Status of the Claims
Claims 67-69, 72-79, and 81-87 are amended.
Claims 67-87 are currently pending and examined herein.
The following Office Action is in response to Applicant’s communication dated 05/01/2026. Rejection(s) and/or objection(s) not reiterated from previous office actions are hereby withdrawn. Specifically, the rejections of claims 67, 69, and 77-87 on the grounds of nonstatutory double patenting as detailed in the previous action are withdrawn in light of the filing of terminal disclaimers (see below). 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 .
Terminal Disclaimer
The terminal disclaimer filed on 05/01/2026 disclaiming the terminal portion of any patent granted on this application which would extend beyond the expiration date of Applications 18/215,296; 17/565,028; 17/565,047; 18/215,299; 18/342,906; 18/342,948; and 18/343,108 has been reviewed and is accepted. The terminal disclaimer has been recorded.
New Claim Rejections - 35 USC § 103
Necessitated by Amendments
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Kim et al., Manzo et al., Hughes et al., and Crnogorac et al.
Claims 67-71 and 77-87 are rejected under 35 U.S.C. 103 as being unpatentable over Kim et al. (US Pat. 7994098; of record) in view of Manzo et al. (US PGPub 2024/0287505; of record), Hughes et al. (CSH Perspec. Biol., 2017, 9(1); of record), and Crnogorac et al (PGPub No: US 2020/0384436; cited in IDS of 05/01/2026).
Regarding claim 67, Kim teaches a method for providing an array (DNA microarray – col. 3, lines 46-52 and 61-64) comprising first and second regions (col. 13, lines 9-14) on a substrate (substrate 100 – Fig. 1: below; col. 3, lines 61-64). Additionally, Kim teaches irradiating the substrate (124 and 126 – Fig. 13; col. 6, line 4) through a mask comprising an opening corresponding to a boundary region between the first and second regions (inverse mask pattern 112 – Fig. 1; col. 6, lines 28-38) thereby blocking (capped 130 – Fig. 14) nucleic acid molecules immobilized in the boundary region (col. 13, lines 47-49).
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Kim Figure 1
Kim also teaches attaching first and second nucleotides to first and second nucleic acid molecules immobilized in the first and second regions, respectively (col. 13, lines 9-21). However, while Kim teaches conventional light directed DNA array synthesis (col. 13, lines 9-21), Kim does not teach attaching oligonucleotide molecules to nucleic acid molecules via ligation.
Manzo teaches a method (Fig. 5: annotated below; p. 2, para [0036]) for attaching oligonucleotide molecules (“second oligonucleotide” – p. 7, para [0116]) via ligation (abstract; p. 5-6, para [0103], lines 5-11) to generate extended nucleic acid molecules (“secondary indexed polynucleotide”).
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Manzo Figure 5, annotated
Additionally, there would be motivation before the effective filing date of the instant application to combine the oligo ligation method of Manzo with the inverse capping method of Kim due to the recognized difficulty of accurately synthesizing long nucleic acid molecules in situ via standard light direct DNA synthesis. As stated by Hughes et al., a challenge arises from sequential base-by-base addition of nucleotides in that the error rate of incorporating each additional nucleotide accumulates over the course of synthesis, limiting the length of oligos that can be synthesized with fidelity (p. 7-8). Additionally, Hughes teaches that synthetic oligos can be assembled together to create longer sequences (p. 8). Furthermore, one of ordinary skill in the art would have a reasonable expectation of success in combining the aforementioned methods because assembly of nucleic acid molecules by ligation is a well-developed technique and, per Manzo, is compatible with immobilized nucleic acids (p. 1, para [0007]; Fig. 5).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to apply the method from Manzo of attaching oligonucleotide molecules to nucleic acid molecules via ligation to generate extended nucleic acid molecules to the method of Kim with a reasonable expectation of success, based on the motivation taught by Hughes.
Kim also does not teach that the extended nucleic acid molecules comprise first and second spatial barcodes.
However, Crnograc discloses a method to fabricate an array wherein extended nucleic acid molecules comprise first and second spatial barcodes (p. 8, ¶[0072]) which correspond to the first and second regions’ spatial locations (p. 8, ¶[0069]; Fig. 1), and wherein the first and second spatial barcodes are different (p. 8, ¶[0071]). Additionally, Crnograc teaches that the disclosed spatial array can be fabricated by synthesizing oligonucleotides using photolithography (p. 9, ¶[0073]), particularly methods that mitigate erroneous DNA synthesis in locations outside the intended regions (p. 9, ¶[0073-4]). While Crnograc uses a different method to mitigate these DNA synthesis errors, this teaching indicates that the fabrication of spatial arrays benefits from methods that mitigate their effects. As the method of Kim serves also serves this purpose, it would have been obvious to fabricate the spatial array of Crnograc using the method of Kim. In doing so, the method of Kim would result in extended nucleic acid molecules that comprise spatial barcodes.
Furthermore, one of ordinary skill in the art would have had a reasonable expectation of success in fabricating the spatial array of Crnograc via the method of Kim because both methods use similar photolithographic techniques, as cited previously, indicating that the method of Kim would be able to spatially allocate building blocks for different regions using photolithography in order to produce the spatially barcoded array of Crnograc.
The method of attaching oligonucleotide molecules to nucleic acid molecules via ligation of Manzo as motivated by Hughes would also be compatible with using the method of Kim to fabricate the spatial array of Crnograc. One of ordinary skill in the art would have a reasonable expectation of success in using the ligation method of Manzo in this combination, as Manzo discloses that this ligation method is used to construct spatial barcodes (p. 9, ¶[0128], lines 13-16). Additionally, the extended nucleic acid of Manzo (see Figure 5, above) contains multiple barcodes (“Index A”, “Index B”, etc.) that could at once be envisioned as the coordinates from the spatial barcodes of Crnograc.
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date to use the method of Kim and Manzo to fabricate the spatial array of Crnograc, yielding the predictable result of first and second extended nucleic acids that comprise different first and second spatial barcodes that correspond to first and second locations on the substrate, with a reasonable expectation of success.
Lastly, Kim does not teach that the irradiating (c) occurs after attaching oligonucleotides in the first (a) and second (b) regions. With regard to the order of steps, the courts have ruled that the selection of any order of performing process steps is prima facie obvious in the absence of new or unexpected results (In re Burhans, 154 F.2d 690, 69 USPQ 330 (CCPA 1946; In re Gibson 39 F.2d 975, 5 USPZ 230 (CCPA 1930; MPEP 2144.04 section IV C). In the instant case, the steps of attaching nucleotides to immobilized nucleic acid molecules are taught by Kim and therefore the claimed order of steps in the instant application is prima facie obvious in the absence of new or unexpected results.
Regarding claim 68, Kim teaches that the boundary region comprises part of the first region or part of the second region (Fig. 21, annotated below).
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Kim Figure 21, annotated
Claims 69-71 are drawn to the dimensions of both the array features and the boundary region between them. The feature dimensions achieved on a microarray are a result of the resolution of the photolithographic apparatus used to pattern the array. While Kim does not disclose dimensions of features or a boundary region, Kim teaches that the optics system described can obtain a “resolution of dimensions as small as 0.5 microns” (col. 9, lines 5-7). This demonstrates that the dimensions of an average diameter between 2 μm and 20 μm for the first and second regions, as well as a length of 1 to 20 μm and a width of about 0.5 μm for the opening corresponding to the boundary region were achievable by the method of Kim.
Furthermore, changes in relative dimensions, such as the relative dimensions of features and a boundary region, have been determined to be obvious. MPEP § 2144.04 (IV)(A) states:
In Gardner v. TEC Syst., Inc., 725 F.2d 1338, 220 USPQ 777 (Fed. Cir. 1984), cert. denied, 469 U.S. 830, 225 USPQ 232 (1984), the Federal Circuit held that, where the only difference between the prior art and the claims was a recitation of relative dimensions of the claimed device and a device having the claimed relative dimensions would not perform differently than the prior art device, the claimed device was not patentably distinct from the prior art device.
As the claimed dimensions do not change the performance of the method – i.e. producing an array – one of ordinary skill in the art would recognize that the method of Kim is compatible with the dimensions of claims 69-71, rendering them obvious.
Regarding claim 77, Kim also teaches applying a positive photoresist to the substrate (col. 9, lines 38-40) wherein the irradiating degrades the positive photoresist to expose nucleic acid molecules in the boundary region (col. 9, lines 27-30), while nucleic acid molecules in the masked region(s) remain covered by the positive photoresist (col. 12, lines 40-42).
Regarding claim 78, Kim further teaches inactivating the exposed nucleic acid molecules (col. 12, lines 43-45).
Regarding claim 79, Kim further teaches that the exposed nucleic acid molecules are modified at the 3’ or 5’ end (col. 12, lines 45-54), rendering the exposed nucleic acid molecules unavailable for ligation (col. 12, lines 58-61).
Regarding claim 80, Manzo teaches modified 3’ends (p. 11, para [0114], lines 10-13) where the modification comprises 3’ ddC (p. 16, para [0180], lines 10-11).
Regarding claim 81, Kim also teaches that the attaching step of (a) and/or (b) comprises photolithography (col. 1, lines 39-61) using a photoresist (col. 1, lines 58-61) or a 5’ photolabile protective group (col. 1, lines 47-48; col. 13, lines 45-47).
Regarding claim 82, the limitations of claim 67, including those recited in 82(II), are discussed above. Additionally, Kim teaches irradiating a substrate comprising an unmasked first region and a masked second region (col. 13, lines 11-14), whereby a photoresist (col. 1, lines 58-61) in the first region is degraded (claim 9) to render the first nucleic acid molecules in the first region available for ligation (col. 13, lines 14-15), whereas the second nucleic acid molecules in the second region are protected by a photoresist in the second region from ligation (claim 9).
Regarding claim 83, the limitations of claim 67, including those recited in 83(IV), are discussed above. Additionally, Kim teaches irradiating a substrate comprising an unmasked second region and a masked first region, whereby a photoresist in the second region is degraded to render the second nucleic acid molecules in the second region available for ligation, whereas the first nucleic acid molecules in the first region are protected by a photoresist in the first region from ligation (col. 13, lines 20-22).
Regarding claim 84, the limitations of claim 82, including those recited in 84(A), are discussed above. Additionally, Manzo teaches a first splint (Figure 5 – annotated above; p. 2, para [0036]) and that the first oligonucleotide comprises a first barcode sequence (p. 7, para [0116], lines 14-15), wherein the first splint hybridizes to the first oligonucleotide and the first nucleic acid molecules in the first region to generate the first extended nucleic acid molecules (Figure 5; p. 2, para [0036]).
Regarding claim 85, the limitations of claim 83, including those recited in 85(D), are discussed above. Additionally, while Kim does not explicitly teach removal of a first photoresist and applying a second photoresist, it is well known to those of ordinary skill in the art that in situ oligonucleotide synthesis using photoresists requires exchange of the photoresist layers in order to irradiate different features on an array. As shown in Figure 4 of Pirrung (2002, cited in IDS of 11/20/2023), the final step of the fabrication cycle involves stripping the photoresist, which is then applied again at the beginning of the next synthesis cycle. Therefore, stripping of a first photoresist before application of a second photoresist is anticipated by the disclosure of using photoresists for oligonucleotide array synthesis by Kim.
Furthermore, Kim teaches parallel combinatorial DNA synthesis as discussed previously in regards to claim 83. Applying the method of Manzo to the synthesis method of Kim, as discussed in regards to claim 67, would thereby result in the steps enumerated in claim 83 additionally using a second splint and barcode, as taught by Manzo and as discussed in regards to claim 84.
Regarding claims 86 and 87, these claims are drawn to continue the method of claim 85 by repeating the steps detailed in claims 84 and 85 in a “Round 2”. Therefore, the additional limitations being set forth in these claims are the repeated steps of claims 84 and 85 being applied to the first and second extended nucleic acid molecules to produce first and second further extended nucleic acid molecules by use of first and second Round 2 oligonucleotides comprising first and second Round 2 barcode sequences. This concept is exemplified by Kim, which states “the process is then repeated, binding another base to a different set of locations” (col. 9, lines 33-35). Furthermore, Manzo additionally discloses the process of ligating a Round 2 oligonucleotide (“third oligonucleotide” – p.12, para [0155]) to an extended nucleic acid molecule (“secondary indexed polynucleotide” – p.12, para [0155]) to obtain a further extended nucleic acid molecule (“tertiary indexed polynucleotide” – p. 13, para [0155]). Taken with the repeated cycles disclosed by Kim, claims 86 and 87 are rendered obvious.
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Response to Arguments
Applicant’s arguments with respect to the newly added “spatial barcode” limitations of claim 67 have been considered but are moot because the new ground of rejection does not rely on any reference applied in the prior rejection of record for any teaching or matter specifically challenged in the argument.
Applicant’s arguments with respect to the limitation of step (c) occurring “after (a) and (b)” of claim 67 have been fully considered but they are not persuasive. Applicant asserts that Kim does not teach steps (a-c) as occurring in the claimed order and that one of ordinary skill would “have no reason” to change the order of the steps based on Kim, nor based on the disclosures of Manzo or Hughes.
As discussed above, Examiner agrees that Kim does not teach steps (a-c) as occurring in the claimed order and that neither Manzo nor Hughes provide motivation to modify Kim thus. However, the court has previously held that changes to the order of performing steps are considered routine expedients available to one of ordinary skill in the art that are obvious in the absence of “new and unexpected results” (In re Burhans, 154 F.2d 690, 69 USPQ 330 (CCPA 1946; In re Gibson 39 F.2d 975, 5 USPZ 230 (CCPA 1930; MPEP 2144.04 section IV C). This indicates that no explicit motivation or suggestion to change the order of the steps of Kim is necessary to establish a case of prima facie obviousness. As Kim teaches steps (a), (b), and (c), it would therefore be obvious to perform step (c) after steps (a) and (b) in the absence of new and unexpected results.
Additionally, applicant argues that changing the order of the steps in Kim would “completely change the reference’s principle of operation” and render the method “unsatisfactory for its intended purpose” of preventing unwanted light directed DNA synthesis. Examiner disagrees on both counts. The method of inverse capping described by Kim is based on the principle of using “conventional capping reagents” to inactivate specific regions of the array, including “conventional phosphoramidite or acetyl (acetyl-anhydride) capping reagents” (col. 12, lines 43-47). Both of these reagents are regularly used to cap DNA molecules and would therefore remain operable regardless of if DNA synthesis has occurred prior to the inverse capping step. Kim even anticipates this use by disclosing that single nucleotides or short polynucleotides can be appended to the substrate prior to inverse capping, which could then proceed without modification (col. 13, lines 47-52). This shows that the principle of operation remains the same regardless of when inverse capping occurs. As nucleic acid molecules can be capped using the method of Kim, this also shows that inverse capping can still be employed for its intended purpose of preventing unwanted DNA synthesis.
Kim et al., Manzo et al., Hughes et al., Crnogorac et al., and Zebala et al.
Claims 72-76 are rejected under 35 U.S.C. 103 as being unpatentable over Kim et al., Manzo et al., Hughes et al., and and Crnogorac et al. as applied to claims 67-71 and 77-87 above, and further in view of Zebala et al. (US Pat. 6159681; of record).
Regarding claim 72, Kim, Manzo, and Hughes teach blocking nucleic acid molecules in the boundary region as well as the method of synthesizing extended nucleic acids by ligation of oligonucleotides to nucleic acid molecules. However, Kim and Manzo do not teach that the nucleic acid molecule is synthesized into the extended nucleic acid molecule prior to being removed, blocked, or inactivated.
Zebala et al. (US Pat. 6159681) teaches removal of nucleic acid molecules (col. 33, lines 37-58) that have been previously synthesized (col. 21-22, lines 58-2). Furthermore, Zebala teaches that removal of nucleic acid molecules can be useful in instances where, “it is desirable to alter the exposed biologic material so as to inhibit detection of a substance of interest in such regions” (col. 33, lines 42-44). It is desirable to remove an extended nucleic acid molecule in a boundary region, as evidenced by Kim disclosing that the negative effects of light diffraction, scattering, and flair can be significantly reduced by inactivating nucleic acid molecules in a boundary region (col. 3, lines 46-60). Additionally, a first oligonucleotide molecule attached to a second nucleic acid molecule is a product of light diffraction, scattering, and flare, which is precisely what is being referred to by Kim. According to the motivations provided by Zebala and Kim, it would therefore be desirable to apply the method Zebala to inactivate a first oligonucleotide molecule attached to a second nucleic acid molecule in a boundary region.
Additionally, Zebala confirms that the disclosed removal of extended nucleic acids is compatible with photolithography synthesis methods (col. 21, line 67) on arrays (col. 17, lines 17-18), so one of ordinary skill in the art would have a reasonable expectation of success in applying the method of Zebala to the method of Manzo and Kim.
Therefore, it would have been obvious to one of ordinary skill in the art before the filing date of the claimed invention to apply the method of removing an extended nucleic acid molecule from Zebala to the method of providing an array of Kim, Manzo, and Crnogorac, based on the motivation taught in Zebala and Kim.
Regarding claims 73 and 74, Zebala further discloses that the inactivation comprises irradiating a nucleic acid molecule with irradiation sufficient to cleave the nucleic acid molecule, as well as removing the cleaved nucleic acid molecule (col. 33, lines 37-58).
Regarding claim 75, cleavage via irradiation is discussed in regards to claim 73 above. Additionally, Kim teaches application of a positive photoresist to the substrate (col. 9, lines 38-40) wherein the irradiating degrades the positive photoresist to expose nucleic acid molecules in the boundary region (col. 9, lines 27-30).
Regarding claim 76, as discussed above, Kim teaches the application of a positive photoresist but is silent on the use of a negative photoresist. However, Zebala teaches application of a negative photoresist to the substrate (col. 3, line 48) and upon irradiation through the mask, the negative photoresist is strengthened to render nucleic acid molecules in the boundary region inactive or inaccessible for ligation (col. 14, lines 55-59; lines 63-67).
The use of negative photoresists in the manufacture of biomolecule microarrays is well known, as evidenced by Zebala, which states, “It will be readily apparent to those skilled in the art that the photoresist may also be selected from a wide variety of negative photoresists” (col. 27, lines 38-40). Though the tone is opposite from the positive photoresist of Zebala, the basic function of the photoresist is unchanged: to differentially pattern accessibility of surface groups using irradiation. As negative photoresists are known in the art and their use in the manufacture of DNA microarrays has been well characterized, one of ordinary skill in the art before the effective filing date of the present application, could have substituted the positive photoresist of Kim with the negative photoresist of Zebala to arrive at the method described in claim 76 with predictable results.
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Response to Arguments
Applicant's arguments filed 05/01/2026 have been fully considered but they are not persuasive. Applicant asserts that Zebala does not provide any reason to modify the method of Kim by performing inverse capping on a first oligonucleotide attached to a second nucleic acid molecule in the boundary region. As cited in the rejections above, Zebala provides the additional motivation to further modify the method of Kim in order to remove extended nucleic acids in a boundary region stating that it is “desirable” to remove biologic material from areas that are not of interest (i.e., a boundary region). As re-ordering the steps of Kim constitutes a routine expedience as discussed previously, this additional motivation from Zebala confirms that one of ordinary skill in the art would recognize that a first oligo attached to a second nucleic acid in a boundary region would be desirable to remove, and that the steps to do so are obvious over the method of Kim.
Applicant also states that modifying the method of Kim in this way would change the operating principle of the method and render it unsatisfactory for its intended purpose. Examiner holds that these assertions have been fully addressed in the previous response to arguments of this action regarding claim 67 (see section 8, 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 nonprovisional extension fee (37 CFR 1.17(a)) 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 mailing date of this final action.
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/ALEXANDRA OLSON/Examiner, Art Unit 1684
/JEREMY C FLINDERS/Primary Examiner, Art Unit 1684
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