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 .
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Applicant’s claim to priority from Foreign Application KR10-2019-0064129 filed 05/30/2019 and from PCT/KR2020/007100 filed 06/01/2020 is hereby acknowledged.
Election/Restrictions
Applicant’s election without traverse of Invention Group III (claim 9, drawn
to a method for stabilizing an RNA sequence) in the reply filed on 03/31/2026 is acknowledged.
While Applicant also elected a species from Group A, such an election is related to unelected Invention Group IV.
Claims 7-8 and 10-15 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 03/31/2026.
Application Status
This application is a National Entry phase application under 35 U.S.C. §371 of PCT/KR2020/007100 filed 06/01/2020.
Preliminary amendments to claims filed 02/23/2022 are hereby acknowledged.
Claims 1-6 are cancelled. Claim 9 is amended; claims 10-15 are newly added (compared to original filed on 11/29/2021).
Claims 7-8 and 10-15 are withdrawn from consideration since they are drawn to unelected inventions. A species was elected in Group A drawn to viruses in the method of claim 12, which is drawn to a non-elected Invention Group IV. Therefore, the species will not be examined.
Claims 7-15 are pending. Claim 9 is under examination and consideration in this office action.
Information Disclosure Statement
The information disclosure statements (IDSs) submitted on 11/29/2021, 12/27/2022, 06/28/2023 and 08/14/2023 are hereby acknowledged. The submissions are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
However, the listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings (Fig. 3g, Fig.4b and Fig.12b) are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings.
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the specification (Table 1 [0091]; [0098]; Table 2 [0099]; [0100]; Table 3 [0107]; Table 4 [0118]; Table 5 [0123]) are not identified by sequence identifiers in accordance with 37 CFR 1.821(d).
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Drawings
The Drawings are objected to because, as stated above, Figures 3g, 4b and 12b present nucleic acid sequences not referred to as sequence identity numbers (SEQ ID NOs).
Specification
The disclosure is objected to because of the following informalities: There is no content in paragraph [0038]. There are numbers for references, but no indication of where to find the full description of these references (see for example [0148]).
Appropriate correction is required.
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (see [0004]). Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
The use of the terms “Thermo” or “ThermoFisher” or “Thermo Scientific”, “Atlas” ([0033], [0104]), “Ribo-Zero” ([0082], [0084]), “Tru-Seq” ([0082]), “MiSeq” ([0082], [0084]), “Invitrogen” ([0033]), “Sepharose” ([0084], [0109], [0111]), “PhiX Controls” ([0084]), Welgene ([0089]), “Illumina” ([0082]-[0084]), “GlutaMAX” ([0089]), “Lipofectamine” ([0090], [0113]), “DharmaFECT I” ([0090]), “ON-TARGETplus” ([0092]), “SMARTpool”, “Dharmacon” ([0092]), “Qiagen” ([0092]), “NEB” ([0098], [0124]), “ Metafectene” ([0098]), “Surveyor” ([0098]), “Novex” ([0104]), “Millipore” ([0104], [0106]), “Ambion”, “ChemiDoc ([0104]), TRIzol ([0106], [0109]), Maxwell 16 LEV” ([0106]), “RNeasy”, “MinElute” ([0106]), “RevertAid”, “SYBR Green” ([0106]), “QuantStudio 3”, “StepOnePlus” ([0106]), “Turbo DNase” ([0109], [0111]), “Amicon”, “Jupiter C18”, “Orbitrap Fusion”, “Lumos” ([0126]), which are trade names or marks used in commerce, has been noted in this application. The terms should be accompanied by the generic terminology; furthermore the terms should be capitalized wherever they appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Rejections - 35 USC § 112
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.
Claim 9 is rejected under 35 U.S.C. §112(a) or 35 U.S.C. §112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
MPEP 2163.II.A.3.(a).i) states, “Whether the specification shows that applicant was in possession of the claimed invention is not a single, simple determination, but rather is a factual determination reached by considering a number of factors. Factors to be considered in determining whether there is sufficient evidence of possession include the level of skill and knowledge in the art, partial structure, physical and/or chemical properties, functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the method of making the claimed invention”.
For claims drawn to a genus, MPEP § 2163 states the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus. See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406.
Nature of the Invention:
Claim 9 recites: “A method for stabilizing an RNA sequence, the method
comprising a step of inserting a stem-loop sequence including a pentaloop structure consisting of the RNA sequence represented by the following general formula into a target RNA sequence: [General Formula] 5'-CNGGN-3', wherein N's are each independently selected from adenosine (A), uracil (U), guanine (G) and cytosine (C).”
It is therefore expected in the instant application a disclosure of a method for stabilizing any RNA sequence, i.e., an mRNA, shRNA, siRNA, single guide RNA, or even a hybrid DNA/RNA, a gapmer, comprising RNA sequence, a ribozyme.
It is also expected a disclosure of stability of RNA , if it is a therapeutic agent, in serum and upon binding of a target sequence.
It is also expected that an example of eukaryotic or prokaryotic RNA. It is expected an example of mammalian RNA, viral RNA, bacterial RNA, plant RNA or yeast RNA.
It is also expected a description of the method step for inserting a pentaloop structure within any RNA and a demonstration of stabilization of said RNA. It is expected a description of a specific target sequence, a location, in 5’ or 3’, in coding region or non-coding, for insertional mutagenesis or for click chemistry. There is no description of further “units” needed and an optimum number of pentaloops needed, nor any modification pattern specific to the region targeted for insertional mutagenesis either.
The State of the Art:
Arnold (Arnold, T.E. et al. “mRNA stabilization by the ompA 5’ untranslated
Region: two protective elements hinder distinct pathways for mRNA degradation”. RNA, Vol. 4 (1998), pp: 319-330) teaches that naturally existing sequences are capable of stabilizing and protecting mRNA from degradation (see title).
The ompA 5’ untranslated region (5’UTR) has a sequence that allows for secondary structures, two hairpins, at position 1-63 and 75-103 (see Figure 1). At the base of the first hairpin, there are two naturally occurring sequences comprising the sequence: “5- CAGGG” from nucleotide 3 to nucleotide 6, and opposite to it in the stem, there is “5’- CCGGU-3’” (see Figure 1).
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Arnold also teaches that the size of the fragments of sequence within the 5’UTR is important for the stability of the ompA mRNA (see Table 1). Arnold teaches a smaller hairpin comprising the motif “5’-CNGGN-3’” is only protective for ompAΔ104D, which has a bigger hairpin and has a methylation pattern that is more distal (see Table 1 and Figure 3).
Therefore, Examiner interprets these teachings as follow: a method of protecting a mRNA sequence would need additional information, as far as chemical modification, and acceptable patterns of modification that do not interfere with the hairpin formation.
Viegas (Viegas, S.C. et al. “Modulating heterologous gene expression with portable mRNA-stabilizing 5’-UTR sequences”. ACS Synthetic Biology, Vol. 7 (2018), pp: 2177-2188) teaches the use of ompA 5’UTR hairpins for stabilizing heterologous gene of interest cloned in a recombinant construct (see title and abstract). Viegas teaches a method of constructing a plasmid for the expression of a gene of interest, inserting the ompA 5’UTR hairpin and shows the increase in mRNA stability of the gene of interest (see Figure 1). Viegas also shows that insertion of additional sequences (“sse”: single stranded element) between the hairpin and the Shine-Dalgarno (SD) sequence increases the expression and stability of the gene of interest (see Figure 3). The additional sequences may contribute to improved entry of ribosomes to the SD region and contribute to additional stability, as they interfere with possible nucleases (see page 2181, left column, lines 7-10 and right column, “The effect of synthetic stem-loops and adjacent single stranded sequences on mRNA decay” section).
Gu (2) (Gu, S. et al. “Weak base pairing in both seed and 3’ regions reduces RNAi off-targets and enhances si/shRNA designs”. Nucleic Acids Research, Vol. 42, No. 19 (2014), pp: 12169-12176) teaches the design of siRNAs and shRNAs with reduced off-targets effects because of their binding stability (see title and abstract).
Gu (1) (Gu, S. et al. “The loop position of shRNAs and pre-miRNAs is critical for the accuracy of Dicer processing in vivo”. Cell, Vol. 151 (2012), pp: 900-911) teaches that insertion of extra 2, 3, or 4 nucleotides within the sequence of shRNA allowing the formation of a bulge can be beneficial for accurate and efficient cleavage by Dicer (see title and Abstract). Figure 5B shows examples of inserted nucleotides forming a bulge, as shown below:
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The position of the bulge and the number of extra nucleotides have a direct impact on the function of the shRNA. Gu(1) teaches that shRNA design for gene silencing must abide by certain rules. Gu (1) states “The Loop-counting rule is as follows: Dicer cleaves precisely when it is able to recognize a single-stranded RNA sequence either from the loop region or internal bulge at a fixed distance (two nucleotides) relative to the site of cleavage. Otherwise, Dicer cleavage is not precise, leading to a range of Dicer cleavage products with variable 5’ start positions” (see page 907, left column, lines 10-15).
Therefore, it is expected a list of potential targets for using shRNAs and an enumeration of residues in sequences around the insertion sites in a targeted shRNA to be stabilized, since Applicant’s claim encompasses all sort of RNA, shRNAs included.
Joshi (Joshi, R. et al. “mRNA-based therapeutics: Advances in drug delivery, comparative innovations, and biomedical applications”. Molecular Pharmaceutics, Vol. 23 (2026), pp: 583-621) reviews methods and systems to improve the stability and promote cellular entry of mRNA drugs (see abstract). Joshi teaches that 5’-Cap structure optimization, modification of nucleotides, poly(A) tail extension, and codon optimization strategies contributed synergistically towards enhance mRNA stability (see page 585, left column, section 1.4). Joshi teaches that various structural modifications have been introduced to enhance the stability and efficacy of mRNA therapeutics, notably 5’-Cap, which improves ribosomal recognition and exonuclease resistance, untranslated regions optimizations, e.g., poly(A) tail sequence optimization (see page 589, section 3, lines 11-27; see page 490, section 4.1). Mostly, stabilization of mRNAs involves chemical modifications and conjugation to molecules for optimum delivery in lipid nanoparticles (LNPs; see section 4.2, page 591).
Therefore, it is expected in the disclosure examples of complexes comprising mRNA from different genes, with linkers, enumeration of residues of sequences of these examples, and position of linkers relative to the claimed “pentaloop”. It is expected a combination of steps and modalities to enhance the mRNA stability.
What the Specification does and does not teach:
The Specification teaches examples that are all centered on viral RNA, more
Specifically, HBV and HCMV RNAs (see {0131]). The Specification discloses methods for analyzing poly(A) tail lengths of these viruses’ RNAs in cells subjected to knockdown of TENT4A and TENT4B protein (see [0133], [0138]). The Specification is mostly for the presentation of a pharmaceutical composition and a method for prevention of treatment of a viral infection (see [0059]-[0061]).
The Specification introduces a method for stabilizing an RNA sequence using the claimed pentaloop using generic statements in paragraphs [0049]-[0057] and [0062], as well as Figure 13. The method as disclosed seems to be drawn to the use of TENT4A/B as stated in [0056]:
“Insertion of the stem-loop structure of the present disclosure into a target RNA
sequence increases the frequency of inducing mixed tailing with TENT4A/B in the target
RNA sequence, resulting in stabilizing the RNA sequence.”
The exemplary embodiment refers to a drawing in Figure 13 of the pentaloop general formula. However, there is no specific example of molecule targeted for stabilization. The Specification does not teach example of stabilizing mutation in specific mRNA, shRNA or other types of RNA.
The Specification does not teach gapmers or ribozymes other than in the context of knocking down TENT4A or TENT4B (see [0090]-[0092]). These examples clearly are drawn to a different invention involving destabilizing viral RNAs to prevent or treat a viral disease.
Conclusion:
Taking into consideration the factors outlined above, including the nature of the
invention, the state of the art, the guidance provided by the applicant and the specific example, it is the conclusion that Applicant does not possess the breath of the claimed invention. There is no specific written example within the Specification that would lead one with ordinary skills in the art to a different conclusion.
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.
Claim 9 is rejected under 35 U.S.C. §102(a)(1) as being anticipated by Zufferey (Zufferey, R. et al. “Woodchuck Hepatitis Virus Posttranscriptional Regulatory Element enhances expression of transgenes delivered by retroviral vectors”. Journal of Virology, Vol 73, No. 4 (1999), pp: 2886-2892), as evidenced by Donello (Donello, J.E. et al. “Woodchuck Hepatitis Virus contains a tripartite posttranscriptional regulatory element”, Journal of Virology, Vol. 72, No.6 (1998), pp: 5085-5092).
Regarding claim 9, it recites “A method for stabilizing an RNA sequence, the
method comprising a step of inserting a stem-loop sequence including a pentaloop structure consisting of the RNA sequence represented by the following general formula into a target RNA sequence: [General Formula] 5'-CNGGN-3', wherein N's are each independently selected from adenosine (A), uracil (U), guanine (G) and cytosine (C).”
Examiner interprets the claim as requiring a method leading to any type of RNA stabilization, in any milieu and context, providing the RNA sequence is modified to insert a stem-loop sequence, without any limitation of length for the stem-loop sequence, providing it includes a pentaloop structure having a sequence according to the general formula “5’-CNGGN-3’”.
Therefore, Zufferey teaches the elements of claim 9, since Zufferey teaches the use of Woodchuck Hepatitis Virus Posttranscriptional Regulatory Element (WPRE) in constructing a HIV-1-based vector comprising a CMV promoter, an open reading frame encoding for a reporter gene (GFP/Luciferase) and a WPRE at the 3’ end or, at the 5’ end of the CMV promoter (see Figure 1).
Zufferey teaches that WPRE enhances the expression of transgenes delivered by HIV-based vectors, by three to five fold (see page 2888, “Results” section). Zufferey also teaches that the stability of the mRNA is increase less than 2-fold (see page 2891, left column, first paragraph, lines 6-8). Zufferey reasons that the increase in efficient processing and sequestering of transcriptional machinery proteins protect the mRNA against degradation, and enhance the stability of the mRNA in the nucleus (page 2891, left column, lines 9-12 ; Discussion section, left column, lines 49-51, and right column, lines 1-3).
Donello teaches that the WPRE contains a tripartite posttranscriptional regulatory element (see title). Figure 5A shows that the element contains a hairpin positioned between nucleotides 1396 and 1475. This element also contains a pentaloop with the sequence: 5’-CUGGA-3’. See also below:
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Therefore, as evidenced by Donello, Zufferey teaches a method to increase mRNA stability using a WPRE comprising a stem-loop sequence including a pentaloop.
The claim is rejected.
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 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.
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 9 is rejected under 35 U.S.C. §103 as being unpatentable over
Orlandini Von Niessen ( Orlandini Von Niessen, A. et al. WO 2017/060314 A2, published April 13, 2017), in view of Arnold (Arnold, T.E. et al. “mRNA stabilization by the ompA 5’ untranslated Region: two protective elements hinder distinct pathways for mRNA degradation”. RNA, Vol. 4 (1998), pp: 319-330) and Viegas (Viegas, S.C. et al. “Modulating heterologous gene expression with portable mRNA-stabilizing 5’-UTR sequences”. ACS Synthetic Biology, Vol. 7 (2018), pp: 2177-2188; and Supporting Doc pdf).
Regarding claim 9, it recites “A method for stabilizing an RNA sequence, the
method comprising a step of inserting a stem-loop sequence including a pentaloop structure consisting of the RNA sequence represented by the following general formula into a target RNA sequence: [General Formula] 5'-CNGGN-3', wherein N's are each independently selected from adenosine (A), uracil (U), guanine (G) and cytosine (C).”
As stated above, Examiner interprets the claim as requiring a method leading to any type of RNA stabilization, in any milieu and context, providing the RNA sequence is modified to insert a stem-loop sequence, without any limitation of length for the stem-loop sequence, providing it includes a pentaloop structure having a sequence according to the general formula “5’-CNGGN-3’”.
Examiner also interprets that the localization of the stem-loop insertion can be at 5’ or 3’ or within an ORF, or within a poly(A) tail, since Applicant’s claim is broad.
Regarding claim 9, Orlandini Von Niessen teaches a method modifying 3’UTR of RNA for stabilization (see title and abstract). Orlandini Von Niessen teaches using 3’UTR of sequence from 2hBg (human beta-globin) , in in vitro translation to provide in vitro-transcribed RNAs for therapeutics (see page 1, lines 1-7 and page 2, lines 28-32).
Orlandini Von Niessen teaches that two consecutive copies of the human beta-globin 3’UTR contribute to higher transcript stability and translational efficiency (see page 2, lines 12-16).
Orlandini Von Niessen teaches the isolation of two sequences that are responsible for mRNA stability and teaches the combination of the sequences for additional effect (see page 125, lines 26-33). The combination of elements I and F results in a 2- to 3-fold increase in half-life compared to 2hBg (see page 127, lines 31-33). Orlandini Von Niessen also teaches the combination of upstream and downstream elements and compares the translational efficiency (see Table 7, page 144).
Orlandini Van Niessen does not teach a stem-loop with a pentaloop structure.
However, Arnold teaches a 5’UTR element in ompA gene that are hairpins that contains two pentaloops (hp1) and a tetraloop (hp2), and contributes to the stability of the ompA mRNA (see title, abstract and Figure 1):
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Dissecting and modifying the hairpins sequence to localize the elements contributing to stability of the mRNA, Arnold teaches ompAΔ104D that increases the mRNA half-life compared to a mutant sequence with deleted hairpins sequences (see Table 1). The modified OmpAΔ104D is represented in Figure 3:
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OmpAΔ104D comprises a tetraloop with the sequence 5’-GGCC-3’.
Viegas teaches the use of ompA 5’UTR hairpins for stabilizing heterologous gene of interest cloned in a recombinant construct (see title and abstract). Viegas teaches a method of constructing a plasmid for the expression of a gene of interest, inserting the ompA 5’UTR hairpin and shows the increase in mRNA stability of the gene of interest (see Figure 1). Viegas teaches the use of single hairpin (see Figures 1 and 3). Viegas teaches the modification of ompA 5’UTR leading to multiple synthetic sequences, sl1 to sl4, each comprising a region with the sequence 5’-NCGGN-3’ (see page 2185, right column). Therefore, Viegas shows that it is possible to further modify the stem and loop regions (see also supporting doc, Figure S3).
In KSR Int 'l v. Teleflex, the Supreme Court, indicated that “The principles underlying [earlier] cases are instructive when the question is whether a patent claiming the combination of elements of prior art is obvious. When a work is available in one field of endeavor, design incentives and other market forces can prompt variations of it, either in the same field or a different one. If a person of ordinary skill can implement a predictable variation, § 103 likely bars its patentability.” KSR Int'l v. Teleflex lnc., 127 S. Ct. 1727, 1740 (2007).
Therefore, it would have been obvious to one with ordinary skills in the art, before the effective filing date of the claimed invention, to have tried and modified the method of stabilizing an RNA as taught by Orlandini Van Niessen, and combined the elements (I and F in 3’ UTR) taught by Orlandini Van Niessen with the element taught by Arnold and modified by Viegas, especially using a minimal sequence for OmpA 5’UTR. One with ordinary skills in the art could have tried and optimized the sequence and the loop, and could have made a pentaloop as taught by Arnold in the original 5’UTR of ompA mRNA. One with ordinary skills in the art motivated in enhancing the half-life of a therapeutic RNA and increasing its production, could have performed this modification with a reasonable expectation of success, and would arrived at the claimed invention.
Conclusion
Claim 9 is rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ALEXANDRA G DACE DENITO whose telephone number is (703)756-4752. The examiner can normally be reached Monday-Friday, 8:30-5:00EST.
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/A.D./Examiner, Art Unit 1636
/NANCY J LEITH/Primary Examiner, Art Unit 1636
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