Detailed Action
► The applicant's response (filed 24SEP 2025) to the Office Action has been entered. Following the entry of the claim amendment(s), Claim(s) 1-2, 5-6, 11, 13, 15-17, 20-23, 26-30, 32, 34—36, 38 and 41-55 is/are pending. Rejections and/or objections not reiterated from the previous office action are hereby withdrawn. The following rejections and/or objections are either newly applied or reiterated. They constitute the complete set presently being applied to the instant application.
► The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA . 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 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 text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claim Rejection(s) under 35 U.S.C. 112(b)/ 112 (pre-AIA ), second paragraph
► Claim(s) 45 is/are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite in that it fails to point out what is included or excluded by the claim language.
Claim 45 is indefinite because the phrase “the affinity labeling” lacks proper antecedent basis in Claim 22. Claim 22 does teach” labeling” but fails to teach “affinity labeling”
Claim Rejection(s) under 35 U.S.C. 102
► Claim 1-2, 5-6, 11, 17, 20-23, 26-27, 36, 38, 42-43 and new Claim(s) 44-46 and 48-55 is/are rejected under 35 U.S.C. 102(a)(2) or (a)(1) as being anticipated by Bjorkbom et al. [JACS 137:14430-14438 (2015) — hereinafter “Bjorkbom”] .
As regards Claim 1, Bjorkbom teach an RNA sequencing method comprising all of the
limitations of Claim 1-2, 5-6, 11, 21 -24, 26-27. See the entire document. For example, Bjorkbom teach a bidirectional direct sequencing method able to determine the primary sequence of given RNA molecules, as well as, the presence and/or location of non-canonical bases, . In particular at the bottom of Column 1 on pg.14431. Bjorkbom a generic procedure that permits RNA oligonucleotides to be sequenced directly, without extraneous labeling or reverse transcription procedures. This method consists of an optimized technique for partial RNA degradation with formic acid, high performance liquid chromatography (HPLC) separation of hydrolytic fragments, online ESI-QTOF mass analysis, and a computational algorithm for read generation from survey mass spectra that generates paired end reads. Together these methods give a simple and robust approach to the sequencing of modified RNA. We further show that in the case of isomeric modifications, such as methylation, the workflow is compatible with tandem MS for disambiguation. Central to the success of the methodology are the formic acid degradation protocol and our ability to correlate fragment masses with chromatographic retention times (RTs), facilitating bidirectional sequencing. With continued improvements in MS sensitivity, we expect this direct sequencing strategy to find utility in pinpointing the chemical identity and position of nucleotide modifications in cellular RNA.
As regards Claim 2 and 5, Bjorkbom explicitly teach the use of HLPC and MS (e.g. ESI-
QTOF) , see the bottom of Column 1 on pg.14431.
As regards Claim 6, note that Bjorkbom teach the use of labeling via biotin and the bulky hydrophobic labeling moiety Cy3. See at least the legend of Fig. 3 on pg.14434.
As regards Claim 11 and new Claim 46, Bjorkbom teach both chemical digestion (i.e. acid hydrolysis), and enzymatic degradation, see at least the para bridging pp.14430-14431.
Claim 17 is drawn, in part, to an embodiment of the method of Claim 1 wherein the RNA sample comprises a mixture of RNAs.
Bjorkbom teach this limitation, see at least at Figure S6 and the legend thereof.
Bjorkbom teach the limitation(s) of Claims 20-21, see the entire document.
Bjorkbom teach the limitation(s) of Claims 22-23, see the entire document.
Bjorkbom teach the limitation(s) of Claims 26-27, see the entire document.
Bjorkbom teach the limitation(s) of Claims 36 and 38, see the entire document.
Bjorkbom teach the limitation(s) of Claims 42-43, see the entire document.
New Claim 44 is drawn, in part, to the embodiment of Claim 1, wherein the 3’ end or the 5’ end of the RNA is labeled with a hydrophobic Cy3 tag or a biotin moiety. Claim 45 is drawn in part to an embodiment of the method of Claim 22 wherein the labeling of the labeling of the 5’ or the 3’ end is selected from a defined group which includes hydrophobic moiety.
Bjorkbom. Clearly teach these limitations see especially the legend of Figure 3.
Bjorkbom teach the limitation(s) of New Claim(s) 48-55, see especially the Figure 3 and the legend thereof.
Claim Rejection(s) under 35 U.S.C. 103
► Claim(s) 15 and new Claim 47 is/are rejected under 35 U.S.C. 103 as being unpatentable over Bjorkbom.
As regards Claims 15, it is unclear as to the timing of the labeling step as Bjorkbom teach that their method lacks an extraneous labeling step. see the last full para in Column 1, on pg. 14431, yet these authors clearly teach a labeling step, see the first full para in Column 2, pg.14432 and legend of Fig. 3 wherein it is taught to label RNA oligonucleotide R4. However, without a showing, it appear that labeling of R4 can be performed both before and/or after the degradation step. The selection of any order of performing process steps is prima facie obvious in the absence of new or unexpected results. See /n re Burhans, 154 F.2d 690, 69 USPQ330 (CCPA 1946).
As regards new Claim 47 it is unclear as to the timing of the degradation step as it relates to the labeling step as Bjorkbom teach that their method lacks an extraneous labeling step. see the last full para in Column 1, on pg. 14431, yet these authors clearly teach a labeling step, see the first full para in Column 2, pg.14432 and legend of Fig. 3 wherein it is taught to label RNA oligonucleotide(s). It appear that labeling of oligos is to occur before the degradation step. Regardless it was well established that the selection of any order of performing process steps is prima facie obvious in the absence of new or unexpected results. See /n re Burhans, 154 F.2d 690, 69 USPQ330 (CCPA 1946).
► Claim(s) 17 is/are rejected under 35 U.S.C. 103 as being unpatentable over Bjorkbom. as applied above against Claim 1 and further in view Burnett et al. [Chemistry & Biology 19: 60- 71 (2012) — hereinafter “Burnett’]
Claim 17 is drawn, in part, to an embodiment of the method of Claim 1 wherein the RNA sample comprises a therapeutic RNA molecule. As outlined above against Claim 1, Bjorkbom teach a method comprising most of the limitation of Claim 17 except these authors do not teach analyzing therapeutic RNA molecules. However, therapeutic RNA molecules and their use in medicine were known as as evidenced by Burnett, see the entire document. Accordingly, absent an unexpected result it would have been prima facie obvious to the PHOSITA at the time of the invention to substitute a therapeutic RNA of Burnett for one or more of the RNAs analyzed by Bjorkbom. Please note that substitution of one known second method/reagent with known properties for a first known method/reagent with known properties would have been prima facie obvious to the ordinary artisan at the time of the invention in the absence of an unexpected result. As regards the motivation to make the substitution recited above, the motivation to combine arises from the expectation that the prior art elements will perform their expected functions to achieve their expected results when combined for their common known purpose. Support for making this obviousness rejection comes from the M.P.E.P. at 2144.07 and 2144.09, as well as, the SCOTUS decision in KSR International. Co. v. Teleflex, Inc., et al., 550 U.S.398 (2007).
► Claim(s) 28-30, 32 and 34 is/are rejected under 35 U.S.C. 103 as being unpatentable over Bjorkbom as applied above against Claims 1 and 22-23 and further in view of Friso et al.[ Analytical Chemisrt 74(17) : 4526 (2002) -hereinaftewr “Friso”].
As outlined above against Claim 1 and 22-23, Bjorkbom teach a method comprising most of the limitation of Claim 28 except these authors do not teach analyzing DNA molecules rather Bjorkbom is focused on the analysis of RNA molecules. However, the analysis of DNA and digestion products thereof , was known as evidenced by at least Friso, see the entire document. Accordingly, absent an unexpected result it would have been prima facie obvious to the PHOSITA at the time of the invention to substitute the DNA of Friso for the RNA of Bjorkbom. Please note that substitution of one known second method/reagent with known properties for a first known method/reagent with known properties would have been prima facie obvious to the ordinary artisan at the time of the invention in the absence of an unexpected result. As regards the motivation to make the substitution recited above, the motivation to combine arises from the expectation that the prior art elements will perform their expected functions to achieve their expected results when combined for their common known purpose. Support for making this obviousness rejection comes from the M.P.E.P. at 2144.07 and 2144.09, as well as, the SCOTUS decision in KSR International. Co. v. Teleflex, Inc., et al., 550 U.S.398 (2007). Bjorkbom teach the limitation(s) of Claim(s) 29-30, 32 and 34, see the entire document noting especially the passages identified above.
Bjorkbom teach the limitation(s) of Claim(s) 29-30, 32 and 34, see the entire document noting especially the passages identified above.
► Claim(s) 35 is/are rejected under 35 U.S.C. 103 as being unpatentable over Bjorkbom as applied above against Claims 1 and further in view of Durairaj et al. [Analytica Chica Acta 173-181(2008) - Durairaj hereinafter ].
As outlined above against Claim 1 and 22-23, Bjorkbom teach a method comprising most of the limitation of Claim 35 except these authors do not explicitly teach analyzing RNA molecules comprising pseudouridine nucleobases wherein the pseudouridine nucleobases are treated with CMC. However, the analysis of RNA molecules comprising pseudouridine nucleobases was known as was the treatment of said pseudouridine containing RNA molecule with CMC as evidenced by Durairaj. see at least the abstract. Accordingly, absent an unexpected result it would have been prima facie obvious to the PHOSITA at the time of the invention to modify the method of Bjorkbom wherein RNAs suspected of comprising and/or known to comprise pseudouridine nucleobases are treated with CMC in order to facilitate the analysis/sequencing of said RNA molecules as suggested by Durairaj.
► Claim(s) 17 and 41 is/are rejected under 35 U.S.C. 103 as being unpatentable over
Bjorkbom as applied above against Claim 1 and further in view Gryaznov et al. [Nucleic Acids
Research 26(18) : 4160-4167 (1998) — hereinafter “Gryaznov’].
Claim 17 is drawn, in part, to an embodiment of the method of Claim 1 wherein the RNA
sample comprises an RNA analog.
As outlined above against Claim 1, Bjorkbom teach a method comprising most of the
limitation of Claim 17 except these authors do not teach analyzing a RNA comprising an RNA analog (e.g. N3’-P5’ linked RNA molecules)). However, RNA analog containing molecules were known as was their use in the art as evidenced by Gryaznov. Accordingly would have been prima facie obvious to the PHOSITA at the time of the invention to substitute the RNA comprising an RNA analog of Gryaznov for one or more of the RNAs analyzed by Bjorkbom. Please note that substitution of one known second method/reagent with known properties for a first known method/reagent with known properties would have been prima facie obvious to the ordinary artisan at the time of the invention in the absence of an unexpected result. As regards the motivation to make the substitution recited above, the motivation to combine arises from the expectation that the prior art elements will perform their expected functions to achieve their expected results when combined for their common known purpose. Support for making this obviousness rejection comes from the M.P.E.P. at 2144.07 and 2144.09, as well as, the SCOTUS decision in KSR International. Co. v.Teleflex, Inc., et al., 550 U.S.398 (2007).
Claim 41 is drawn, in part, to an embodiment of the method of Claim 17 wherein the
analog of the RNA molecule is one comprising an N3’-P5’ linked phosphonamidite RNA.
Gryaznov teach this limitation, see at least the abstract.
Response to Applicant’s Amendment / Arguments
► Applicant's arguments with respect to the claimed invention have been fully and carefully considered but are moot in view of the new ground(s) of rejection.
The applicant has traversed the of rejection of Claim 1 arguing that Bjorkbom does not teach labeling of the RNA to be analyzed and points to the last full para in Column 1 of pg. 14431 wherein Bjorkbom expressly teach RNA sequencing analysis without extraneous labeling. In response the examiner readily concedes the labeling point. However, later in the reference Bjorkbom also expressly teach an embodiment in which RNA oligos are labeled and then sequenced, see Figure 3 and the legend thereof. As such the examiner finds that Bjorkbom anticipates and/or reasonably suggest two embodiments (i.e. both a labeling embodiment and an embodiment lacking a labeling step).
Conclusion
C1. Applicant's amendment necessitated the new grounds of rejection. Accordingly, THIS ACTION IS MADE FINAL. See M.P.E.P. § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 C.F.R. § 1.136(a).
A SHORTENED STATUTORY PERIOD FOR RESPONSE TO THIS FINAL ACTION IS SET TO EXPIRE THREE MONTHS FROM THE DATE OF THIS ACTION. IN THE EVENT A FIRST RESPONSE IS FILED WITHIN TWO MONTHS OF THE MAILING DATE OF THIS FINAL ACTION AND THE ADVISORY ACTION IS NOT MAILED UNTIL AFTER THE END OF THE THREE-MONTH SHORTENED STATUTORY PERIOD, THEN THE SHORTENED STATUTORY PERIOD WILL EXPIRE ON THE DATE THE ADVISORY ACTION IS MAILED, AND ANY EXTENSION FEE PURSUANT TO 37 C.F.R. § 1.136(a) WILL BE CALCULATED FROM THE MAILING DATE OF THE ADVISORY ACTION. IN NO EVENT WILL THE STATUTORY PERIOD FOR RESPONSE EXPIRE LATER THAN SIX MONTHS FROM THE DATE OF THIS FINAL ACTION.
C2. Any inquiry concerning this communication or earlier communications from the examiner should be directed to Ethan Whisenant whose telephone number is (571) 272-0754. The examiner can normally be reached Monday-Friday from 8:30 am -5:30 pm EST or any time via voice mail. If repeated attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Anne Gussow, can be reached at (571) 272-6047.
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/ETHAN C WHISENANT/Primary Examiner, Art Unit 1683 ethan.whisenant@uspto.gov