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 01/30/2026, in which claims 1, 6, 16 and 17 were previously presented, claims 18-21 were canceled and claims 22-28 were newly added. Claims 1, 6, 16, 17 and 22-28 are currently pending.
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withdrawn.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 Non-FINAL.
Oath/Declaration
Acknowledgement is made of the Declaration filed on 01/30/2026. The declaration is found to be proper and therefore, entered.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 25-28 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Thiaville et al (Proc. Natl. Acad. Sci. U.S.A. 113 (11) E1452-E1459). This is a NEW Rejection necessitated by the amendment filed by Applicant on 01/30/2026.
Regarding claims 25-28, 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).
Response to Amendments - Claim Rejections - 35 USC § 102
The previous rejection of claims 1, 6 and 16-21 under 35 U.S.C. 102(a)(1) has been withdrawn in view of Applicant’s filing of the declaration of 01/30/2026.
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. 102(a)(1) as being anticipated 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). This is a NEW Rejection.
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 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 22-28 are rejected 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). This is a NEW rejection.
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 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 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.
Regarding claims 25-28, 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+ synthesis pathway, 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).
Hutinet is only cited to show physical clustering analysis of the 9g phage genome 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 plasmid 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).
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 and 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.
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 as taught by Kasarjian.
Response to Arguments - Claim Rejections - 35 USC § 103
The previous rejection of claims 1, 6 and 16-21 under 35 U.S.C. 103 as being unpatentable has been withdrawn and rewritten in view of Applicant’s arguments and amendments to the claims filed on 01/30/2026.
Conclusion
No claims are allowed.
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/ALEXANDRA ROSE LIPPOLIS/Examiner, Art Unit 1637
/CELINE X QIAN/Primary Examiner, Art Unit 1637
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