DETAILED ACTION
Status of Application
The response and amendments filed 19 September 2025 are acknowledged and have been considered in their entireties. Claims 1-2, 4-5 and 7-17 remain pending and claims 9-11 remain withdrawn from further consideration as being drawn to a nonelected species. Thus, claims 1-2, 4-5, 7-8 and 12-17 are subject to examination on the merits.
Maintained Rejection – Necessitated by Amendments
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.
Claim(s) 1-2, 4-5, 7-8 and 12-17 are rejected under 35 U.S.C. 103 as being unpatentable over Chong et al. (Bioresource and Bioprocessing, 2019 – cited previously) in view of Swarts et al. (Nat. Struct. Mol. Biol., 2014 – cited previously), Wu et al. (J. Adv. Res., 2020 – cited previously), Smallheiser & Gomes (Biology Direct, 2015 – cited previously, hereafter Smallheiser) and the sequence deposited as Uniprot G2QEV0 (See attached and https://www.uniprot.org/uniprotkb/G2QEV0/entry - cited previously).
Chong et al. teach the characterization of a recombinant thermotolerant Argonaute protein by recombinantly expressing said protein, testing which 16bp guides (which are complementary to target nucleotide sequences) said protein utilizes inclusive of 5'-Phosphorylated ssDNA, 5'-hydroxylated ssDNA, and 5'-Phosphorylated ssRNA (wherein it is taught it capable of using them all), and testing the argonaute protein’s substrate cleaving activity on both target RNA and DNA sequences. The temperature, time, and concentration of divalent cations and reaction conditions are all also tested to ascertain the most optimal results for activity (See Methods). For example, a concentration range of divalent cations from 0.005 to 2.5mM, of Fe2+, Co2+, Ni2+, Cu2+, Zn2+, Mg2+, Mn2+ and Ca2+ are all tested to see which afforded the Argonaute protein the most optimal endonuclease activity (manganese/Mn2+ afforded the highest enzymatic activity); and a temperature range for optimal activity is also tested (55 to 95 oC). Chong et al. state: “Therefore, exploring argonaute proteins with unique enzyme properties is desired for understanding their diverse catalytic mechanisms and promoting their applications in biotechnology.” – See Abstract, Background. Chong et al. teach ratios of the Ago protein to gRNA/DNA to target RNA/DNA of 3.125:2.5:1 for activity assays and 2.5:2:1 for temperature assays which are tested at a requisite temperature in a reaction buffer that comprises a solution of divalent metal cations of MnCl2 (this equates to Ago:target:guide of 3.125:1:2.5 and 2.5:1:2 as per the current claim construction) – See pp. 6-7.
Chong et al., however, do not teach the characterization of eukaryotic Argonaute proteins for target DNA cleavage, specifically one comprising SEQ ID NO: 1, nor utilizing temperatures of 37 oC (claim 1/14) nor a molar ratio of Ago:target:guide of 5:1:2.
Swarts et al. teach “….the Ago protein is the key player in eukaryotic RNA interference (RNAi) pathways (Box 1), in which Ago utilizes short 5′-phosphorylated RNA guides to target complementary RNA transcripts. The Ago proteins belong to the PIWI protein superfamily, defined by the presence of a PIWI (P element–induced wimpy testis) domain. In addition, all eAgos feature an N (N-terminal) domain, a PAZ (PIWI-Argonaute-Zwille) domain and a MID (middle) domain, along with two domain linkers, L1 and L2 (Fig. 1 and Box 2).” – See p. 1, 1st paragraph. And: “Despite low sequence similarity between pAgos and eAgos (12% identity between various pAgos and hAGO2), their structural and functional features are remarkably similar (Box 2).” – See p. 5, 2nd paragraph.
Wu et al. teach (See abstract)
“Argonaute proteins are highly conserved in almost all organisms. They not only involve in the biogenesis of small regulatory RNAs, but also regulate gene expression and defend against foreign pathogen invasion via small RNA-mediated gene silencing pathways. As a key player in these pathways, the abnormal expression and/or mis-modifications of Argonaute proteins lead to the disorder of small RNA biogenesis and functions, thus influencing multiply biological processes and disease development, especially cancer. In this review, we focus on the post-translational modifications and novel functions of Argonaute proteins in alternative splicing, host defense and genome editing.”
And (Concluding remarks):
a comprehensive understanding the functions of Argonaute proteins will help us better reveal and explore the causes of disease development. Meanwhile, it is expected to discover more Argonaute proteins with genome-editing functions in
future, which will bring the gospel to the treatment of human genetic diseases.
Smallheiser teaches the general consensus that eAgo only bind and utilize RNA without also considering its role and interaction with DNA has been naïve (See Abstract, and p. 2, 1st col., last paragraph). They present several lines of reasoning as to why those skilled in the art should be testing eAgo for interactions with both RNA and DNA (See Abstract, Evidence for interactions of Argonaute with DNA and DNA-like nucleic acids, p. 2). Their conclusory remarks are that they predict that the field of eukaryotic Ago-DNA binding and functions, which has not existed previously, has the potential to rise and become prominent in the near future. Their rationale for this is as follows.
It is stated (Evidence for interactions of Argonaute with DNA and DNA-like nucleic acids, p. 2):
Over the past decade, eukaryotic Argonaute proteins have shown a steady increase in the number of its well documented protein and RNA binding partners, its subcellular locales and its biological functions [6,7]. Not only does Ago interact with a variety of classes of short RNAs [6], it binds longer structured ncRNAs such as pre-miRs and certain tRNAs, as well as single stranded RNAs [8,9]. In fact, Ago can bind directly to mRNAs [10] and can inhibit protein translation even in the absence of RNA guide strands, e.g. when tethered to the mRNA [11] or when using Smaug as a protein-based guide [12].
It is not absurd to wonder if eukaryotic Ago might interact with DNA as well, since isolated domains of Argonaute proteins do bind DNA in the test tube. For example, the human Ago2 MID domain, which binds to the 5′ end of small RNAs, shows no strong binding preference towards the sugar conformation in the nucleic acids. RNA and DNA have comparable dissociation constants (Kd =35 μM for DNA, 53 μM for RNA) [13]. In addition, the crystal structure of human Ago2 reveals that it does not have any direct hydrogen bonds to the 2′ hydroxyl groups of the guide strand for RNA recognition, which may explain why DNA bases and 2′ fluoro substitutions are well tolerated in the antisense strand of siRNAs [14]. Drosophila melanogaster Ago2 has similar binding affinity to 21nt ssDNA and ssRNA of the same sequence, and recognizes 21 bp dsDNA [15,16]. The PAZ domain of D. melanogaster Ago1 shows binding to 26 nt ssDNA, albeit with lower affinity than to the equivalent ssRNA sequence [17].
The sequence of instant SEQ ID NO: 1 is known and has 100% identity to that of deposited as G2QEV0_MYCTT/THET4 (See Supplemental Content, 20230501_105802_us-18-172-482-1.align50.rup file, Result #1 and reproduced below; as well as the UniProt deposit G2QEV0_MYCTT cited previously) and encoded by nucleotide sequence having 100% identity to SEQ ID NO: 3 (See Supplemental Content, 20230501_110025_us-18-172-482-3.n2p50.rup file, Result #1). It is clear that the protein, while it appears to not have been previously isolated, has been identified as being an Argonaute protein with a PIWI domain and is from the thermophilic biomass-degrading fungi formerly called Myceliophthora thermophila (MYCTT) and presently called Thermothelomyces thermophilus (THET)
RESULT 1
G2QEV0_MYCTT
ID G2QEV0_MYCTT Unreviewed; 1082 AA.
AC G2QEV0;
DT 16-NOV-2011, integrated into UniProtKB/TrEMBL.
DT 16-NOV-2011, sequence version 1.
DT 22-FEB-2023, entry version 48.
DE RecName: Full=Piwi domain-containing protein {ECO:0000259|PROSITE:PS50822};
GN ORFNames=MYCTH_2306810 {ECO:0000313|EMBL:AEO58979.1};
OS Myceliophthora thermophila (strain ATCC 42464 / BCRC 31852 / DSM 1799)
OS (Sporotrichum thermophile).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina; Sordariomycetes;
OC Sordariomycetidae; Sordariales; Chaetomiaceae; Thermothelomyces.
OX NCBI_TaxID=573729 {ECO:0000313|EMBL:AEO58979.1, ECO:0000313|Proteomes:UP000007322};
RN [1] {ECO:0000313|EMBL:AEO58979.1, ECO:0000313|Proteomes:UP000007322}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 42464 / BCRC 31852 / DSM 1799
RC {ECO:0000313|Proteomes:UP000007322};
RX PubMed=21964414; DOI=10.1038/nbt.1976;
RA Berka R.M., Grigoriev I.V., Otillar R., Salamov A., Grimwood J., Reid I.,
RA Ishmael N., John T., Darmond C., Moisan M.-C., Henrissat B., Coutinho P.M.,
RA Lombard V., Natvig D.O., Lindquist E., Schmutz J., Lucas S., Harris P.,
RA Powlowski J., Bellemare A., Taylor D., Butler G., de Vries R.P.,
RA Allijn I.E., van den Brink J., Ushinsky S., Storms R., Powell A.J.,
RA Paulsen I.T., Elbourne L.D.H., Baker S.E., Magnuson J., LaBoissiere S.,
RA Clutterbuck A.J., Martinez D., Wogulis M., de Leon A.L., Rey M.W.,
RA Tsang A.;
RT "Comparative genomic analysis of the thermophilic biomass-degrading fungi
RT Myceliophthora thermophila and Thielavia terrestris.";
RL Nat. Biotechnol. 29:922-927(2011).
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DR EMBL; CP003005; AEO58979.1; -; Genomic_DNA.
DR RefSeq; XP_003664224.1; XM_003664176.1.
DR AlphaFoldDB; G2QEV0; -.
DR SMR; G2QEV0; -.
DR STRING; 78579.XP_003664224.1; -.
DR GeneID; 11513933; -.
DR KEGG; mtm:MYCTH_2306810; -.
DR VEuPathDB; FungiDB:MYCTH_2306810; -.
DR eggNOG; KOG1041; Eukaryota.
DR HOGENOM; CLU_004544_4_1_1; -.
DR InParanoid; G2QEV0; -.
DR OrthoDB; 3060088at2759; -.
DR Proteomes; UP000007322; Chromosome 4.
DR GO; GO:0003676; F:nucleic acid binding; IEA:InterPro.
DR CDD; cd02846; PAZ_argonaute_like; 1.
DR CDD; cd04657; Piwi_ago-like; 1.
DR Gene3D; 3.40.50.2300; -; 1.
DR Gene3D; 2.170.260.10; paz domain; 1.
DR Gene3D; 3.30.420.10; Ribonuclease H-like superfamily/Ribonuclease H; 1.
DR InterPro; IPR014811; ArgoL1.
DR InterPro; IPR032472; ArgoL2.
DR InterPro; IPR032474; Argonaute_N.
DR InterPro; IPR036085; PAZ_dom_sf.
DR InterPro; IPR003165; Piwi.
DR InterPro; IPR045246; Piwi_ago-like.
DR InterPro; IPR012337; RNaseH-like_sf.
DR InterPro; IPR036397; RNaseH_sf.
DR PANTHER; PTHR22891:SF174; ARGONAUTE-1, ISOFORM A; 1.
DR PANTHER; PTHR22891; EUKARYOTIC TRANSLATION INITIATION FACTOR 2C; 1.
DR Pfam; PF08699; ArgoL1; 1.
DR Pfam; PF16488; ArgoL2; 1.
DR Pfam; PF16486; ArgoN; 1.
DR Pfam; PF02171; Piwi; 1.
DR SMART; SM01163; DUF1785; 1.
DR SMART; SM00950; Piwi; 1.
DR SUPFAM; SSF101690; PAZ domain; 1.
DR SUPFAM; SSF53098; Ribonuclease H-like; 1.
DR PROSITE; PS50822; PIWI; 1.
PE 4: Predicted;
KW Reference proteome {ECO:0000313|Proteomes:UP000007322}.
FT DOMAIN 728..1049
FT /note="Piwi"
FT /evidence="ECO:0000259|PROSITE:PS50822"
FT REGION 1..99
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 191..225
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 1082 AA; 118184 MW; 40E540714FF060D8 CRC64;
Query Match 100.0%; Score 5691; DB 16; Length 1082;
Best Local Similarity 100.0%;
Matches 1082; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MSDSRGRGYGGGRGGGRGGRGGQAGEGFRGGGGRGGYPGGGRGGGDGYRGGRGGGGGEFR 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MSDSRGRGYGGGRGGGRGGRGGQAGEGFRGGGGRGGYPGGGRGGGDGYRGGRGGGGGEFR 60
Qy 61 GGRGGRGDFRGGRGGGGRGGRGGYGGSGPDVFLGAGPSIPAPDAAVTELEDRWIEKHGIQ 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 GGRGGRGDFRGGRGGGGRGGRGGYGGSGPDVFLGAGPSIPAPDAAVTELEDRWIEKHGIQ 120
Qy 121 SRTTGASELESKMADLSLGTISMPKRPGFGTGGNPVVLWANYFNVNLKLGAVYRYDLRVI 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 SRTTGASELESKMADLSLGTISMPKRPGFGTGGNPVVLWANYFNVNLKLGAVYRYDLRVI 180
Qy 181 SKKLTKEQDDALSKQQESASKKAKGKPKQASGQQPNAPKDAREAKGKKLSEVIKLALDRL 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 SKKLTKEQDDALSKQQESASKKAKGKPKQASGQQPNAPKDAREAKGKKLSEVIKLALDRL 240
Qy 241 PGEPAIA TEYKQQLVTTEKLQVPPDGLMQVELAEPGRNPETWYVRFDGPSSINIAGLMDY 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 PGEPAIA TEYKQQLVTTEKLQVPPDGLMQVELAEPGRNPETWYVRFDGPSSINIAGLMDY 300
Qy 301 VRSLEDKNDGVFPKFPEEIDALGIVLGHTARANLNTAAIGSSRFFAIDQARKDQASMPPD 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 VRSLEDKNDGVFPKFPEEIDALGIVLGHTARANLNTAAIGSSRFFAIDQARKDQASMPPD 360
Qy 361 SRIEILRGYVQSVRPATGRLLLNTNVTHAVFRKAVKLDELFQKCGLANLHLPQQRPNHAL 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 SRIEILRGYVQSVRPATGRLLLNTNVTHAVFRKAVKLDELFQKCGLANLHLPQQRPNHAL 420
Qy 421 RTLDGLNKFLAKSRIECKVPGERPGEFFKIQRGMAGLATTKDGKDEDQKPEFTESGFRFG 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 RTLDGLNKFLAKSRIECKVPGERPGEFFKIQRGMAGLATTKDGKDEDQKPEFTESGFRFG 480
Qy 481 TPATVRFYLRKPKDLGAKPPPGLSFDTMVLVSDYYKARYGIRADPGLPLINVGTAGKPIY 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 TPATVRFYLRKPKDLGAKPPPGLSFDTMVLVSDYYKARYGIRADPGLPLINVGTAGKPIY 540
Qy 541 ILAEFCTLLPGQPLKARLSPQEQDAMIRFACRPPPENALSVTTSARELLALDNNMLLDKF 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 ILAEFCTLLPGQPLKARLSPQEQDAMIRFACRPPPENALSVTTSARELLALDNNMLLDKF 600
Qy 601 GITVDKHLITVKGRELPPPAVGYLRGNSIERVTPENGGWLMKGVKVCKSGRRIANWAFLV 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 601 GITVDKHLITVKGRELPPPAVGYLRGNSIERVTPENGGWLMKGVKVCKSGRRIANWAFLV 660
Qy 661 IGKARPPIDFGTIKSAVGGFARFLNNNMGIDMNMQPVPANGYQTAGTSEEDLRNAFRTIS 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 661 IGKARPPIDFGTIKSAVGGFARFLNNNMGIDMNMQPVPANGYQTAGTSEEDLRNAFRTIS 720
Qy 721 KQKPQPEFILVLLPDKDATTYNIVKKLGDVEYGITTVCVRQEMLTKEQGQMGYFANVGLK 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 721 KQKPQPEFILVLLPDKDATTYNIVKKLGDVEYGITTVCVRQEMLTKEQGQMGYFANVGLK 780
Qy 781 VNLKFGGINHRVRDETGLVDKTMFVGYDVTHPTNLPGGAGDNAPSLVGLVASVDNSLAQW 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 781 VNLKFGGINHRVRDETGLVDKTMFVGYDVTHPTNLPGGAGDNAPSLVGLVASVDNSLAQW 840
Qy 841 PAVTWENKSRVEQVGGKTDEGQFIAHFKDRLRLWQKHNSNRLPENIVIFRDGVSEGQFSM 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 841 PAVTWENKSRVEQVGGKTDEGQFIAHFKDRLRLWQKHNSNRLPENIVIFRDGVSEGQFSM 900
Qy 901 VLEKELPNIRQACQETYPARPNAQPRLSLIVSVKRHQTRFYPTDRNHIHPRSKSPKEGTV 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 901 VLEKELPNIRQACQETYPARPNAQPRLSLIVSVKRHQTRFYPTDRNHIHPRSKSPKEGTV 960
Qy 961 VDRGVTNVRYWDFFLQAHASLQGTARPAHYTVLLDEIFRHKFGPNAADALETLTHNMCYA 1020
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 961 VDRGVTNVRYWDFFLQAHASLQGTARPAHYTVLLDEIFRHKFGPNAADALETLTHNMCYA 1020
Qy 1021 YGRATKAVSICPPAYYADLVAARARIHKSELFENVQSLASSEQSSVSRRKVHDRLKDTMY 1080
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1021 YGRATKAVSICPPAYYADLVAARARIHKSELFENVQSLASSEQSSVSRRKVHDRLKDTMY 1080
Qy 1081 YI 1082
||
Db 1081 YI 1082
In addition, said protein G2QEV0_MYCTT/THET4 has been characterized in UniProt which also indicates it is a Piwi-containing domain protein, the structure has been predicted with Alpha-fold indicating a disordered N-terminus and the Piwi-domain from amino acids 728-1049 – See p. 2.
Therefore, it would have been obvious to one of ordinary skill in the art prior to the effective filing date of claimed invention to characterize available Argonaute type proteins comprising PIWI-domains including the available instant SEQ ID NO: 1 (and encoded by SEQ ID NO: 3) because Chong et al., Swarts et al. and Wu et al. all teach the importance of characterizing new Argonaute proteins as they are so beneficial for various applications in biotechnology and because Smallheiser provide a line of evidence as to why eAgo should be looked at for DNA interactions. It would be therefore obvious to said skilled artisan and motivate a skilled artisan to characterize new Argonaute proteins utilizing the protocol as established by Chong et al., which is an in vitro method of forming an Argonaute protein complexed to a guide nucleotide sequence, testing the four different kinds of guide sequences (DNA and RNA) known to work with various Argonaute proteins to ascertain which ones work, testing the cleavage (or not) of the complementary target sequences of both DNA and RNA as Smallheiser suggests this should be done for eAgo, and at which range of temperatures are required/optimal, and which divalent cations are required/optimal, given it is well known that Argonaute proteins require said cations for nuclease activity to occur and they function with varying conditions (See Wu et al., p. 318, 2nd col., 2nd paragraph: “In some Argonaute proteins, which are structurally similar to ribonuclease H (RNase H), the PIWI domain contains a slicer active site that cleaves target RNA complementary with small RNA [38]. In the cleavage-compatible conformation, several highly conserved amino acid residues, such as DDX/DEDX (X stands for D or H), form a slicer activity center with an Mg2+ cation [15,39].” One skilled in the art would have a reasonable expectation of success in doing this for SEQ ID NO:1 given the organism is known, the protein sequence is known and it has been identified as a RNase-like protein have a PAZ and PIWI domain and Argonaute like protein (See UniProt information) and given the detailed protocols established by Chong et al. and the evidence for eAgo DNA interactions presented by Smallheiser.
Finally, with regard to the Ago:target:guide ratios of 5:1:2 as in claims 1 and 14, as noted in MPEP 2144.05(I), a prima facie case of obviousness exists where ranges or amounts do not overlap but are close, as it the case with the molar ratios taught by Chong et al., and when it is held that there is no criticality in the range or concentrations/amounts.
Therefore, the combined references render the instant claims as prima facie obvious.
Applicant’s Response and Examiner’s Rebuttal:
Applicant’s traverse the rejection of record and state that none of Chong et al., Swarts et al., Wu et al., or Smallheiser et al. (nor the sequence G2QEV0) teach the limitations of cleaving the target DNA in vitro by the eAgo complex having a molar ratio of Ago:target DNA/RNA:guide of 5:1:2 at a temperature of 37oC in the solution of divalent metal cations.
On p. 5-6, Applicant’s assess what each reference teach and what they do not teach and notes that none of them individually teach the limitations of the instant claims. However, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986).
Regarding Applicant’s first point and second point, regarding the combination of references, it is asserted that no prior art had identified any eAgo that could cleave target DNA in vivo and that Chong et al. is only relevant for a testing method for pAgo’s. The Examiner acknowledges these statements and argument, however, this is why the rejection has been made as a 103 rejection and it would have been obvious to one of ordinary skill to utilize the methods of Chong et al. to test RNA and DNA activity for eAgo’s when considering the secondary references suggestions to do so.
Third, Applicant’s state that Smallheiser merely suggest a hypothesis, citing extensive literature, but that does not mean that eAgo’s do exhibit DNA-binding activity either in vivo or in vitro.
The Examiner acknowledges this argument, however, a hypothesis provides ample motivation to investigate/test the hypothesis. That is exactly what a good hypothesis does in fact, provide motivation and means for testing whether it is true or false (or maybe somewhere in between).
Fourth, it is argued that Smallheiser only suggest that isolated domains of eAgo bind DNA but that this does not mean that a full-length protein, with its more complex structure, will do the same. The Examiner acknowledges there is no guarantee that a full length protein will behave the same as domain of said protein. However, again, this is an easy testable hypothesis (e.g. Full length human Ago2 will bind DNA because the isolated MID domain of the same protein binds DNA). And the actual testing methods and parameters and now to achieve and test this hypothesis is specifically laid out in the protocols of Chong et al. There need only a reasonable expectation of success and not an absolute guarantee of success which is the standard which Applicant’s seem to be applying (See MPEP 2143.02).
Applicant’s fifth argument is that Smallheisers main question about eAgo binding to DNA has only to do with DNA as a guide (See Remarks, top of p. 7). But Smallheiser actually warns against taking snippets of information like this out of context. The very next paragraph states (See p. 2, 2st col., last paragraph):
These are not merely statements of scientific consensus regarding the nature of guides for eukaryotic Ago, but also serve rhetorical functions. For example, they heighten the contrast between mammalian and prokaryotic Argonautes, and emphasize the importance and novelty of the DNA interference phenomenon. Moreover, they also have the unintended effect of warning away readers who might naively wonder whether eukaryotic Ago proteins are also capable of interacting with DNA in any biologically relevant fashion at all. Like a policeman, these statements say: “Move along, folks, show’s over; nothing to see here. Move along quickly now!”
They then go one to demonstrate many publications that point to not only potential interactions of eAgo with guide DNA but with other kinds of DNA molecules as well.
Applicant’s sixth point is that binding activity does not equate to cleavage activity (See Remarks, p. 7, middle of page).
The Examiner acknowledges this, however, again this is an easy testable hypothesis again that Chong et al. have laid out every parameter and element to test on any Ago protein. The protocol tests for guides for DNA and RNA; for cleavage of DNA and RNA; for all of the temperature ranges to test, for the required ions to test, etc.; and again, Smallheiser provides the motivation to test these exact same parameters with eAgo’s. Again, while there is no absolute guarantee of success, there is a reasonable expectation.
Thus, for these reasons, the rejection is maintained.
Conclusion
No claim is 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 SUZANNE M NOAKES whose telephone number is (571)272-2924. The examiner can normally be reached M-F (7-4).
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/SUZANNE M NOAKES/Primary Examiner, Art Unit 1656 07 October 2025