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 .
This action is in response to the amendment filed 07/28/2026, in which claims 1 and 24 were amended, claims 6, 16, 17, 22 and 23 were previously presented and claims 8-15 were withdrawn due to a restriction election set forth in a previous Office Action. Claims 1, 6, 16, 17, 22, 23 and 24 are currently under examination.
Applicant’s arguments have been thoroughly reviewed, but are not persuasive for the
reasons that follow. Any rejection and objections not reiterated in this action have been
withdrawn. This action is FINAL.
Response to Amendments - Claim Rejections - 35 USC § 102
The previous rejection of claims 25-28 under 35 U.S.C. 102(a)(1) has been withdrawn in view of Applicant’s cancelation of the claims filed on 07/28/2026.
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.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 1, 16, 17 and 22-24 are rejected under 35 U.S.C. 103 as being unpatentable by Thiaville et al (Proc. Natl. Acad. Sci. U.S.A. 113 (11) E1452-E1459; Cited in a prior Office Action) in view of Kholod et al (Bio Techniques, 31 :2, 322-328; Cited in a prior Office Action). This was a previous rejection mailed in the prior Office Action on 04/26/2026.
Regarding claims 1, 16, 17 and 22-24, Thiaville teaches a plasmid comprising the dpd cluster which functions as a restriction-modification (R-M) system to modify DNA with 7-deazaguanine derivatives like 2′-deoxy-7-amido-7-deazaguanosine (dADG) (Page E1455, Column 2). Thiaville teaches the plasmid was transformed into S. Montevideo WT and YYF3022 strains (Page E1455, Column 2).
Thiaville does not teach a two-plasmid system.
Kholod teaches the development of a co-expression system requires the construction of two plasmids containing compatible replication origins that would yield approximately equal copy numbers of both vectors in the bacterial cells such as E. coli (Page 324, Column 2). Kholod teaches that the two-plasmid system is in order to allow more efficient co-expression and purification of large protein complexes (Page 325, Column 3).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the teachings of Thiaville to include the two-plasmid system as taught by Kholod because Thiaville teaches it is within the ordinary skill in the art to use a plasmid comprising the dpd cluster which functions as a restriction-modification (R-M) system to modify DNA with 7-deazaguanine derivatives like 2′-deoxy-7-amido-7-deazaguanosine (dADG) and Kholod teaches the two-plasmid system in order to allow more efficient co-expression and purification of large protein complexes.
One would have been motivated to make such a modification in order to receive the expected benefit of efficient co-expression and purification of large protein complexes as taught by Kholod.
Claims 1, 6, 16, 17 and 22-24 are rejected under 35 U.S.C. 103 as being unpatentable over Tsai et al (Scientific Reports Vol 7, 8348, Pages 1-13; 2017; Cited in a prior Office Action) as evidenced by Hutinet et al (RNA Biology, Vol. 14, No. 9, Pgs. 1175-1184; 2017; Cited in a prior Office Action) in view of Kasarjian et al (Nucleic Acids Research, 2003, Vol. 31, No. 5 e22, pgs. 1-10; Cited in a prior Office Action) and Kholod et al (Bio Techniques, 31 :2, 322-328; Cited in a prior Office Action). This was a previous rejection mailed in the prior Office Action on 04/26/2026.
Regarding claims 1, 6, 16, 17 and 22-24, Tsai teaches E. coli phage 9g contains the modified base deoxyarchaeosine (dG+) in its genome (Abstract). Tsai teaches the incorporation of the Phage 9g including (dG+) modification into several strains of E. coli bacteria to test for phage restriction activity in vivo (Page 6; Paragraph 1 and Table 1). Tsai teaches the examination for the use of phage 9g DNA as a template in PCR using thermostable DNA polymerases wherein eight sets of PCR primers were synthesized based on phage 9g coding sequences for primase, DNA ligase, DNA polymerase (two subunits/ORFs), and five predicted genes involved in the dG+ synthesispathway, namely GTP cyclohydrolase (GCYH), 6-pyruvoyl-tetrahydropterin synthase (PTPS), glutamine amidotransferase (GAT)-QueC enzyme, QueE-like radical activating enzyme, and archaeosine-tRNA-ribosyltransferase (aTGT, a.k.a. tRNA guanosine transglycosylase) (Page 5, Paragraph 1). Thus, Tsai teaches an E. coli bacteria genetically modified to comprise phage 9g, including a dG+ modification, and encoding archaeosine-tRNA-ribosyltransferase (aTGT, a.k.a. tRNA guanosine transglycosylase) and glutamine amidotransferase (GAT)-QueC enzyme.
Hutinet is only cited to show physical clustering analysis of the 9g phage genome that had revealed that the dpdA gene clustered with a gat-queC homolog, suggesting that G+ might be inserted in this phage (Page 1179, Column 2). This shows that the Tsai’s nucleic acid sequence must include the dpdA gene due to including the gat-QueC homolog.
Tsai does not teach the nucleic acid sequences from the phage within a two-plasmid system to be delivered to either an E. coli or B. subtilis bacterium.
Kasarjian teaches that the subcloning of phage DNA to a plasmid for transfection to a host bacterium, such as an E. coli, is more efficient than transfection of genetic material from the phage to the bacterium specifically in the context of enzyme gene delivery (Page 1, Column 2 and Page 3, Figure 1). Kasarjian teaches subcloning of the phage DNA into a plasmid to be transfected into the bacterium is more efficient due to many bacterial strains not being susceptible to infection by phages commonly used in laboratories (Page 1, Column 2).
Kasarjian does not teach a two-plasmid system.
Kholod teaches the development of a co-expression system requires the construction of two plasmids containing compatible replication origins that would yield approximately equal copy numbers of both vectors in the bacterial cells such as E. coli (Page 324, Column 2). Kholod teaches that the two-plasmid system is in order to allow more efficient co-expression and purification of large protein complexes (Page 325, Column 3).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the teachings of Tsai to include the subcloning of the E. coli phage 9 DNA sequences into a plasmid as taught by Kasarjian because Tsai teaches it is within the ordinary skill in the art to use an E. coli phage 9 to infect an E. coli cell to transduce genetic material comprising a nucleic acid sequence with the dpdA gene clustered with a gat-queC homolog, Kasarjian teaches subcloning of the phage DNA into a plasmid to be transfected into the bacterium is more efficient due to many bacterial strains not being susceptible to infection by phages commonly used in laboratories and Kholod teaches the two-plasmid system in order to allow more efficient co-expression and purification of large protein complexes.
One would have been motivated to make such a modification in order to receive the expected benefit of improved delivery of the desired nucleic acid sequences to the host E. coli bacterium using a two-plasmid system as taught by Kasarjian and Kholod, respectively.
Response to Arguments - Claim Rejections - 35 USC § 103
The previous rejection of claims 1, 16, 17 and 22-24 under 35 U.S.C. 103 as being unpatentable by Thiaville et al (Proc. Natl. Acad. Sci. U.S.A. 113 (11) E1452-E1459) in view of Kholod et al (Bio Techniques, 31 :2, 322-328) has been maintained in view of Applicant’s arguments and amendments to the claims filed on 07/28/2026. Applicant’s arguments have been fully considered but are not found to be persuasive.
Applicant argues a person of ordinary skill in the art would not have looked at Kholod’s protein co-expression platform for guidance in modifying Thiaville’s naturally occurring deazapurine DNA modification system. Applicant continues to argue that the rejection cannot be sustained with mere conclusory statements, and the rejection here supplies no such reasoning connecting the teachings of Thiaville to the particular advantage identified in Kholod. Applicant argues Kholod is aimed at purifying protein-protein complexes and therefore the objective is absent from the DNA modification system of Thiaville, thus the “expected benefit” is unrelated to the claimed invention. Applicant continues to argue that while Kholod proposes that its vectors might enable the large scale production of modified proteins by co-expression of a substrate protein with an enzyme that will modify it, the modification is of a protein substrate; therefore, Kholod provides no suggestion to place a heterologous nucleic acid on a second plasmid, much less to modify the heterologous nucleic acid with deazaguanine bases, nor suggest that a second plasmid should function as a target nucleic acid substrate rather than as a protein-expression vector.
However, the intended uses of the components cited in the prior art references do not negate the teachings that the components within the prior art references. The instantly claimed invention is a product therefore, any product/component taught by the prior art references would therefore teach those specific components of the claimed product. Specifically, Kholod teaching the two-plasmid system for the purpose of purifying protein complexes does not negate that is relied on for teaching that the development of a co-expression system requires the construction of two plasmids containing compatible replication origins that would yield approximately equal copy numbers of both vectors in the bacterial cells such as E. coli (Page 324, Column 2), as well as that the two-plasmid system is in order to allow more efficient co-expression and purification of large protein complexes (Page 325, Column 3). It is the teachings of Kholod that provide the expected benefit of providing the system of Thiaville’s in a two-plasmid co-expression system rather than a single plasmid system. Kholod teaches two-plasmid systems for co-expression wherein the plasmids are heterologous nucleic acids encoding large proteins (Page 2, Columns 2 and 3).
The previous rejection of claims 25-28 under 35 U.S.C. 103 as being unpatentable over Tsai et al (Scientific Reports Vol 7, 8348, Pages 1-13; 2017) as evidenced by Hutinet et al (RNA Biology, Vol. 14, No. 9, Pgs. 1175-1184; 2017) in view of Kasarjian et al (Nucleic Acids Research, 2003, Vol. 31, No. 5 e22, pgs. 1-10) and Kholod et al (Bio Techniques, 31 :2, 322-328) has been withdrawn in view of Applicant’s cancelation of the claims filed on 07/28/2026.
The previous rejection of claims 1, 6, 16, 17 and 22-24 under 35 U.S.C. 103 as being unpatentable over Tsai et al (Scientific Reports Vol 7, 8348, Pages 1-13; 2017) as evidenced by Hutinet et al (RNA Biology, Vol. 14, No. 9, Pgs. 1175-1184; 2017) in view of Kasarjian et al (Nucleic Acids Research, 2003, Vol. 31, No. 5 e22, pgs. 1-10) and Kholod et al (Bio Techniques, 31 :2, 322-328) has been maintained in view of Applicant’s arguments and amendments to the claims filed on 07/28/2026. Applicant’s arguments have been fully considered but are not found to be persuasive.
Applicant argues neither Tsai nor Hutinet discloses a bacterium comprising a first plasmid encoding a transglycosidase and an amindotransferase and a second plasmid comprising a heterologous nucleic acid. Applicant continues to argue that Kasarjian only teaches merely tools used to evaluate restriction activity and Kholod, as discussed above, teaches the use of two protein-expression vectors that express separate proteins within the same bacterial cell. Applicant argues that a person of ordinary skill in the art would not have looked to Kasarjian’s restriction-assay plasmids or Kholod’s protein co-expression platform for guidance in modifying the naturally occurring phage systems as described in Tsai and Hutinet; therefore, the rejection here supplies no reasoning connecting the teachings of Tsai and Hutinet to objectives identified in Kasarjian and Kholod, much less why a person of ordinary skill in the art would have combined those teachings to arrive at the specific two-plasmid architecture. Applicant continues to argue that the cited art is directed to different technologies that have different objectives, and the Office has not articulated why a person of ordinary skill in the art would have expected any benefit from combining these disparate teachings to create a bacterium comprising a first plasmid encoding a transglycosidase and an amidotransferase and a second plasmid comprising a heterologous nucleic acid. Applicant argues that while Kasarjian may teach that phage DNA fragments can be cloned into plasmids and Kholod may teach that two plasmids may coexist within the same bacterial cell, neither reference suggests that a second plasmid should serve as a heterologous nucleic acid substrate for modification by a transglycosidase/amidotransferase system, additionally, nor does Tsai or Hutinet provide any suggestion that their naturally occurring phage system should be re-engineered into the specific two-plasmid architecture.
However, the intended uses of the components cited in the prior art references do not negate the teachings that the components within the prior art references. The instantly claimed invention is a product therefore, any product/component taught by the prior art references would therefore teach those specific components of the claimed product. Specifically, Tsai is not recited in the rejection to teach the entirety of the claimed invention. Tsai is relied on for teaching an E. coli phage 9g contains the modified base deoxyarchaeosine (dG+) in its genome (Abstract). Tsai teaches the incorporation of the Phage 9g including (dG+) modification into several strains of E. coli bacteria to test for phage restriction activity in vivo (Page 6; Paragraph 1 and Table 1). Tsai teaches the examination for the use of phage 9g DNA as a template in PCR using thermostable DNA polymerases wherein eight sets of PCR primers were synthesized based on phage 9g coding sequences for primase, DNA ligase, DNA polymerase (two subunits/ORFs), and five predicted genes involved in the dG+ synthesispathway, namely GTP cyclohydrolase (GCYH), 6-pyruvoyl-tetrahydropterin synthase (PTPS), glutamine amidotransferase (GAT)-QueC enzyme, QueE-like radical activating enzyme, and archaeosine-tRNA-ribosyltransferase (aTGT, a.k.a. tRNA guanosine transglycosylase) (Page 5, Paragraph 1). Thus, Tsai teaches an E. coli bacteria genetically modified to comprise phage 9g, including a dG+ modification, and encoding archaeosine-tRNA-ribosyltransferase (aTGT, a.k.a. tRNA guanosine transglycosylase) and glutamine amidotransferase (GAT)-QueC enzyme. In addition, Hutinet was only cited as evidence to show that physical clustering analysis of the 9g phage genome that had revealed that the dpdA gene clustered with a gat-queC homolog, suggesting that G+ might be inserted in this phage. Kasarjian is recited as teaching that the subcloning of phage DNA to a plasmid for transfection to a host bacterium, such as an E. coli, is more efficient than transfection of genetic material from the phage to the bacterium specifically in the context of enzyme gene delivery (Page 1, Column 2 and Page 3, Figure 1). Finally, Kholod is recited for teaching the two-plasmid system for the purpose of purifying protein complexes does not negate that is relied on for teaching that the development of a co-expression system requires the construction of two plasmids containing compatible replication origins that would yield approximately equal copy numbers of both vectors in the bacterial cells such as E. coli (Page 324, Column 2), as well as that the two-plasmid system is in order to allow more efficient co-expression and purification of large protein complexes (Page 325, Column 3). It is the teachings of Kholod that provide the expected benefit of providing the system of Tsai’s in a two-plasmid co-expression system rather than a single plasmid system. Kholod teaches two-plasmid systems for co-expression wherein the plasmids are heterologous nucleic acids encoding large proteins (Page 2, Columns 2 and 3). Thus, in combination, one of ordinary skill of the art would have been motivated to combine the teachings of Tsai as evidenced by Hutinet in view of Kasarjian and Kholod to reach the claimed invention.
Thus, Applicant’s arguments are not found to be persuasive, and the previous rejections have been maintained.
Conclusion
No claims are allowed.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ALEXANDRA ROSE LIPPOLIS whose telephone number is (703)756-5450. The examiner can normally be reached Monday-Friday, 8:00am to 5:00pm EST.
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/ALEXANDRA ROSE LIPPOLIS/Examiner, Art Unit 1637
/CELINE X QIAN/Primary Examiner, Art Unit 1637
