DETAILED ACTION
Status of the Claims
Claims 1, 5, 42, 46, and 48 are amended.
Claims 50-53 are newly added.
Claims 2, 9, 13, 16-24, 26-29, 31-38, 40-41, 43, and 47 are canceled.
Claims 1, 3-8, 10-12, 14-15, 25, 30, 39, 42, 44-46, and 48-53 are currently pending and are examined herein.
The following Office Action is in response to Applicant’s communication dated 12/29/2025. Rejection(s) and/or objection(s) not reiterated from previous office actions are hereby withdrawn. Specifically, the rejection of claims 1, 3-8, 10-12, 14-15, 25, 30, 39, 42, and 44-45 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112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement is withdrawn in light of amendments made by Applicant to the claims in the 12/29/2025 response. The following rejection(s) and/or objection(s) are either reiterated or newly applied. 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 .
Priority
This application claims the benefit of prior-filed application No. 62/614,307 under 35 U.S.C. 120, 121, 365(c), or 386(c) or under 35 U.S.C. 119(e). If the prior-filed application is an international application designating the United States, it must be entitled to a filing date in accordance with PCT Article 11; if the prior-filed application is an international design application designating the United States, it must be entitled to a filing date in accordance with 37 CFR 1.1023; and if the prior-filed application is a nonprovisional application under 35 U.S.C. 111(a), the prior-filed application must be entitled to a filing date as set forth in 37 CFR 1.53(b) or 1.53(d) and include the basic filing fee set forth in 37 CFR 1.16. See 37 CFR 1.78(d)(1). If the prior-filed application is a provisional application, the prior-filed application must be entitled to a filing date as set forth in 37 CFR 1.53(c) and the basic filing fee must be paid within the time period set forth in 37 CFR 1.53(g). See 37 CFR 1.78(a)(2).
This application is not entitled to the benefit of the prior-filed application because the prior-filed application was not entitled to a filing date as being incomplete. Applicant is required to delete the reference to the prior-filed application. Please see MPEP § 211.01.
Therefore 01/05/2019 (i.e., the date of filing of PCT/US2019/012444) is the date for the purposes of prior art concerning the claims.
New Claim Objections
Necessitated by Amendments
Claims 51 and 52 are objected to as being dependent upon a rejected base claim, but would be free from the prior art if rewritten in independent form including all of the limitations of the base claim and any intervening claims. Appropriate correction is required.
Modified Claim Rejections – 35 U.S.C. 103(a)
Necessitated by Amendments
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.
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.
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 set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied 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.
Yun et al., Kuimelis et al., and Zhou et al.
Claims 1, 3-8, 10-12, 14-15, 25, 30, 39, 42, 44-46, 48-50, and 53 are rejected under 35 U.S.C. 103 as being unpatentable over Yun et al. (U.S. PGPub 2011/0189608 A1, cited in the IDS of 10/02/2020, of record) in view of Kuimelis et al. (U.S. 7,910,312 B2, of record) and further in view of Zhou et al. (WO 2016/168825 A1, published Oct. 20, 2016).
Regarding claim 42, Yun teaches a photoresist composition comprising:
about 2.5-4.5% by weight of a photoacid generator (e.g., as per ¶0039)
about 2.5-4.5% by weight a photosensitizer (e.g., as per ¶0039)
about 3.0-4.0% by weight a matrix (e.g., as per ¶0039), and
about 86.7-91.8% by weight a solvent (e.g., as per ¶0039).
Regarding claims 44-45, Yun discloses identical ranges of weight percentages of photosensitizer and photoacid generators (e.g., as per ¶0039).
Note that in accordance with MPEP § 2144.05(I), in the case where the claimed ranges “overlap or lie inside ranges disclosed by the prior art” a prima facie case of obviousness exists. In the present case, Yun discloses “approximately 1 to 20 wt % of a resin, approximately 1 to 10 wt % of a photoacid generator, approximately 1 to 10 wt % of a sensitizer, and balance of a solvent”, as per ¶0039.
Regarding the limitation of claim 42 that states “wherein the photoresist composition is capable of forming a high contrast pattern of oligonucleotides on a microarray comprising a transition from full chemistry to no chemistry of between about 100 nm”, this is a recitation of intended use of the instant claimed photoresist composition and a recitation of the intended use of the claimed invention must result in a structural difference between the claimed invention and the prior art in order to patentably distinguish the claimed invention from the prior art. If the prior art structure is capable of performing the intended use, then it meets the claim. Please see MPEP 2111.02, citing In re Sinex, 309 F.2d 488, 492, 135 USPQ 302, 305 (CCPA 1962) (statement of intended use in an apparatus claim did not distinguish over the prior art apparatus), and MPEP 2112.01 citing In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990) stating that “discovery of an unobvious property and use does not overcome the statutory restraint of section 102 when the claimed composition is known”. In the present case, since the claimed ranges of photoresist components fall within the ranges of the applied prior art, then there is a prima facie case for the photoresist composition to also be capable of forming a high contrast such as the claimed high contrast. Similarly, regarding the limitation of claim 42 regarding the oligonucleotides comprising at least one zipcode sequence, it is noted that the claim is drawn to a photoresist composition “wherein the photoresist composition is capable of forming a high contrast pattern of oligonucleotides on a microarray”. Importantly, the claim does not require the presence of oligonucleotides, only that the photoresist composition is capable of forming said microarray, which is a statement of intended use of the composition. Again, if the prior art structure is capable of performing the intended use, then it meets the claim.
However, it is noted that the Yun reference is silent on the presence of an acid scavenger in the photoresist, as set forth in claim 42.
Kuimelis similarly discloses photoresists for the synthesis of nucleic acid biopolymers on arrays involving a photoacid generator to remove DMT protective groups, further disclosing the addition of acid scavengers to the photoresist (e.g., 0.25% by weight of polyvinylpyridone as per Examples 2-3 in col. 21-23).
It would have been prima facie obvious to a person of ordinary skill in the art prior to the effective filing date of the application to add an acid scavenger as per Kuimelis to the photoresist of Yun. One of ordinary skill in the art would have been motivated to do so since Kuimelis teaches the benefits of adding an acid scavenger, such as “to modulate contrast/sensitivity and decrease background (e.g., spontaneous detritylation)”, as per col. 20, lines 17-20.
One of ordinary skill in the art would have had a reasonable expectation of success as of the application’s effective filing date in combining the teachings of the prior art references to arrive at the invention as presently claimed since the simple addition (and any routine optimization) of an additional component to the photoresist would be within the grasp of the skilled artisan.
Regarding claim 1 and 14, Yun in view of Kuimelis disclose a method of forming a pattern of oligonucleotides on a microarray (e.g., as per col. 19-20 of Kuimelis, and/or Fig. 1-7 of Yun), comprising:
forming a photoresist layer by applying a photoresist composition onto an underlying layer of a substrate (e.g., as per col. 20 of Kuimelis, and/or ¶0047 and Fig. 2 of Yun), wherein the photoresist composition comprises the photoresist as above, wherein the underlying layer comprises a plurality of functional groups protected by protective groups (e.g., as per col. 20 of Kuimelis, and/or ¶0045 and/or Fig. 1 of Yun);
exposing a dose of light through a patterned mask onto the substrate (e.g., as per col. 20 of Kuimelis, and/or ¶0054 and/or Fig. 3 of Yun); and
removing protective groups on a section of the plurality of functional groups within at least one exposed region of the substrate (e.g., as per col. 20 of Kuimelis, and/or ¶0014 and/or ¶0040 of Yun); thereby forming a pattern on the substrate;
wherein the pattern comprises the at least one exposed region, and wherein the at least one exposed region is no more than 950 nm, 900 nm, 850 nm, 800 nm, 750 nm, or 700 nm in at least one dimension (e.g., as per Kuimelis col. 20, lines 12-16).
Regarding the limitation of claim 1 that states “the pattern is a high contrast pattern comprising a transition from full chemistry to no chemistry of between about 100 nm”, it is noted that In re Best (195 USPQ 430) and In re Fitzgerald (205 USPQ 594) discuss the support of rejections wherein the prior art discloses subject matter which there is reason to believe inherently includes functions that are newly cited or is identical to a product instantly claimed. In such a situation the burden is shifted to the applicants to "prove that subject matter shown to be in the prior art does not possess characteristic relied on" (205 USPQ 594, second column, first full paragraph). In the instant case, Kuimelis discloses that with the addition of the acid scavenger, nucleic acid features on the order of 100-1000 nm can be produced (e.g., as per col. 20, lines 11-17) and Yun in Fig. 16A-B and ¶0133 show features that are 460 and 760 nm high with very sharp transitions from trough to pillar top, such that there is reason to believe that the claimed range of chemistry transitions are achievable subject to no more than routine optimization. See MPEP 2144.05.
However, Yun in view of Kuimelis do not mention the use of zipcode sequences comprising an upper zipcode sequence and a lower zipcode sequence in the produced oligonucleotide patterns, as set forth in claims 1, 46, and 48-50.
Similar to Yun in view of Kuimelis, Zhou discloses forming dense patterns of oligonucleotides using photolithography and photoacid generators (e.g., as per para [0068]-[0070]). Zhou further discloses these spatial oligonucleotide barcode arrays as comprising oligonucleotides densely patterned on a surface wherein the oligonucleotides comprise capture probes as well as spatial barcode sequences (e.g., 5-35 bases in length as per para [0054]), wherein said spatial barcodes identifies an x, y coordinate and/or an x, y, z coordinate for the plurality of oligonucleotides (e.g., as per para [0004]-[0005] and/or Fig. 3A). Zhou discloses that the spatial barcode can reside at the 5’ end of the oligonucleotide (e.g., as per para [0030]). Zhou also discloses the presence of other elements in the oligonucleotide, such as sequencing adaptors, primer sequences, and other barcode sequences (e.g., as per para [0028] and/or Fig. 3A), as set forth in claim 53. This “spatial barcode” as taught by Zhou therefore anticipates and/or renders obvious the “zipcode” sequences of the presently rejected claims. Zhou does not specifically state that their “zipcode” sequence comprises an “upper zipcode” sequence and a “lower zipcode” sequence, as set forth in claims 1, 42, 46, 48-50, and 53. However, it is noted that the “zipcode” sequences of Zhou are 3-35 bases in length (e.g., as per para [0054]) and therefore can reasonably be deconstructed to two (or more) subsequences, as supported by the rationales recited in MPEP § 2144.04, absent factual evidence to the contrary.
It would have been prima facie obvious to a person of ordinary skill in the art prior to the effective filing date of the application to include the “zipcode” sequences of Zhou in the patterned oligonucleotides of Yun in view of Kuimelis. One of ordinary skill in the art would have been motivated to do so since Zhou teaches the advantages of adding such sequences as per para [0002].
In accordance with MPEP 2141 citing KSR International Co. v. Teleflex Inc. (KSR), 550 U.S. 398, 82 USPQ2d 1385,1395 (2007), "[t]he combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results”, and as per MPEP 2143(I)(A), the rationale to support a conclusion that the claim would have been obvious is that all the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions, and the combination yielded nothing more than predictable results to one of ordinary skill in the art. In the present case, all of the elements of the spatial barcoded array were well known in the art, as per Yun, Kuimelis, and Zhou, the mere combining of the individual elements in one embodiment in the manner of the claimed invention results in no change in the elements respective functions, and the combination yields nothing more than predictable results.
One of ordinary skill in the art would have had a reasonable expectation of success as of the application’s effective filing date in combining the teachings of the prior art references to arrive at the invention as presently claimed since this would merely require the addition of the appropriate bases.
Regarding claim 3, Yun in view of Kuimelis disclose the above, further comprising:
contacting the functional groups within the at least one exposed region of the substrate with a first nucleotide reagent, thereby coupling a fraction of the functional groups within the at least one exposed region of the substrate with a first nucleotide (e.g., as per col. 20 of Kuimelis, and/or ¶¶0063-0065 and/or Fig. 4 of Yun).
Regarding claim 4, Yun in view of Kuimelis disclose the above, further comprising:
exposing another dose of light through another patterned mask onto the substrate (e.g., as per col. 20 of Kuimelis, and/or ¶0068 and/or Fig. 5 of Yun);
removing protective groups on another section of the plurality of functional groups within at least another exposed region of the substrate (e.g., as per col. 20 of Kuimelis, and/or ¶0068 and/or Fig. 5 of Yun); thereby forming another pattern on the substrate.
Note that while Kuimelis specifically recites preferentially producing arrays of oligonucleotides with features on the order of 100-1000 nm (e.g., as per col. 20 lines 15-16), the reference is silent on the explicit measuring of these feature sizes by using super resolution microscopy, as set forth in claims 1 and 4. Kuimelis does recite measuring the feature sizes of some of the arrays produced (e.g., as per TABLE 1 in col. 22) using SEM, which is reasonably a super resolution microscopy method, although these particular features are larger than 1 micron. As per MPEP § 2143(I)(A), the rationale to support a conclusion that the claim would have been obvious is that all the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions, and the combination yielded nothing more than predictable results to one of ordinary skill in the art. In the instant case, all of the elements of the super resolution microscopy were well known in the art, as per Kuimelis, the mere combining of the individual elements in one embodiment in the manner of the claimed invention results in no change in the elements respective functions, and the combination yields nothing more than predictable results. In the present case, the results of measuring sub-micron oligonucleotide features would reasonably be predictable, since SEM can achieve resolutions on the order of nanometers.
Regarding claim 5, Yun in view of Kuimelis disclose the above, further comprising:
(g) contacting the functional groups within the at least another exposed region of the substrate with a second nucleotide reagent, thereby coupling another fraction of the functional groups within the at least another exposed region of the substrate with a second nucleotide (e.g., as per col. 20 of Kuimelis, and/or ¶0069 and/or Fig. 6 of Yun).
Regarding claim 6, Yun in view of Kuimelis disclose the above, the first nucleotide is different from the second nucleotide (e.g., as per col. 20 of Kuimelis, and/or Fig. 6 of Yun).
Regarding claim 7, Yun in view of Kuimelis disclose the above, the at least one exposed region is different from the at least another exposed region (e.g., as per col. 20 of Kuimelis, and/or Fig. 5 of Yun).
Regarding claim 8, Yun in view of Kuimelis disclose the above, further comprising:
(e) forming another photoresist layer by applying another photoresist composition onto the substrate, wherein the another photoresist composition comprises another photoacid generator and another photosensitizer, wherein the underlying layer comprises a plurality of functional groups protected by protective groups;
(f) exposing another dose of light through another patterned mask onto the substrate;
(g) removing protective groups on another section of the plurality of functional groups and/or a nucleotide protective group on a nucleotide functional group on the first nucleotide within at least another exposed region of the substrate;
thereby forming another pattern on the substrate, wherein the another pattern comprises the at least another exposed region (e.g., “the process further includes repeating all the steps to obtain the desired polymer array” as per col. 17 of Kuimelis, and/or “[t]his basic sequence of events is repeated to add additional monomer units, preferably nucleotides, thus assembling the probe array” as per col. 20 of Kuimelis, and/or “[a] probe array having a desired sequence can be fabricated by repeatedly performing the protection and deprotection steps” as per ¶0045 of Yun).
Regarding claim 10, Yun in view of Kuimelis disclose the above, further comprising:
(h) contacting the functional groups and/or the nucleotide functional group on the first nucleotide within the at least another exposed region of the substrate with a second nucleotide reagent, thereby coupling another fraction of the functional groups and/or the nucleotide functional group within the at least another exposed region of the substrate with a second nucleotide (e.g., as per col. 20 of Kuimelis, and/or ¶0069 and/or Fig. 6 of Yun).
Regarding claim 11, Yun in view of Kuimelis disclose the above, the first nucleotide is different from the second nucleotide (e.g., as per col. 20 of Kuimelis, and/or Fig. 6 of Yun).
Regarding claim 12, Yun in view of Kuimelis disclose the above, the at least one exposed region is different from the at least another exposed region (e.g., as per col. 20 of Kuimelis, and/or Fig. 5 of Yun).
Regarding claim 25, Yun in view of Kuimelis disclose the above, further comprising:
(d) contacting the substrate with a reagent for oligonucleotide synthesis; and
(e) repeating steps (a)-(d) and/or (b)-(d) with another reagent for oligonucleotide synthesis; thereby forming a pattern of oligonucleotides (e.g., “the process further includes repeating all the steps to obtain the desired polymer array” as per col. 17 of Kuimelis, and/or “[t]his basic sequence of events is repeated to add additional monomer units, preferably nucleotides, thus assembling the probe array” as per col. 20 of Kuimelis, and/or “[a] probe array having a desired sequence can be fabricated by repeatedly performing the protection and deprotection steps” as per ¶0045 of Yun).
Regarding claim 30, Yun in view of Kuimelis disclose the above, wherein when no more than one-third of the dose of light is directed to the at least one exposed region, another photoacid generator within the at least one exposed region does not produce another acid from the another photoacid generator (e.g., both Yun and Kuimelis disclose embodiments wherein there is a single photoacid generator, in which cases there would reasonably be no “another photoacid generator” and thus no “another acid”).
Regarding claim 39, Yun in view of Kuimelis disclose the above, wherein step (b) is conducted by using an oligonucleotide synthesizer (note that reasonably the device used by Yun and/or Kuimelis to synthesize the oligonucleotides can reasonably be considered as an oligonucleotide synthesizer, given the broadest reasonable interpretation of the term in light of the specification).
Regarding claims 46-49, the steps (a)-(c) are prima facie obvious for the same reasoning as shown above for claim 1. Claims 46-49 have addition limitations that the formed pattern comprises one or more oligonucleotides wherein each comprises at least one zipcode sequence, wherein the zipcode sequence comprises an upper zipcode sequence and a lower zipcode sequence that determine the spatial location of the zipcode sequence on the array in one-, two-, or three-dimensional space.
The specification states “the term ‘zipcode’ generally refers to a known, determinable, and/or decodable sequence, such as, for example, a nucleic acid sequence (DNA sequence or RNA sequence), a protein sequence, and a polymer sequence (including synthetic polymers, carbohydrates, lipids, etc.), that allows the identification of a specific location of the sequence, e.g., the nucleic acid, in one, two or multiple dimensional spaces” (e.g., as per ¶0038). Thus, the terms “zipcode” and “zipcode sequence” are reasonably functional limitations for the synthesized oligonucleotides. As per MPEP 2173.05(g), a “claim term is functional when it recites a feature ‘by what it does rather than by what it is’”. The same MPEP section states that “[t]here is nothing inherently wrong with defining some part of an invention in functional terms” and that “[a] functional limitation must be evaluated and considered, just like any other limitation of the claim, for what it fairly conveys to a person of ordinary skill in the pertinent art in the context in which it is used.” MPEP 2114(II) further explains that "[A]pparatus claims cover what a device is, not what a device does" citing Hewlett-Packard Co. v. Bausch & Lomb Inc., 909 F.2d 1464, 1469, 15 USPQ2d 1525, 1528 (Fed. Cir. 1990) (emphasis in original), further stating that a "recitation with respect to the manner in which a claimed apparatus is intended to be employed does not differentiate the claimed apparatus from a prior art apparatus” if the prior art apparatus teaches all the structural limitations of the claim, citing Ex parte Masham, 2 USPQ2d 1647 (Bd. Pat. App. & Inter. 1987). In the instant case, the only structural limitations imposed on the zipcode sequences of the oligonucleotides by their intended use in the claims is their ability to represent information, such as by their nucleotide sequences. However, since nucleic acid sequences can be associated with or correlated to information, then their ability to store and provide (spatial) information is inherent to their structure. Accordingly, the “zipcode sequence” limitations of the present claims do not distinguish over the prior art. Alternatively and in addition, it is noted that “zipcode” sequences as per the present claims were known in the art, such as by Zhou, as detailed above.
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Response to Arguments
The 12/29/2025 remarks argue: not all elements are taught.
Applicant's arguments have been fully considered but they are not persuasive for at least the following reasons.
Specifically, the remarks assert that neither Yun nor Kuimelis disclose zipcode sequences. In response, it is noted that this has been fully addressed in the rejection of the claims, above.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any extension fee pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the date of this final action.
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/JEREMY C FLINDERS/Primary Examiner, Art Unit 1684