FINAL ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
This action is responsive to the Amendment and Response filed 08 December 2025. Claims 8-9 and 11-12 have been amended. Claims 1-4, 8-9, 11-14, 17, 20, 22-24, 27, 29-31, and 34 remain under consideration. Applicant’s amendments and arguments have been thoroughly reviewed, and have overcome the following objections/rejections set forth in the prior Office action:
The objection related to a missing SEQ ID NO on page 58 of the specification; and
The rejections of claims 8-9 and 11-14 under 35 USC 103 (as all of these claims now require the combination a reporter switch and kill switch as specified in claim 14, and Applicant’s arguments regarding the combination of Popp et al and Pearce et al at pages 12-14 of the Response have been found persuasive regarding the nonobviousness of such sensor constructs).
Claim 14 is objected to (see paragraph 5 below), while claims 1-4, 8-9, 11-13, 17, 20, 22-24, 27, 29-31, and 34 remain rejected for the reasons given below, which include new grounds of rejection necessitated by Applicant’s amendments. It is noted that the prior Office action of 08 September 2025 contained a typographical error in the original statement of rejection in paragraph 9; the examiner regrets any confusion caused by this typographical error, which resulted from insertion of an incorrect form paragraph (however the grounds of rejection as set forth in the body of the rejection remain unchanged, and therefore the rejection has been made final). Any rejections and/or objections not reiterated in this action have been withdrawn. This action is FINAL.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Allowable Subject Matter
Claim 14 is objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims. It is reiterated that Applicant’s arguments regarding the prior rejection of the claim under 35 USC 103 were found persuasive; see above.
Claim Rejections - 35 USC § 112(d)/fourth paragraph
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
THE FOLLOWING ARE NEW GROUNDS OF REJECTION NECESSITATED BY APPLICANT’S AMENDMENTS:
Claims 8-9 and 11-13 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, because these claims have been amended to depend from a following claim (claim 14), and therefore fail to “contain a reference to a claim previously set forth”, as required by 35 U.S.C. 112(d). It is noted that claim 13 does not directly depend from claim 14, but is rejected herein because it depends from claim 12 (which as amended now depends from claim 14). Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim Rejections - 35 USC § 103
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.
Claim(s) 1-4, 17, and 20 remain rejected under 35 U.S.C. 103 as being unpatentable over Popp et al (Scientific Reports 7:15058, 13 pages [Nov 2017]; previously cited).
Independent claim 1 remains drawn to a “cell-based DNA sensor comprising a competent cell comprising a genetic circuit, wherein the genetic circuit comprises:”
-a “pair of homology arms in a DNA strand, wherein the homology arms comprise” first and second arms homologous to first and second portions of a target DNA, with the first and second arms being ‘separated within the DNA strand by an interstitial region of the DNA strand”; and
at least one of “a reporter switch and a kill switch”, wherein:
the reporter switch “comprises a reporter gene and a negative regulator of the reporter gene, wherein the reporter gene comprises a promoter and a coding sequence that are not comprised within the interstitial region of the DNA strand, and wherein the negative regulator of the reporter gene is comprised within the interstitial region”; and
the kill switch “comprises one or more genetic elements configured for inhibiting growth of the competent cell, wherein at least one of the one or more genetic elements is comprised within the interstitial region”.
With regard to the boundaries of claim 1, it is again noted that: a) only “at least one of” the recited “reporter switch” and “kill switch” are required; and b) no set boundaries are provided (either in the claim itself or, e.g., via a limiting definition in the specification) for the recited “interstitial region”, such that while this “interstitial region” must be located between the first and second arms, the claim does not require that only the “interstitial region” be so located. Additionally, it is noted that the specification does not provide any kind of limiting definition for “cell-based DNA sensor” beyond what is stated in the claim regarding the required components of a “competent cell comprising a genetic circuit”, such that the claim requires “a competent cell comprising a genetic circuit”, where the genetic circuit meets the requirements set forth in the claims.
Popp et al teach a variety of “genetic building blocks” , including new integrative vectors, adapted for use with B. subtilis (see entire reference, particularly the Abstract). Among the vectors taught by Popp et al are multiple vectors including the inducible promoter PxylA “in combination with its repressor xylR (xylR-PxylA)”, further teaching that “the xylA promoter responds to xylose by de-repressing the native regulator XylR” (see page 2 at the final paragraph, bridging to page 3). Popp et al illustrate such a vector in Figure 2 (page 6), particularly in panels A and B, where such a construct – with PxylA located upstream of a coding sequence for red fluorescent protein, and downstream of (oppositely oriented) xylR – is flanked by lacA’ and ‘lacA homology arms (it is noted that the legend of Figure 1 at page 5 teaches that boxes as are depicted in Figure 6 for lacA “represent flanking homology regions used as integrate sites for double homologous recombination into the B. subtilis chromosome” (see both Figure 1 and 2, as well as the descriptions of Table 1). It is noted that this construct of Popp et al meets the requirements of the ‘genetic circuit” of claim 1 with regard to the embodiment of a circuit including a “reporter switch” (as it is again noted that specific boundaries for the “interstitial region” are not provided). While Popp et al do not necessarily disclose a “competent cell” including this particular construct, they do teach that B. subtilis has the ”ability to become naturally competent” (page 2, lines 1-3), and it is noted that the specification provides B. subtilis as an example of preferred cell type for this reason (see, e.g., paragraph 31 of the corresponding published application). Further, Popp et al teach that use of their constructs involves transformation of bacteria such as B. subtilis (as well as E. coli), i.e., procedures that employ competent cells (page 11).
With regard to the benefits of their constructs, Popp et al teach that they have provided “a powerful and stand-alone collection of standardized genetic parts, all adhering to the BioBrick cloning standards”, allowing for genetic modification of B. subtilis “for performing a large variety of different experiments” (page 10, top paragraph).
In view of the teachings of Popp et al, 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 have prepared a competent B. subtilis cell comprising a construct as depicted in Figures 2A and B of Popp et al, and thereby to have prepared a “cell-based DNA sensor” meeting the requirements of claim 1. An ordinary artisan would have been motivated to have prepared such a cell for the benefits taught by Popp et al, i.e., of facilitating any of a variety of experiments of interest to a practitioner, using genetic parts meeting BioBrick cloning standards.
With further regard to dependent claim 2, it is reiterated that Popp et al teach that xylR is a repressor of PxylA. Regarding claim 3, red fluorescent protein (RFP) as disclosed by Popp et al meets the requirement of a fluorescent protein gene. Regarding claim 4, XylR also meets the requirement of constituting a negative regulator of a selectable marker. Regarding claim 17, it is an inherent property the lacA’ and ‘lacA homology “arms” of the construct of Popp et al that they are homologous to native/naturally occurring lacA target sequences (which meets the requirements of the claim). With regard to claim 20, Popp et al also teach evaluating and comparing fluorescence of different cells – which are demonstrated by Popp et al as exhibiting “detectably different” fluorescence – in a common 96 well plate, which meets the requirement of a “composition” comprising multiple cell types as taught by Popp et al (see, e.g., page 6 [starting at the last paragraph] – page 9, including Figure 5, and page 11). Popp et al thus suggest preparing any of a variety of compositions meeting the requirements of the claim, for the benefit of evaluating and comparing constructs, fluorescent reporters, etc., based on the interests of a practitioner, and providing the benefit of allowing accurate comparisons (via the use of a common plate/composition).
The reply of 08 December 2025 traverses the rejection on the following grounds.
Applicant argues that Popp et al do not teach a configuration of reporter gene and negative regulator thereof meeting the requirements of the claims, urging that the entire region located between lacA’ and ‘lacA must be considered as the interstitial region, and that therefore Popp et al “fails to teach a reporter gene not included in an interstitial region separating a first homology arm and a second homology arm as recited in the claims” (Reply page 7 to page 8). Applicant urges that the broadest reasonable interpretation (BRI) of the claims relied upon in the Office action “is inconsistent with the usage of the claim terms in the specification and drawings as well as the ordinary and customary meanings of such terms”, noting that the specification “defines the interstitial region as being ‘formed’ by the spacing of the homology arms”, referring to the specification at page 12, lines 6-11, and arguing that it “would not make sense to say that the spacing of the homology arms ‘forms’ the interstitial region if the interstitial region did not take up the entire space between the homology arms and other regions were included therebetween” (Reply page 9). The Reply further argues that this definition of interstitial region ‘is consistent with the recitation of the interstitial region in the claims as ‘separating’ the homology arms”, urging that the term “separating” and grammatical variants thereof “is clearly used in the specification to indicate a full span between two homology sequences”, referring to the specification at page 12 lines 15-22 (Reply page 9), and further arguing that the usage of the term “separate” in the specification is consistent with its ordinary and customary meaning (for which a dictionary definition has been provided)(Reply page 10). Next, Applicant urges that an “interpretation of ‘interstitial region’ as not spanning the entire distance between the homology arms….is not only inconsistent with the specification and claims…but also renders the disclosed embodiments inoperable”, as operability of these embodiments “relies on the excision of elements ‘within the interstitial region’ in the presence of a homologous target while leaving behind elements ‘not comprised within the interstitial region’ to permit detection and/or selection” (Reply pages 10-11). Finally, the Reply asserts that “the Office Action’s interpretation of ‘interstitial region’ as constituting one of several nondemarcated, functionally irrelevant…sub-portions between the homology arms is completely arbitrary, and finds no support in the specification or cited prior art” (Reply page 11).
These arguments have been thoroughly considered but are not persuasive.
Regarding Applicant’s argument that the entire region located between lacA’ and ‘lacA of Popp et al’s constructs must be considered as “the interstitial region”, and that constructs as taught by Popp et al are thus not encompassed by the BRI of the claims, it is reiterated that the specification does not in fact define “interstitial region” in the manner urged by Applicant (although the embodiment discussed throughout Applicant’s arguments is certainly embraced by the claims, and is a disclosed preferred embodiment of the invention). Several terms are defined in the specification – for example, “competent cell” (page 10), “homologous” and “homology” (page 12), “sequence identity” (page 13), “gene” (page 14), etc. – however, a similar type of definition is not provided for the term(s) “interstitial” and/or “Interstitial region”. Applicant refers to multiple statements on page 12 of the specification, the first of which states:
The homology arms in each pair are configured to excise a portion of DNA from the DNA strand through homologous recombination with a target DNA. To perform this function, the homology arms are spaced apart on the DNA strand to form an interstitial region therebetween and together have homology to one or more homologous sequences in the target DNA. Homologous recombination of the homology arms with the target DNA thereby excises the interstitial region from the DNA strand.
While this language clearly embraces embodiments in which the entire region between homology arms is considered an “interstitial region”, this is not a requirement based on this language of the specification; rather, the “homology arms” must be “spaced apart on the DNA strand to form an interstitial region therebetween and together have homology to one or more homologous sequences” in target DNA. The examiner agrees that regions not bound by the “homology arms” cannot reasonably be considered as within the “interstitial region”; however, Applicant’s argument that “interstitial region” is equivalent to the entirety of the region located within the homology arms is not consistent with Applicant’s disclosure. Lacking a provided limiting definition for “interstitial” or “interstitial region” in the specification, a standard dictionary definition of the term “interstitial” may be relied upon; such a definition (Merriam-Webster) has been cited herein, which states that one meaning of “interstitial” is: “occurring in or being an interval or intervening space or segment”. Based on this definition, the examiner’s interpretation of “interstitial” as meaning “occurring in….an interval or intervening space or segment” is reasonable and is within the BRI of what is claim (whereas Applicant is effectively arguing that the claims must be limited to the meaning “being an interval or intervening space or segment”, without this limiting definition having been provided in the original disclosure).
Regarding Applicant’s arguments pertaining to the claim language “the first homology arm and the second homology arm are separated within the DNA strand by an interstitial region of the DNA strand”, and the general meaning of the term “separating” and grammatical variants thereof, such homology arms may be separated by an “interstitial region” without the entirety of the sequence located between the arms necessarily corresponding to the “interstitial region”; again, while such a preferred configuration/embodiment is clearly embraced by the claim language, there are multiple embodiments embraced by the actual claim language. Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993). It is also noted that the portion of the specification cited in the Reply at page 9 bridging to page 10 (specification page 12, lines 15-22) is referencing homologous sequences in the target DNA, not the homology arms of the DNA strand of the sensor (and further, various embodiments of the target DNA are discussed on page 12, including both embodiments in which the homology arms “are homologous to a single, continuous sequence in the target DNA” as well as “to two separated sequences”, etc.; this discussion of different types of target DNAs does not support a more limited interpretation of the term “interstitial region”).
Regarding Applicant’s arguments that the operability of the invention relies on a configuration in which the “interstitial region” spans “the entire distance between the homology arms”, which arguments focus on a requirement for excision of some elements (and “non-excision” of others) to achieve detection/selection, it is noted that the claims under consideration are directed to products (which are not limited to any particular use/application); while such arguments could potentially be persuasive with regard to methods requiring, e.g., use/functioning of the recited products in a particular way, the teaching of the cited art are sufficient to meet all of the present requirements of the products actually claimed.
Finally, regarding Applicant’s assertion that the Office action interprets interstitial region as encompassing, e.g., “several nondemarcated, functionally irrelevant…sub-portions”, etc., this is simply not the case; the term “interstitial region” has been interpreted in a manner consistent with Applicant’s actual disclosure, as well as a standard definition of the term “interstitial”. This interpretation is not arbitrary, nor does the rejection suggest that the interstitial region is “nondemarcated” (on the contrary, the claims have been interpreted as requiring an “interstitial region” that is bound by first and second homology arms, consistent with the language of the claims as well as the guidance in the original disclosure).
Claim(s) 22-24, 27, 29-31, and 34 remain rejected under 35 U.S.C. 103 as being unpatentable over Popp et al as applied to claims 1-4, 17, and 20, above, and further in view of Hammond et al (GB2563577 [26 December 2018]; previously cited).
The teachings of Popp et al are set forth above. While Popp et al teach competent cells comprising constructs meeting the requirements of independent claim 1, Popp et al do not teach methods meeting the requirements of the instant claims.
Hammond et al teach methods for selection and characterization of genetically transformed cells, which Hammond et al state has particular relevance to such activities with regard to “genetic circuits…that have been inserted into transformed cells” (i.e., cells of the type suggested by the teachings of Popp et al, as discussed above); see entire reference, particularly page 1. Hammond et al teach that such cells comprising genetic circuits “are designed with a specific purpose in mind and have to be tested, or characterized, to ensure the transformed cell responds as intended”, noting that such characterization “usually involves exposing the transformed cells to one or more analytes and/or conditions that trigger a desired response from the genetic circuit” (page 1). To address the labor intensive nature of manually performing the required testing, Hammond et al propose an apparatus and methods for screening transformed cells, including cells comprising multiple reporters (including fluorescent or luminescent markers) for measurement (see pages 2-5, as well as page 9 and 16-17). Hammond et al also disclose methods in which transformed and untransformed cells are mixed, with the transformed cells comprising “a genetic design to be tested”, which methods may include incubating/growing the cells together (as well as testing) (see, e.g., pages 5-7). With particular regard to claims 25 and 31, it is noted that Hammond et al teach that bacterial cells are a preferred embodiment (see, e.g., page 19). With further regard to claim 22 and claims dependent therefrom, as well as claim 30, it is noted that growth/culturing (including without lysis) is taught at, e.g., pages 15, 18; Figures 1-2). With further regard to claims 27 and 34, it is reiterated that Hammond et al teach the use multiple cells (or a single cell) comprising multiple different reporters are taught at, e.g., pages 5-7, 9, 16-17). With regard to “detection”, it is also noted that Hammond et al teach that their methods achieve detection, such as via the detection of fluorescent or luminescent markers, as noted above.
In view of the teachings of Hammond et al, 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 have performing testing on the competent cells suggested by Popp et al (including multiple such cells) via the methods taught by Hammond et al, and thereby to have performed methods meeting the requirements of claims 22-24, 27, 29-31, and 34. An ordinary artisan would have been motivated to have performed such testing in this manner by Hammond et al’s teachings that their methods allow for more rapid characterization and analysis of cells of the type taught by Popp et al as compared to traditional methods. Further, given the detailed guidance provided by Hammond et al, an ordinary artisan would have had a reasonable expectation of success in performing the testing as taught by Hammond et al on any of the cells/constructs taught and/or suggested by Popp et al.
The reply of 08 December 2025 traverses the rejection on the following grounds.
First, Applicant states that the rejection is traversed for the same reasons that the rejection over Popp et al was traversed (which reasons are summarized above) (Response page 15); the response to those arguments set forth above therefore applies equally herein. Second, the rejection is traversed on the grounds that the Office action “has not provided any reasoning or described with any particularity how the constructs and cells of Popp et al could be used in the apparent detection methods of Hammond et al” (Response page 15). This argument has been thoroughly considered but is not persuasive. As set forth in the rejection itself, Hammond et al teach improved methods for selection and characterization of genetically transformed cells, and an ordinary artisan would have been motivated to have tested constructs/competent cells such as those of Popp et al via the methods of Hammond et al simply for the benefit of performing rapid characterization and analysis of cells of the type as taught by Popp et al (rather than, e.g., a traditional, more time consuming type of characterization). Claim 22 and claims dependent therefrom broadly encompass any “detecting target DNA with the cell based DNA sensor” comprising culturing and detecting, while claim 29 and claims dependent therefrom broadly encompass analogous methods to detect a “target cell”; as any methods in which such a “culturing” and “detecting” as recited are performed are embraced by the claims, the teachings of the cited art are sufficient to suggest what is claimed.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/DIANA B JOHANNSEN/Primary Examiner, Art Unit 1682