on page 182). Further, no evidence of unexpected results has been presented. Accordingly, inclusion of these reagents at the required concentrations is obvious in view of the guidance in MPEP 2144.05 I, 2144.06, and 2144.07.
The claims of the ‘602 patent do not recite providing the lyophilized pellet on the bottom of a tube, in a well of a multi-well container, or attached to a mobile solid support (e.g., a bead or a strip) as recited in the instant claims 52-56, but providing these pellets would have been obvious to the ordinary artisan. More specifically, the ordinary artisan would have recognized that any of these commonly used ways of providing the freeze-dried pellet would have been suitable, and accordingly, would have been provided to so provide the freeze-dried pellets of the ‘602 patent. See also pages 29-30 of Piepenburg 1, which discuss suitable ways of providing a freeze-dried pellet for RPA.
The limitations of the instant claims 57-59 are recited in, e.g., claims 3, 9, and 13 of the ‘602 patent.
Further regarding the instant claim 62, claim 1 of the ‘602 patent states that the composition may contain a crowding agent. Claim 21 of the ‘602 patent states that the crowding agent may be PEG. The claims of the ‘602 patent do not specify the concentration of the crowding agent. Therefore, they do not teach that the PEG concentration in the freeze-dried pellets is low enough that the solution used to rehydrate the pellets before their intended use in an amplification reaction must also contain PEG. This would have been obvious to the ordinary artisan, however. More specifically, the ordinary artisan would have recognized that it is generally desirable to optimize concentrations and that the PEG concentration in the freeze-dried pellets could be (1) sufficient for amplification (i.e., present in an amount that does not require the rehydration solution to also contain PEG); (2) absent such that the rehydration solution must contain a sufficient amount of PEG for amplification; and (3) present in an intermediate amount, such that the rehydration solution must also contain PEG so that the resulting solution will contain enough PEG for amplification. The ordinary artisan would have recognized that each of these options could be suitable, and accordingly, would have been motivated to select any desired option with a reasonable expectation of success.
Thus, the instant claims 42-59, 61, and 62 are not patentably distinct from claims 1-21 of the ‘602 patent in view of Piepenburg 1.
12. Claim 60 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-21 of U.S. Patent No. 10,329,602 B2 in view of Piepenburg et al. (WO 2005/118853 A2; “Piepenburg 1” below) and further in view of Piepenburg et al. (WO 2008/035205 A2; “Piepenburg 2” below).
The instant claim 60 depends from the instant claim 42 and requires the freeze-dried pellet to contain at least one of the following: (i) T6 uvsX H66S recombinase as the recombinase, (ii) Rb69 uvsY as the recombinase loading protein, and (iii) Rb69 gp32 as the single-stranded DNA binding protein.
As discussed above, the instant claims 42-59, 61, and 62 are not patentably distinct from the claims of the ‘602 patent in view of Piepenburg 1.
Neither the claims of the ‘602 patent nor Piepenburg 1 teach or suggest freeze-dried pellets with any of components recited in the instant claim 60.
The teachings of Piepenburg 2, though, remedy this deficiency. In particular, Piepenburg 2 teaches that RPA can be practiced using the T4 or T6 uvsX recombinase (page 8, lines 10-15). The reference also teaches that the T4 and Rb69 gp32 proteins are functional equivalents useful in RPA (page 8, lines 10-20) and that the claimed T6 uvsX recombinase having an H66S mutation is an improvement compared to the wild-type form (see page 9, lines 8-12 and Example 4 on pages 58-59). Piepenburg 2 also teaches that the uvsY recombinase loading protein from Rb69 can be used in RPA mixtures also containing the Rb69 gp32 protein and a T6 uvsX recombinase (see, e.g., page 83, lines 7-21).
It would have been prima facie obvious for one of ordinary skill in the art at the time of the invention to select the Rb69 gp32 protein and/or the Rb69 uvsY recombinase loading protein disclosed in Piepenburg 2 as the gp32 protein and uvsY recombinase loading protein contained in the freeze-dried pellets of the ‘602 patent. As discussed in MPEP 2144.06, it is prima facie obvious to substitute art-recognized equivalents known to be useful for the same purpose in the absence of unexpected results. It is also prima facie obvious to select a known material based on its suitability for the intended purpose in the absence of unexpected results (MPEP 2144.07). In this case, the teachings of Piepenburg 2 establish that the T4 gp32 protein and T4 uvsY recombinase loading proteins recited in the claims of the ‘602 patent and the claimed gp32 and uvsY proteins from Rb69 are equivalents useful for the same purpose, and no persuasive evidence of unexpected results has been presented with respect to the inclusion of either of these Rb69 proteins in the claimed freeze-dried pellets. Accordingly, their substitution in the freeze-dried pellets of the ‘602 patent is prima facie obvious.
It also would have been prima facie obvious to select the T6 H66S uvsX recombinase disclosed in Piepenburg 2 for as the uvsX recombinase in the freeze-dried pellets of the ‘602 patent. Since the teachings of Piepenburg 2 also indicate that the claimed T6 uvsX H66S recombinase is a functional equivalent of the uvsX recombinase used in the freeze-dried pellets of the ‘602 patent and no persuasive evidence of unexpected results has been presented concerning the inclusion of this uvsX recombinase in the claimed freeze-dried pellets, this substitution is also prima facie obvious in view of MPEP 2144.06 and 2144.07. Additional motivation is provided by the teaching in Piepenburg 2 that the T6 uvsX H66 recombinase is an improvement relative to T4 uvsX recombinase (Piepenburg 2 at pages 58-59).
Thus, the instant claim 60 is not patentably distinct from the claims of the ‘602 patent in view of Piepenburg 1 and further in view of Piepenburg 2.
Conclusion
13. No claims are currently allowable.
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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/ANGELA M. BERTAGNA/Primary Examiner, Art Unit 1637