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 .
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 10/10/2025 has been entered.
Application Status
This action is written in response to applicant’s correspondence received on 10/10/2025. Claims 1-3, 6, 10-15, and 17-18 are pending. Claims 4-5, 7-9, and 16 have been cancelled. Claim 18 is newly added. Claims 1-3, 6, 12, and 14 have been amended. All pending claims are currently under examination.
Duplicate Claim Warning
Applicant is advised that should claim 15 be found allowable, claim 18 will be objected to under 37 CFR 1.75 as being a substantial duplicate thereof. When two claims in an application are duplicates or else are so close in content that they both cover the same thing, despite a slight difference in wording, it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim. See MPEP § 608.01(m).
In the present case, claim 15 recites “The method according to claim 1, wherein the treating four or more oligonucleotide raw material fragments in total in the presence of an oligonucleotide ligase is performed at 16 to 50°C,” while claim 18 recites “The method according to claim 1, wherein the treating is performed at a temperature from 16 to 50°C.” The claims are therefore worded slightly differently. However, there is only one “treating” recited in claim 1, from which both claims 15 and 18 depend. Therefore, recitation of “the treating four or more oligonucleotide raw material fragments in total in the presence of an oligonucleotide ligase” in claim 15 and “the treating” in claim 18 appear to be referring to the same “treating” where furthermore the same temperature range is recited.
Information Disclosure Statement
The Information Disclosure Statement (IDS) filed 12/10/2025 has been reviewed.
Claim Rejections - 35 USC § 103 – Updated in Response to Amendment
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.
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.
Claims 1-3, 6, 10-15, and 17-18 are rejected under 35 U.S.C. 103 as being unpatentable over Sosic (Sosic A et al. Bioconjug Chem. 2014 Feb 19;25(2):433-41) in view of Jung (Jung S et al. J Control Release. 2010 Jun 15;144(3):306-13), Torchia (Torchia C et al. Nucleic Acids Res. 2008 Nov;36(19):6218-27), and Kraynack (Kraynack BA et al. RNA. 2006 Jan;12(1):163-76).
Regarding claim 1, Sosic teaches a method for producing a modified oligonucleotide comprising a complementary portion having 28-37 nucleotide length, where the method comprises forming the modified oligonucleotide by treating four or more oligonucleotide raw material fragments in total in the presence of an oligonucleotide ligase (Title, Table 1, and e.g., Figure 5A). Sosic discloses that T4 DNA ligase was used (Abstract). Furthermore, Sosic teaches that the oligonucleotides vary in length (e.g., 9, 12, 16, 18, 19, 21, and 28 nucleotides, Table 1). Sosic teaches that eight single strand oligonucleotide raw material fragments were combined to form double stranded oligos (e.g., d+d’ combined into D, Table 1). Furthermore, Sosic teaches that resulting nucleotides would be the product of at least four oligonucleotide raw material fragments (see Figure 5A, which depicts at least four raw fragments).
Additionally, regarding the claim limitation that the modified oligonucleotide is “siRNA,” Sosic teaches that siRNA molecules attract great interest owing to their versatility to treat a wide range of diseases and their potential high selectivity (Abstract). Sosic further teaches that modified siRNA have demonstrated an improved cell internalization and stability with respect to free nucleic acids (Introduction, first paragraph). Sosic therefore directly teaches a motivation to create modified oligonucleotides that are siRNAs, because such molecules are known to be useful as therapeutics in disease contexts (Abstract).
Concerning steps (i) and (ii), Sosic teaches that the 5’ overhangs of the fragment links D, DF, and S are cohesive to A and upon ligation represent an EcoRI restriction site (page 439, left column, paragraphs 1-2 and Figure 4A). Thus, Sosic teaches that one or more fragment linking sites are present in the complementary portion in each strand with two or more fragment linking sites total (Figures 4A-5A, page 439, left column, paragraphs 1-2). Furthermore, Sosic teaches that a sticky end is present when the modified oligonucleotide is divided that is 1-10 nucleotides in length (see EcoRI sticky end site, Figure 4A).
Concerning step (iii), Sosic teaches that at least one oligonucleotide of the raw material fragment has been modified (page 435, left column, third paragraph, and Abstract, “PEGylated nucleic acids”).
Regarding step (iv), Sosic teaches raw material fragments which are between 5 and 17 nucleotides in length (e.g., fragments “s” and “s’” in Table 1). Given that Sosic teaches raw material fragments between 5-17 nts in length, a practitioner could immediately envision that all four could be 5-17 nts in length. Furthermore, Sosic teaches that the TBA fragment is a 15-mer added to a 6T tail that makes aptamers partly complementary to T, thus further teaching raw materials which are between 5-17 nts in length (page 434 right column second paragraph to page 435 left column, first paragraph).
Regarding step (v) claim 1, Sosic teaches raw material fragments with complementary portions between 11-27 nucleotides in length (e.g., see sequence “D” in Table 1, where complementarity region is 18 nucleotides).
Sosic, while teaching that siRNAs should be manufactured due to their therapeutic importance, did not specifically make siRNAs in their method. Sosic, while teaching the ligation of DNA using double-stranded DNA ligase, does not specifically teach a double stranded RNA ligase. Sosic, while teaching a motivation to modify oligonucleotides to enhance stability, does not teach that the modification is a 1’,2’,3’,or 4’ -O-C1-6 alkyl modification.
Sosic references Jung in the Introduction, first paragraph (line 7). Thus, Sosic and Jung directly overlap is subject matter and field of endeavor, as evidenced by the fact that Sosic directly references Jung. A practitioner would thus reasonably be directed to the teachings of Jung based on Sosic, as Jung is referenced by Sosic concerning siRNA molecules. Jung teaches that siRNA molecules are 19-21 nucleotides in length and can target mRNA molecules (Introduction, first line). Jung teaches and reduces to practice siRNA molecules with modifications and cleavable linking sites (Abstract). Jung teaches siRNA molecules that are 19-21 nucleotides in length, and that siRNA molecules are designed to bind to mRNA targets (Jung, Introduction, first paragraph). Thus, Jung teaches that siRNA molecules have complementary regions which are between 11-27 nucleotides in length.
Furthermore with regards to the length of the siRNA and its complementary regions, Jung who teaches that siRNAs can be between 19-21 nucleotides in length which target mRNA (i.e., have complementary regions). Thus, a practitioner would understand that the methods and products of Sosic could and should be designed with such lengths to act as siRNAs because Sosic teaches that siRNAs are known to be useful as therapeutics (Abstract and Introduction of Sosic). Jung also teaches sense and antisense strands of siRNA, and therefor teaches siRNAs are double-stranded RNA molecules (Abstract).
Sosic and Jung, while teaching the ligation of double-stranded DNA using a DNA ligase (Sosic, Abstract) and the ligation of RNA molecules using RNA ligase (Jung, page 307, right column, third paragraph), and furthermore teach that siRNAs are double-stranded RNA molecules which have important therapeutic roles (Sosic and Jung Abstracts), do not specifically teach double-stranded RNA ligases.
Torchia is a research article which teaches RNA ligases and their uses (Title, Abstract, and see document). Torchia teaches that there are different families of RNA ligases, including the single-strand break repair family Rnl1, and the double-strand ligation family Rnl2 (page 6218, right column, paragraphs 2-3). Torchia also teaches that such ligases, their structure, and their functionality is already known (page 6218, right column, final paragraph into page 6219, left column). Thus, Torchia teaches that double-stranded RNA ligases such as Rnl2 family ligases are known ligases with predictable functionality (page 6218, right column, final paragraph into page 6219, left column). Given that Jung teaches that siRNA is double-stranded RNA (Conclusion), a practitioner would be able to immediately envision using a double-stranded RNA ligase such as those taught by Torchia in order to make siRNAs as taught and suggested by Sosic/Jung.
Kraynack is a research article that teaches siRNA molecules comprising 2’-O-methyl modifications (Title, Abstract, and throughout). Kraynack teaches that such siRNA molecules comprising 2’O-methyl modifications have been reduced to practice (Abstract and Introduction). Kraynack teaches that it is known that 2’-O-methyl modifications in siRNA molecules show an increase in their resistance to nuclease degradation (page 163 final paragraph into page 164 first paragraph). Thus, Kraynack teaches a direct motivation to incorporate 2’-O-methyl modifications into siRNA molecules.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use the method taught by Sosic to manufacture siRNA as taught by Jung because Sosic teaches a direct motivation to make siRNA molecules, namely, that siRNAs are known to be important molecules used in therapeutics. Furthermore, there is a reasonable expectation of success in making siRNAs because Sosic already reduced to practice their methods with other oligonucleotides of similar length and furthermore references Jung who also teaches that siRNAs have been reduced to practice.
Furthermore, a practitioner would be motivated to substitute the DNA ligase taught by Sosic for a double-stranded RNA ligase such as Rnl2 as taught by Torchia because Sosic teaches that double-stranded RNA products such as siRNA are known to be useful to produce, which would require ligation by a double-strand break ligation such as Rnl2 (Sosic, Abstract). Additionally, such a substitution would result in predictable results because Torchia teaches that the structure and functionality of Rnl2 family ligases is already well-understood (page 6218, right column paragraphs 2-4 into page 6219, left column). Sosic already teaches a motivation to apply their synthesis method do double-stranded RNA product such as siRNA because Sosic teaches the value of producing siRNA; a practitioner would therefore understand that they would simply use available tools in the industry (i.e., double-stranded RNA ligases) in order to make the product suggested by Sosic.
Additionally, it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the oligonucleotide modifications taught by Sosic/Jung with the 2’-O-methyl modification taught by Kraynack because such a modification is the simple substitution of one known prior art element for another with predictable results. In the present case, a practitioner would simply substitute and/or augment the modifications taught by Sosic/Jung with the 2’-O-methyl modification taught by Kraynack with predictable results as Kraynack has already reduced to practice functional siRNA molecules with said 2’-O-methyl modification. Furthermore, a practitioner would be motivated to combine the prior art because Kraynack teaches that the 2’-O-methyl modification has the advantageous benefit of reducing nuclease degradation.
Regarding claim 2, Sosic teaches sticky ends which are 4 nucleotides in length (Figure 4A).
Regarding claim 3, Sosic teaches raw oligonucleotide fragments that are 9, 12, 16, 18, 19, and 21 nucleotides in length (Table 1).
Regarding claim 6, Torchia teaches that the RNA ligase is in the Rnl2 family (page 6218, right column, paragraphs 2-3)
Regarding claim 10, Sosic teaches that equal amounts of the complementary strands (i.e., a ratio of 1:1) of each pair were mixed (page 435, right column, first paragraph).
Regarding claim 11, Sosic teaches subjecting the raw material fragments to a treatment with a monovalent cationic salt whose concentration is 10 mM or less (“10 mM NaCl,” page 435, right column, second paragraph).
Regarding claim 12, Jung teaches siRNA manufacturing which proceeds at room temperature (page 307, left column, third paragraph).
Regarding claims 13-14, Sosic teaches that siRNA molecules should be manufactured as therapeutics.
Sosic does not specifically teach that contaminants in the product should be suppressed and that the oligos should be purified.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the teachings of Sosic and Jung to suppress contamination of the product because such a claim limitation amounts to nothing more than routine laboratory optimization. Furthermore, Sosic teaches that siRNAs are to be used as therapeutics; a practitioner making siRNAs would therefore be motivated to suppress contaminants as a routine part of making a therapeutic product. Similarly, it would be obvious to a practitioner of ordinary skill to purify the oligo product rendered obvious by Sosic and Jung, because Sosic teaches that such siRNA products are therapeutics; a practitioner would be motivated to purify the product so that it could be used as intended by Sosic (i.e., as a therapeutic).
Regarding claims 15 and 18, Sosic teaches ligation reactions occurring at 16oC (page 435, right column first paragraph, final line).
Regarding claim 17, Kraynack teaches that the -O-C1-6 alkyl is 2’-O-methyl (Abstract, throughout).
Response to Arguments
The Applicant’s arguments filed 10/10/2025 have been considered but are not persuasive. The Applicant argues that Sosic teaches terminally added PEG and merely references Jung as an example of a siRNA with terminally added PEG, not suggesting to enzymatically make modified siRNA. This argument is not persuasive because it mischaracterizes the teachings of the prior art. Sosic in fact directly teaches the importance of siRNA as therapeutic molecules because of their versatility in treating diseases (Abstract). This is a direct motivational teaching to manufacture siRNA molecules using enzymatic methods such as those taught by Sosic, who reduced their method to practice.
The Applicant argues that Jung, while teaching the length of siRNA to be 19-21, does not suggest making molecules this small. This argument is not persuasive because the teaching that siRNA is fully functional at 19-21 nucleotides in length and also a very important therapeutic class of molecule is a suggestion to make a molecule as small as 19-21 nucleotides in length, so that a practitioner could make therapeutically relevant molecules (i.e., siRNA). Contrary to the Applicant’s arguments, the combination of Sosic and Jung certainly motivates a practitioner to make siRNA molecules, which were known to be short and functional (19-21 nts). By teaching that siRNA molecules are important therapeutic molecules, a practitioner would understand that a molecule as short as 19-21 nts would be made, in order to follow the teachings and suggestions of Sosic/Jung (i.e., to make the valuable siRNA molecule).
The Applicant argues that Sosic/Jung focus on terminally added PEG, and that there is no motivation to make other, non-terminal modifications. This argument is not persuasive. As an initial matter, the Applicant argues that the claims are now directed to non-terminal modifications. However, this argument is moot because the claims do not require that the modifications be non-terminal modifications. The Applicant only offers a piecemeal analysis of the combination of prior art references, arguing that no motivation exists to apply any other modifications. However, as disclosed and discussed above, other chemical modifications are widely known in the art, specifically associated with siRNAs (Kraynack). For instance, Kraynack teaches that the 2’-O-methyl modification of siRNA is advantageous because of its stabilizing effects on the molecule (page 163 final paragraph into page 164 first paragraph, Kraynack). The Applicant’s arguments do not take into consideration the fact that a person of ordinary skill in the art would understand the importance of introducing well-known modifications into siRNA, as already taught by Kraynack.
The Applicant argues that the modifications recited unpredictably alter ligase activity. This argument is not persuasive because it is an argument of counsel not supported by any evidence of record. Applicants have provided only arguments of counsel, and arguments of counsel cannot take the place of factually supported objective evidence. See, e.g., In re Huang, 100 F.3d 135,139-40, 40 USPQ2d 1685, 1689 (Fed. Cir. 1996); In re De Blauwe, 736 F.2d 699, 705, 222 USPQ 191, 196 (Fed. Cir. 1984).
The Applicant argues that there is no motivation in Jung to introduce non-cleavable modifications. This argument is not found to be persuasive because Kraynack teaches a motivational reason to include 2’-O-methyl modifications in siRNA, so that they stabilize the molecule page 163 final paragraph into page 164 first paragraph, Kraynack). The Applicant’s argument does not take into consideration that other knowledge in the art could be applied to the same molecule (i.e., siRNA), where Kraynack certainly provides a motivation to include the well-known 2’-O-methyl modification into siRNA. Furthermore, a practitioner would understand that the PEG modification and 2’-O-methyl modification are different, and that not all “non-cleavable” modifications necessarily interfere with a molecule’s functionality. The fact that Kraynack teaches and reduces to practice siRNA modified with 2’-O-methyl, and also teaches that it reduces unwanted degradation is sufficient motivation to use a 2’-O-methyl modification in an siRNA molecule, which is within the skill of a person of ordinary skill. Furthermore, there is a predictable expectation of success because this is already a known modification which has been reduced to practice (Kraynack).
The Applicant argues that the invention requires a double-stranded RNA ligase. However, Torchia teaches double-stranded RNA ligases; such ligases are therefore known. Furthermore, a practitioner would immediately understand that siRNA is a double-stranded RNA (e.g., Jung Conclusion, first sentence). Given the motivational teaching to make siRNA, a practitioner would understand that a double-stranded RNA ligase should be used. Furthermore, this is in keeping with the double-stranded ligation strategy taught by Sosic, with the exception that the ligase of the present invention is an RNA ligase where Sosic taught a double-stranded DNA ligase. In short, double-stranded RNA ligases were known and furthermore a practitioner would be motivated to use a double-stranded ligase in order to make siRNA (which is double-stranded RNA).
The Applicant argues that Sosic does not teach oligos which are less than 28 nucleotides. This argument is not persuasive. While it appears that Sosic teaches DNA oligos which are 28 nucleotides, it should be pointed out that Sosic does also teach and suggest making siRNA, which as evidenced by Jung is 19-21 nucleotides in length. Such a teaching is in fact a teaching and suggestion to make oligos as short as 19-21 nucleotides, even if the oligo fragments of Sosic were 28 nucleotides in length. Furthermore, Sosic does also teach partially double-stranded aptamer formation, where the complementary region (in the form of an adapter) is as short as 12 nucleotides (see Figure 6, and description on page 439, right column, paragraph 3). Thus, the complementary region of Sosic appears to tolerate strategies where the region is shortened.
Furthermore, the Applicant argues that motivation exists to lengthen fragment regions but not to shorten them. This argument is not persuasive because Sosic teaches a motivational teaching to make siRNA, which as evidenced by Jung is shorter than the fragments made my Sosic. There is therefore a motivation to shorten the fragments of Sosic, so as to make siRNA. The Applicant argues that there is no motivation of shortening the annealing region; however, shortening the annealing region would not necessarily be required, where the complementary region could be shortened instead to arrive at the recited siRNA design. Taken in totality, and given the strong motivational teaching in Sosic to make shorter oligos (i.e., siRNA), Sosic and Jung do not teach away from making shorter oligos than Sosic. Even if an increase in secondary products exists, a practitioner would still be motivated to manufacture the valuable therapeutic product siRNA.
The Applicant argues that it is not obvious to use a double-stranded RNA ligase, as Sosic uses a double-stranded DNA ligase. This argument is not found persuasive because of the motivational teaching of Sosic to make siRNA (a double-stranded RNA ligase). A practitioner would understand that in order to modify the teaching of Sosic to make siRNA an RNA ligase would be suited for this task. Additionally, the Applicant references unpredictable results shown in Figure 18. This argument is not found persuasive because the specification and drawings do not appear to contain a Figure 18.
The Applicant argues that Torchia and Kraynack do not remedy the deficiencies of Sosic/Jung. These arguments are not persuasive because the combination of Sosic/Jung/Torchia/Kraynack does not appear to contain deficiencies.
Double Patenting – Updated in response to amendment
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-3, 6, 10-15, and 17-18 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-9 of U.S. Patent No. 11,525,132 B2 (‘132) in view of Sosic (Sosic A et al. Bioconjug Chem. 2014 Feb 19;25(2):433-41) and Jung (Jung S et al. J Control Release. 2010 Jun 15;144(3):306-13), Torchia (Torchia C et al. Nucleic Acids Res. 2008 Nov;36(19):6218-27), and Kraynack (Kraynack BA et al. RNA. 2006 Jan;12(1):163-76).
Regarding claim 1, claims 3-8 of ‘132 recite:
3. A method for producing a nucleic acid product, said method comprising linking two or more nucleic acid materials in the presence of a ligase mutant according to claim 1 to form said nucleic acid product, wherein said two or more nucleic acid materials are selected from the group consisting of one or more single-stranded nucleic acid materials, one or more double-stranded nucleic acid materials, and a mixture thereof.
4. The method according to claim 3, wherein said two or more nucleic acid materials are RNA.
5. The method according to claim 3, wherein said two or more nucleic acid materials are four or more single-stranded RNAs.
6. The method according to claim 3, wherein said nucleic acid product contains a complementary portion having a base length of 12 to 27.
7. The method according to claim 3, wherein said two or more nucleic acid materials are DNA and/or a modified nucleic acid.
8. The method according to claim 3, wherein said two or more nucleic acid materials have a concentration of 1 μM or more.
9. The method according to claim 3, wherein said nucleic acid product is siRNA.
Thus, claims 3-9 of ‘132 recite the claim limitations of instant claim 1 with the exception that claims 3-9 of ‘132 do not recite that the complementary regions comprise sticky ends.
Regarding claim 1, Sosic teaches a method for producing a modified oligonucleotide comprising a complementary portion having 28-37 nucleotide length, where the method comprises forming the modified oligonucleotide by treating four or more oligonucleotide raw material fragments in total in the presence of an oligonucleotide ligase (Title, Table 1, and e.g., Figure 5A). Sosic discloses that T4 DNA ligase was used (Abstract). Furthermore, Sosic teaches that the oligonucleotides vary in length (e.g., 9, 12, 16, 18, 19, 21, and 28 nucleotides, Table 1). Sosic teaches that eight single strand oligonucleotide raw material fragments were combined to form double stranded oligos (e.g., d+d’ combined into D, Table 1). Furthermore, Sosic teaches that resulting nucleotides would be the product of at least four oligonucleotide raw material fragments (see Figure 5A, which depicts at least four raw fragments).
Additionally, regarding the claim limitation that the modified oligonucleotide is “siRNA,” Sosic teaches that siRNA molecules attract great interest owing to their versatility to treat a wide range of diseases and their potential high selectivity (Abstract). Sosic further teaches that modified siRNA have demonstrated an improved cell internalization and stability with respect to free nucleic acids (Introduction, first paragraph). Sosic therefore directly teaches a motivation to create modified oligonucleotides that are siRNAs, because such molecules are known to be useful as therapeutics in disease contexts (Abstract).
Concerning steps (i) and (ii), Sosic teaches that the 5’ overhangs of the fragment links D, DF, and S are cohesive to A and upon ligation represent an EcoRI restriction site (page 439, left column, paragraphs 1-2 and Figure 4A). Thus, Sosic teaches that one or more fragment linking sites are present in the complementary portion in each strand with two or more fragment linking sites total (Figures 4A-5A, page 439, left column, paragraphs 1-2). Furthermore, Sosic teaches that a sticky end is present when the modified oligonucleotide is divided that is 1-10 nucleotides in length (see EcoRI sticky end site, Figure 4A).
Concerning step (iii), Sosic teaches that at least one oligonucleotide of the raw material fragment has been modified (page 435, left column, third paragraph, and Abstract, “PEGylated nucleic acids”).
Regarding step (iv), Sosic teaches raw material fragments which are between 5 and 17 nucleotides in length (e.g., fragments “s” and “s’” in Table 1). Given that Sosic teaches raw material fragments between 5-17 nts in length, a practitioner could immediately envision that all four could be 5-17 nts in length. Furthermore, Sosic teaches that the TBA fragment is a 15-mer added to a 6T tail that makes aptamers partly complementary to T, thus further teaching raw materials which are between 5-17 nts in length (page 434 right column second paragraph to page 435 left column, first paragraph).
Regarding step (v) claim 1, Sosic teaches raw material fragments with complementary portions between 11-27 nucleotides in length (e.g., see sequence “D” in Table 1, where complementarity region is 18 nucleotides).
Sosic, while teaching that siRNAs should be manufactured due to their therapeutic importance, did not specifically make siRNAs in their method. Sosic, while teaching the ligation of DNA using double-stranded DNA ligase, does not specifically teach a double stranded RNA ligase. Sosic, while teaching a motivation to modify oligonucleotides to enhance stability, does not teach that the modification is a 1’,2’,3’,or 4’ -O-C1-6 alkyl modification.
Sosic references Jung in the Introduction, first paragraph (line 7). Thus, Sosic and Jung directly overlap is subject matter and field of endeavor, as evidenced by the fact that Sosic directly references Jung. A practitioner would thus reasonably be directed to the teachings of Jung based on Sosic, as Jung is referenced by Sosic concerning siRNA molecules. Jung teaches that siRNA molecules are 19-21 nucleotides in length and can target mRNA molecules (Introduction, first line). Jung teaches and reduces to practice siRNA molecules with modifications and cleavable linking sites (Abstract). Jung teaches siRNA molecules that are 19-21 nucleotides in length, and that siRNA molecules are designed to bind to mRNA targets (Jung, Introduction, first paragraph). Thus, Jung teaches that siRNA molecules have complementary regions which are between 11-27 nucleotides in length.
Furthermore with regards to the length of the siRNA and its complementary regions, Jung who teaches that siRNAs can be between 19-21 nucleotides in length which target mRNA (i.e., have complementary regions). Thus, a practitioner would understand that the methods and products of Sosic could and should be designed with such lengths to act as siRNAs because Sosic teaches that siRNAs are known to be useful as therapeutics (Abstract and Introduction of Sosic). Jung also teaches sense and antisense strands of siRNA, and therefor teaches siRNAs are double-stranded RNA molecules (Abstract).
Sosic and Jung, while teaching the ligation of double-stranded DNA using a DNA ligase (Sosic, Abstract) and the ligation of RNA molecules using RNA ligase (Jung, page 307, right column, third paragraph), and furthermore teach that siRNAs are double-stranded RNA molecules which have important therapeutic roles (Sosic and Jung Abstracts), do not specifically teach double-stranded RNA ligases.
Torchia is a research article which teaches RNA ligases and their uses (Title, Abstract, and see document). Torchia teaches that there are different families of RNA ligases, including the single-strand break repair family Rnl1, and the double-strand ligation family Rnl2 (page 6218, right column, paragraphs 2-3). Torchia also teaches that such ligases, their structure, and their functionality is already known (page 6218, right column, final paragraph into page 6219, left column). Thus, Torchia teaches that double-stranded RNA ligases such as Rnl2 family ligases are known ligases with predictable functionality (page 6218, right column, final paragraph into page 6219, left column). Given that Jung teaches that siRNA is double-stranded RNA (Conclusion), a practitioner would be able to immediately envision using a double-stranded RNA ligase such as those taught by Torchia in order to make siRNAs as taught and suggested by Sosic/Jung.
Kraynack is a research article that teaches siRNA molecules comprising 2’-O-methyl modifications (Title, Abstract, and throughout). Kraynack teaches that such siRNA molecules comprising 2’O-methyl modifications have been reduced to practice (Abstract and Introduction). Kraynack teaches that it is known that 2’-O-methyl modifications in siRNA molecules show an increase in their resistance to nuclease degradation (page 163 final paragraph into page 164 first paragraph). Thus, Kraynack teaches a direct motivation to incorporate 2’-O-methyl modifications into siRNA molecules.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to use to modify claims 3-9 of ‘132 to include sticky ends to manufacture siRNA as rendered obvious by Sosic/Jung because such a modification is the simple combination of known prior art elements to yield predictable results. Sosic teaches a direct motivation to make siRNA molecules, namely, that siRNAs are known to be important molecules used in therapeutics. Furthermore, the methods of Sosic use sticky ends (figure in the Abstract). There is a reasonable expectation of success in making siRNAs because Sosic already reduced to practice their methods with other oligonucleotides of similar length and furthermore references Jung who also teaches that siRNAs have been reduced to practice.
Furthermore, a practitioner would be motivated to substitute the DNA ligase taught by Sosic for a double-stranded RNA ligase such as Rnl2 as taught by Torchia because Sosic teaches that double-stranded RNA products such as siRNA are known to be useful to produce, which would require ligation by a double-strand break ligation such as Rnl2 (Sosic, Abstract). Additionally, such a substitution would result in predictable results because Torchia teaches that the structure and functionality of Rnl2 family ligases is already well-understood (page 6218, right column paragraphs 2-4 into page 6219, left column). Sosic already teaches a motivation to apply their synthesis method do double-stranded RNA product such as siRNA because Sosic teaches the value of producing siRNA; a practitioner would therefore understand that they would simply use available tools in the industry (i.e., double-stranded RNA ligases) in order to make the product suggested by Sosic.
Additionally, it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the oligonucleotide modifications taught by Sosic/Jung with the 2’-O-methyl modification taught by Kraynack because such a modification is the simple substitution of one known prior art element for another with predictable results. In the present case, a practitioner would simply substitute and/or augment the modifications taught by Sosic/Jung with the 2’-O-methyl modification taught by Kraynack with predictable results as Kraynack has already reduced to practice functional siRNA molecules with said 2’-O-methyl modification. Furthermore, a practitioner would be motivated to combine the prior art because Kraynack teaches that the 2’-O-methyl modification has the advantageous benefit of reducing nuclease degradation.
The claim elements of instant claim 1 are therefore obvious in view of claims 3-9 of ‘132 in view of Sosic/Jung/Torchi/Kraynack.
Regarding claim 2, Sosic teaches sticky ends which are 4 nucleotides in length (Figure 4A).
Regarding claim 3, Sosic teaches raw oligonucleotide fragments that are 9, 12, 16, 18, 19, and 21 nucleotides in length (Table 1).
Regarding claim 6, Torchia teaches that the RNA ligase is in the Rnl2 family (page 6218, right column, paragraphs 2-3)
Regarding claim 10, Sosic teaches that equal amounts of the complementary strands (i.e., a ratio of 1:1) of each pair were mixed (page 435, right column, first paragraph).
Regarding claim 11, Sosic teaches subjecting the raw material fragments to a treatment with a monovalent cationic salt whose concentration is 10 mM or less (“10 mM NaCl,” page 435, right column, second paragraph).
Regarding claim 12, Jung teaches siRNA manufacturing which proceeds at room temperature (page 307, left column, third paragraph).
Regarding claims 13-14, Sosic teaches that siRNA molecules should be manufactured as therapeutics.
‘132/Sosic/Jung does not specifically teach that contaminants in the product should be suppressed and that the oligos should be purified.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the teachings of ‘132, Sosic and Jung to suppress contamination of the product because such a claim limitation amounts to nothing more than routine laboratory optimization. Furthermore, Sosic teaches that siRNAs are to be used as therapeutics; a practitioner making siRNAs would therefore be motivated to suppress contaminants as a routine part of making a therapeutic product. Similarly, it would be obvious to a practitioner of ordinary skill to purify the oligo product rendered obvious by Sosic and Jung, because Sosic teaches that such siRNA products are therapeutics; a practitioner would be motivated to purify the product so that it could be used as intended by Sosic (i.e., as a therapeutic).
Regarding claims 15 and 18, Sosic teaches ligation reactions occurring at 16oC (page 435, right column first paragraph, final line).
Regarding claim 17, Kraynack teaches that the -O-C1-6 alkyl is 2’-O-methyl (Abstract, throughout).
Response to Arguments
The Applicant has not offered an argument regarding the double patenting rejection. The rejection is therefore maintained.
Conclusion
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/D.C.R./Examiner, Art Unit 1635
/KIMBERLY CHONG/Primary Examiner, Art Unit 1636