DETAILED ACTIONNotice 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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on July 8 2024 has been entered.
Application Status
Claims 1-6 and 9-22 are pending.
Claims 1, 9, 10, 11, 12, 13, and 17 have been amended.
Claims 7-8 are canceled.
New claims 17-22 have been added. Examination on the merits commences on claims 1-6 and 9-22.
Applicants are informed that the rejections and/or objections of the previous Office action not stated below have been withdrawn from consideration in view of the Applicant' s arguments and/or amendments. Applicant’s amendments and arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow.
Claim Rejections - 35 USC § 112(a) – Scope of Enablement – Modified Maintained
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-6 and 9-22 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while enabling for a method of a short-stranded DNA staple oligonucleotides between 30 and 100 bases hybridizing to a specific target RNA to bring guanine repeat sequences closer together so as to form a guanine-quadruplex structure (G4), does not reasonably enable the method for the genus of all oligonucleotides able to target any target RNA to be capable of the specific claimed G4 disrupting folding pattern. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
The test of enablement is whether one skilled in the art could make and use the claimed invention from the disclosures in the specification coupled with information known in the art without undue experimentation (United States v. Telectronics., 8 USPQ2d 1217 (Fed. Cir. 1988)). Whether undue experimentation is needed is not based upon a single factor but rather is a conclusion reached by weighing many factors. These factors were outlined in Ex parte Forman, 230 USPQ 546 (Bd. Pat. App. & Inter. 1986) and again in In re Wands, 8 USPQ2d 1400 (Fed. Cir. 1988), and the most relevant factors are indicated below:
Nature of the Invention and Breadth of claims
The claims are drawn to a method of an oligonucleotides for bringing guanine repeat sequences in a target RNA closer together so as to form a guanine-quadruplex structure (G4). According to the claims, “oligonucleotides” are described only by their function, i.e., molecules capable of bringing guanine repeat sequences in a target RNA closer together so as to form a guanine-quadruplex structure (G4). Dependent claims limit the structure of the oligonucleotides as having a folding direction facing the G4 for hybridization (claim 2 and 8), the oligonucleotides is DNA or RNA (claim 4 and 9), and the oligonucleotides is a dimer (claim 5 and 10). However, the claimed language does not limit the structure of the oligonucleotides in length, modification, secondary/tertiary structure, or further function, and therefore could encompass any means, directly or indirectly, for targeting an RNA to bring guanine repeat sequences closer together. The genus of “oligonucleotides” is broad and diverse in the art. Oligonucleotides can be single stranded or double stranded, DNA or RNA, modified with 2’, 5’, and 3’ modifications. Single stranded oligonucleotides may have a double stranded region, and double stranded oligonucleotides may have a single stranded region. Some oligonucleotides include structural genes, genes containing control and termination regions, self-replicating systems such as viral or plasmid DNA, single-stranded and double-stranded siRNA and other RNA interference reagents (RNAi or iRNA agents), shRNA, antisense oligos. Nucleotide, ribozyme, microRNA, microRNA mimetic, supermir, aptamer, antimir, antagomir, Ul adapter, triplex-forming oligonucleotide, G-quadruplex oligonucleotide, RNA activator, immunostimulatory oligo, and decor oligonucleotides, among others. Accordingly, enablement of the method requires one skilled in the art to be able to use any oligonucleotides for bringing guanine repeat sequences in a target RNA closer together to form a guanine-quadruplex structure (G4) so as to inhibit protein translation and treat a protein-related disease in a subject.
Guidance from the Specification
The specification discloses a variety of nucleic acids that can serve as oligonucleotides that hybridize a target RNA. The specification teaches, “In the present invention, a predetermined oligomer is used to bring the four guanine repeat regions present on RNA closer together. This oligonucleotides functions to bring the first guanine repeat sequence and the second guanine repeat sequence, the second guanine repeat sequence and the third guanine repeat sequence, or the third guanine repeat sequence and the fourth guanine repeat sequence close to each other such that the four guanine repeat sequences are brought closer together as a whole, and the oligomer is herein referred to as "Staple nucleic acid." ([0016] and Fig 1a). The specification teaches the known DNA origami method, which is a technique for creating a nanostructure by allowing a single-stranded circular DNA exceeding 7,000 bases to be self-assembled with 200 designed short-stranded DNAs (Staple oligomers) of more than 30 bases ([0015] and Figure 2). The specification also teaches limited examples of the target RNA used include mRNA, TPM3, and MYD88, where TPM3 is a gene associated with muscle contraction, and MYD88 is an adapter protein that mediates Toll and interleukin (IL) 1 receptor signaling [0017].
From the working examples, Example 1 of the specification teaches a purchased DNA oligonucleotide with preparation of 2+2_100nt RNA and 2+2_100ntMut A RNA [0024-0025] where the prepared dsDNAs are used as a template so as to transcribe RNAs from dsDNAs [0035]. The specification teaches the staple nucleic acid inside loops of 26-40 nucleotides [0051] and an outside loop of 30 nucleotides [0053]. Staple Nucleic acids: TPM3_30nt, 26nt, and MYD88_30nt, 26nt or milliQ (control) were introduced into the HEK293T cells for translational control by forming an RNA G-quadruplex (Fig 4 [0058]). Fig. 5b demonstrates the gene expression inhibitory effects of the staple nucleic acids by constructing an RNA G- quadruplex [0061]. The specification teaches the target nucleic acid is an RNA G-quadruplex structure that is a stable higher-order RNA structure constructed when a guanine sequence of 3 or more continuous bases is present at 4 sites with a close spacing of less than 7 bases (Figure 1b). When this RNA G-quadruplex structure is present in the 5' untranslated region (5' UTR) of mRNA, it suppresses the protein synthesis reaction by ribosomes (Figure 1c and [0014]).
Although the specification discloses several embodiments of “oligonucleotides” as short-stranded DNAs (Staple oligomers) of more than 30 bases and less than 100 bases the specification fails to teach representative species of oligonucleotides which sufficiently describe the full genus of oligonucleotides capable of bringing guanine repeat sequences in a target RNA closer together to form a guanine-quadruplex structure (G4) such that a skilled artisan could predictably disrupt protein translation via the claimed folding pattern in a method of treating a protein-related disease in a subject. As such, the scope of enablement in the disclosure does not bear a reasonable correlation to the scope of the claims. MPEP 2164.08.
State of the Art
The genus of “oligonucleotides” is broad and diverse in the art. Oligonucleotides can be single stranded or double stranded, DNA or RNA, modified with 2’, 5’, and 3’ modifications. Single stranded oligonucleotides may have a double stranded region, and double stranded oligonucleotides may have a single stranded region. Some oligonucleotides include structural genes, genes containing control and termination regions, self-replicating systems such as viral or plasmid DNA, single-stranded and double-stranded siRNA and other RNA interference reagents (RNAi or iRNA agents), shRNA, antisense oligos. Nucleotide, ribozyme, microRNA, microRNA mimetic, supermir, aptamer, antimir, antagomir, Ul adapter, triplex-forming oligonucleotide, G-quadruplex oligonucleotide, RNA activator, immunostimulatory oligo, and decor oligonucleotides, among others.
Regarding oligonucleotides as nucleic acid ligands for G-4 quadruplex structures, Kruisselbrink of record teaches the existence of 376,000 potentially mutagenic G4 (G-4 quadruplex) DNA sites in the human genome (pg 900 para 1; Kruisselbrink of record, Evelien, et al. Current Biology 18.12 (2008): 900-905) and that those G4 DNA sequences that have the potential to fold into replication blocking quadruplex structures are intrinsically mutagenic in live animals (pg 903 col 2 para 5). Kruisselbrink teaches the instability of G4 complexes requires a specialized genome-protection mechanism to prevent massive genome rearrangements at G4 DNA sites (pg 903 col 2 para 5). Thus, the instability and mutagenesis of G-4 structures undermines the predictability of any non-specific oligonucleotides able to hybridize a G-4 complex so as to interfere with translational events.
Regarding oligonucleotides as nucleic acids, “Guide RNA” is a known RNA that binds to an RNA-guided nuclease and binds to a target site, where for example, E. coli have naturally occurring CRISPR/Cas systems and therefore E. coli cells contain guide RNAs (Diez-Villasenor et al. of record, Microbiology (2010), 156: 1351-1361). The RNA “staple nucleic acid” is also described in the art. Wilner et. al., teaches that appropriate selection of staple units may lead to predesigned nanoscale 2D or 3D shapes and patterns of DNA (Figure 10; Wilner, Ofer I. of record, and Itamar Willner. Chemical reviews 112.4 (2012): 2528-2556.). Wilner teaches one of the challenges in the self-assembly of DNA-origami-based nanostructures involves the appropriate design of the staple strands (pg 2537 col 2 para 2). Wilner teaches the design of programmed origami-based DNA assemblies provide the basis to organize ordered systems of nanoparticles, nanotubes, and proteins on origami scaffolds (pg 2537 col 2 para 2). Figure 1 of Wilner teaches schematic structural and functional features of staple nucleic acids including (A) single-stranded sticky end; (B) duplex hybridization; (C) hairpin nanostructure; (D) G-quadruplex; (E) triplex hybrid; (F) DNAzyme structure; (G) metal-bridged duplex; and (H) aptamer nanostructure (pg 2529 para 1). Although the specification teaches [0015] that this DNA origami method for producing a DNA nanostructure can be applied to artificially induce an RNA G-quadruplex structure, the many examples and applications of Wilner’s staple nucleic acids as well as those described by Díez-Villaseñor demonstrate the vast genus of oligonucleotides such that a skilled artisan would find it unpredictable to stably hybridize what Kruisselbrink describes as an already mutatagenic G4 complex, especially without specificity of design length, secondary structure, and how they relate to function.
As the prior art establishes, there is substantial variation within the genus of oligonucleotides and thus target oligonucleotides. Applicant fails to adequately describe a sufficient variety of species to reflect the variation within the genus of target oligonucleotides. Furthermore, the description of a representative number of species from the specification is not representative of the entire genus. Given the lack of guidance in the art and specification regarding common structural characteristics shared by members of the genus of “oligonucleotides” and lack of predictability of undefined modifications, secondary structure, or function, the specification disclosure is not sufficient to show that the Applicant was in possession of all “oligonucleotides” at the time the invention was filed. However, given evidence in the art and specification, short-stranded DNAs (Staple oligonucleotides) of between 30 and 100 bases are sufficiently enabling for hybridized target RNA G-quadruplex formation and subsequent inhibition of protein translation.
After a thorough search of the related art, in the method of oligonucleotides targeting for G-quadruplex formation, evidence in the art is lacking as to whether any oligonucleotides can be used to induce G-quadraplex formation in a target RNA so as to inhibit protein translation in a subject with a protein related disease. Taking this into consideration, the lack of related examples in the specification, the lack of knowledge in the art of the unpredictability G-quadruplexes, and the large genus of “oligonucleotides” recited in the claims, it is the conclusion that undue experimentation would be required to use the described invention with the entire genus of “oligonucleotides.”
Allowable Subject Matter
Regarding claims 1-6 and 9-22, a thorough search of the prior art does not appear to teach, suggest or provide a motivation for a staple oligonucleotide that hybridizes with its partial nucleic acid regions to areas proximal to two separate guanine repeat sequences on target RNA so as to inhibit target protein expression in the treatment of protein related disease. The closest prior art is Rouleau and Phan. Rouleau teaches construction and use of antisense oligonucleotides (ASO) to successfully modulate specific RNA G4 formation in human cells in a method to promote or inhibit translation of reporter genes as well as endogenously expressed mRNAs following modulation of G4 formation (pg 604 para 2). Rouleau Teaches a 19-mer ASO (Table S2), pro-H2G4, was designed to specifically bind and, thus, disrupt this long stem-loop structure, therefore enabling G4 formation. Rouleau teaches in figure 4B the G sequences brought closer together (Claim 1, 7, and 11) by adjacent hybridization of the ASO oligonucleotides. Phan teaches targeting of single-stranded mRNAs with complementary oligonucleotides for G4 mediated gene regulation at the translational level where upon binding its target mRNA, the antisense oligonucleotide either triggers degradation of the mRNA by RNase H-dependent mechanism, or inhibits the translational machinery by acting as a steric block [0004], i.e. oligonucleotides G-4 hybridized composition inhibits translation (claim1). Phan teaches an n adaptor G•A base pair can be utilized to bridge a duplex across the diagonal corners of a tetrad (Fig 4 and [0023]).
However, the claimed invention as newly amended is an alternative oligonucleotide which binds specifically, one region of the oligonucleotide hybridizes near one guanine repeat sequence, while another region hybridizes near a different guanine repeat sequences which causes the intervening RNA sequence between the two binding sites to fold so hybridizing to two different guanine repeat sequence regions on a target sequence such that the staple nucleic acid of the invention brings these G-rich regions spatially closer together.
Response to Arguments
Applicant’s argue (Remarks pg 10) regarding 35 U.S.C. §112, that the Examiner has wrongly focused on the breadth of the claims without properly considering the level of skill for a person of ordinary skill in the art (POSITA) of the present invention. Applicants further argue that a POSITA is aware of teachings related to G4 complexes, hybridization and origami-based nanostructure and such a POSITA would have that understanding when also reading the present specification and would be able to practice the invention without "undue experimentation". Applicant’s arguments have been thoroughly reviewed and found unpersuasive. The specification, while enabling for a method of a short-stranded DNA oligonucleotides between 30 and 100 bases which hybridize to a target RNA to bring guanine repeat sequences closer together so as to form a guanine-quadruplex structure (G4), does not reasonably enable the method for the genus of all staple oligonucleotides such RNA and does not reasonably enable the method of targeting any target so as to cause the claimed folding patterns. Example 1 from the specification teaches DNA oligonucleotides, however, the broad genus of staple oligonucleotides includes various other iterations of stable nucleic acids. Furthermore, given Applicants arguments related to the novelty of applying the claimed staple oligonucleotides to influence G4 folding and target RNA expression, a person of ordinary skill in the art would not be so informed as to reasonably predict the how any staple oligonucleotide of unspecified length and structure would fold according to the claimed patterns for all possible target RNAs without undue experimentation.
Applicant’s arguments (Remarks pg 11-12) relate to the withdrawn 35 U.S.C. §§101 and 102 rejection therefore the arguments are moot.
Regarding 35 U.S.C. §103, Applicant’s arguments (remarks pg 13) regarding the deficiencies of the references of record have been thoroughly examined and found persuasive, given the description of allowable subject matter noted above.
Conclusion
No claims are allowable.
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/JOHN CHARLES MCKILLOP/Examiner, Art Unit 1637
/EKATERINA POLIAKOVA-GEORGANTAS/Primary Examiner, Art Unit 1637