DETAILED ACTION
Status of the Application
Claims 1, 4-5, 7, 11-14, 16-17, 22-23, 47-49, 52-53, 76-80 are pending.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant’s amendment of claims 1, 4-5, 7, 12-14, 16-17, 22-23, 47-49, 76, 79, addition of claim 80, and cancellation of claim 75 as submitted in a communication filed on 7/22/2025 is acknowledged.
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 7/22/2025 has been entered.
As indicated in the prior Office action, Applicant elected Group 23 without traverse, which is drawn in part to an engineered Cas effector protein that comprises SEQ ID NO: 131, the heterologous polypeptide of SEQ ID NO: 1, and the combination of a wedge domain, a Rec1 domain, a Rec2 domain, a PAM interacting domain, a RuvC domain, a bridge helix and a Nuc domain, in a communication filed on 3/11/2024.
New claim 80 is directed in part to the elected invention. Claims 1 (linking), 4-5, 7, 11-14, 16-17, 22-23, 47-49, 52-53, 76-80 are at issue and will be examined to the extent they encompass the elected invention. Embodiments related to SEQ ID NO: 2-17, 125-130, 132, 157-168, 169-174 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 3/11/2024.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Rejections and/or objections not reiterated from previous office actions are hereby withdrawn.
Claim Objections
Claim 7 is objected to due to the recitation of “second_Cas12a protein”. The underscore between “second” and “Cas12a” should be removed. Appropriate correction is required.
Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA )
Claims 1, 4-5, 7, 11-14, 16-17, 22-23, 47-49, 52-53, 76-80 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor, or for pre-AIA the applicant regards as the invention.
Claim 1 (claims 4-5, 7, 11-14, 16-17, 22-23, 76-80 dependent thereon) is indefinite in the recitation of “a first CRISPR-Cas effector polypeptide comprises…a first portion of the wedge domain and the Rec1 domain of a first Cas12a protein….second CRISPR-Cas effector polypeptide comprises…a first portion of the RuvC domain, the bridge helix, a second portion of the RuvC domain…and a third portion of the RuvC domain of a second Cas12a protein…” for the following reasons. As written, it is unclear if the first CRISPR-Cas effector polypeptide comprises any fragment of a wedge domain (e.g., any fragment of 2 amino acids of a wedge III domain) of a Cas12a protein and any fragment of a Rec1 domain of a Cas12a protein, or if the first CRISPR-Cas effector polypeptide comprises any fragment of a wedge domain of a Cas12a protein and a complete Rec1 domain of a Cas12a protein. In addition, as written, it is unclear if the second CRISPR-Cas effector polypeptide comprises 3 fragments of any RuvC domain that together make one of a RuvC 1 domain, a RuvC II domain or a RuvC III domain, or if the first portion of the RuvC domain in the second CRISPR-Cas effector polypeptide is an entire RuvC I domain, the second portion of the RuvC domain is an entire RuvC II domain and the third portion of the RuvC domain is an entire RuvC III domain. Moreover, even if the three portions make up all of RuvC I, RuvC II, and RuvC III domains, it is unclear if, for example, the first portion of a RuvC domain can comprise all of a RuvC I domain and part of a RuvC II domain, the second portion can comprise only a fragment of the second RuvC III domain, and the third portion can comprise a fragment of the second RuvC II domain and all of a RuvC III domain. For examination purposes, it will be assumed that the first CRISPR-Cas effector polypeptide comprises a fragment of any wedge domain and a fragment of the Rec1 domain of a first Cas12a protein, and the second CRISPR-Cas effector polypeptide comprises the Rec2 domain, the PAM-interacting domain, the bridge helix, and the Nuc domain of a second Cas12a protein. Correction is required.
Claim 12 (claim 13 dependent thereon) is indefinite in the recitation of “wherein the C-terminal amino acid residue of the first CRISPR-Cas effector polypeptide and the N-terminal amino acid residue of the second CRISPR effector polypeptide are two consecutive amino acids in the same Cas12a protein and the heterologous….is between the two consecutive amino acids” for the following reasons. The first CRISPR-Cas effector polypeptide and the second CRISPR-Cas effector polypeptide are not required to be complete fragments of the “same” Cas12a protein such that the two fragments constitute the entire “same” Cas12a protein. For example, the first CRISPR-Cas effector polypeptide can comprise a portion of a wedge domain and a portion of the Rec1 domain since the term “a first portion of the wedge domain and the Rec1 domain” can be interpreted as a portion of a wedge domain and a portion of an Rec1 domain. Therefore, the C-terminal amino acid of the first CRISPR-Cas effector polypeptide and the N-terminal amino acid residue of the second CRISPR effector polypeptide are not required to be consecutive amino acids of the “same” Cas12a protein. Since the claim requires any two consecutive amino acids found in the “same” Cas12a protein, these consecutive amino acids can be found anywhere within the “same” Cas12a protein. If, for example, one has an engineered Cas effector protein wherein the first and second CRISPR-Cas effector polypeptides are not complete fragments of the “same” Cas12a protein but the C-terminus of the first CRISPR-Cas effector polypeptide and the N-terminus of the second CRISPR-Cas effector polypeptide form a dipeptide which is found anywhere in the “same” Cas12a protein, is the engineered Cas effector protein encompassed or excluded from the scope of the claim?. For examination purposes, claim 12 will be interpreted as a duplicate of claim 7. Correction is required.
Claim 13 is indefinite in the recitation of “wherein the two consecutive amino acids are selected from amino acid residues 270-350 of the same Cas12a protein” for the following reasons. It is unclear as to how the option to select the two amino acid residues can be longer than two amino acids. Amino acids 270-350 is a fragment of 81 amino acids. In addition, in the absence of the sequence identifier associated with amino acids 270-350, it is unclear as to how the identity of the two amino acids is defined by the limitation, namely the sequence of the dipeptide that is required at the junction between the first and second CRISPR-Cas polypeptides. For examination purposes, claim 13 will be interpreted as a duplicate of claim 7. Correction is required.
Claim 14 is indefinite in the recitation of “wherein the heterologous polypeptide comprises an amino acid sequence having at least 90% sequence identity to one or more of SEQ ID NO: 1 and 169-174” for the following reasons. The limitation is unclear and confusing because it is not possible to have at least 90% sequence identity to SEQ ID NO: 1 and one or more of the recited sequences when the sequence identity among the recited sequences is not high. For example, the amino acid sequence identity between SEQ ID NO: 1 and SEQ ID NO: 169 is 10%, while the amino acid sequence identity between SEQ ID NO: 1 and SEQ ID NO: 170 is 19%. See alignments below. Therefore, if the heterologous polypeptide has an amino acid sequence at least 90% sequence identical to SEQ ID NO: 1, it cannot have at the same time an amino acid sequence at least 90% identical to SEQ ID NO: 169 or SEQ ID NO: 170. If the intended limitation is “at least 90% sequence identity to SEQ ID NO: 1, 169, 170, 171, 172, 173, or 174”, the claim should be amended accordingly. Correction is required.
Query = SEQ ID NO: 1
Sbjct = SEQ ID NO: 169
NW Score Identities Positives Gaps
-94 14/144(10%) 23/144(15%) 91/144(63%)
Query 1 ENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVD 60
T G++ LK H + +
Sbjct 1 CRVT-----------------GVQ------LKNHLIAS---------------------- 15
Query 61 QELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQ 120
HI P + + R D + G
Sbjct 16 --------------HIKPWAVSNNQE-------RLDGHNG-------------------- 34
Query 121 LLNAKLITQRKFDNLTKAERGGLS 144
L+ D+L
Sbjct 35 -----LLLAPHVDHLFDKGFISFE 53
Query = SEQ ID NO: 1
Sbjct = SEQ ID NO: 170
NW Score Identities Positives Gaps
-23 30/158(19%) 55/158(34%) 35/158(22%)
Query 1 -ENQTTQKGQKNSRERMKRIE--EGIKELGSQILKEHPVENTQLQNEKLYLYYLQN--GR 55
N+ + K + R E K L Q + +N+K Y + +N R
Sbjct 1 MPNRPLKPCNKIGCTNLTRDRYCEQHKHLAEQRQRTR-------RNDKEYDKHKRNQQAR 53
Query 56 DMYVDQELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMK 115
Y +E + RL+ D+ + Q LK+ I V+ + VV +
Sbjct 54 AFYHSREWERVRLAVLARDNYLCQHCLKEKKITRAVIV--------------DHVVPLLV 99
Query 116 NYWRQLL--NAKLITQRKFDNLTKAE-------RGGLS 144
++ ++L N + + Q + T + R G
Sbjct 100 DWSKRLDMDNLQSLCQSCHNRKTAEDKRRYGQGRSGKF 137
Claim 47 (claims 48-49, 52-53 dependent thereon) is indefinite in the recitation of “..a first polypeptide that comprises the Rec1 domain of a Cas12a protein; a second polypeptide that comprises the Rec2 domain, the PAM-interacting domain, the RuvC domain, the bridge helix, and the Nuc domain of the Cas12a protein” for the following reasons. As written, it is unclear if the Rec2 domain, the PAM-interacting domain , the RuvC domain, the bridge helix and the Nuc domain are those of the same Cas12a protein from which the Rec1 domain in the first polypeptide originates. For examination purposes, it will be assumed that the Cas12a protein from which the Rec2 domain, the PAM-interacting domain, the RuvC domain, the bridge helix, and the Nuc domain originates may be the same or a different Cas12a protein from which the Rec1 domain originates. Correction is required.
Claim 48 is indefinite in the recitation of “wherein the C-terminal amino acid residue of the first polypeptide and the N-terminal amino acid residue of the second polypeptide are two consecutive amino acids in the Cas12a protein and the two consecutive amino acid residues are selected from amino acid residues 283-293 of the Cas12a protein…is between the two consecutive amino acid residues” for the following reasons. It is unclear as to how the option to select the two amino acid residues can be longer than two amino acids. Amino acids 283-293 is a fragment of 11 amino acids. In addition, in the absence of the sequence identifier associated with amino acids 283-293, it is unclear as to how the identity of the two amino acids is defined by the limitation, namely the sequence of the dipeptide that is required at the junction between the first and second CRISPR-Cas polypeptides. Furthermore, as indicated above with regard to claim 47, it is unclear if the Cas12a protein referred to with regard to the second polypeptide is the same Cas12a protein referred to with regard to the first polypeptide. Therefore, it is unclear which is the Cas12a protein associated with the two consecutive amino acids. For examination purposes, it will be assumed that claim 48 is a duplicate of claim 47 as interpreted. Correction is required.
Claim 49 is indefinite in the recitation of “wherein the engineered Cas effector protein further comprises the wedge domain of the Cas12a protein” for the following reasons. As indicated above with regard to claim 47, it is unclear if the Cas12a protein referred to with regard to the second polypeptide is the same Cas12a protein referred to with regard to the first polypeptide. Therefore, it is unclear which is the Cas12a protein that is referred to with regard to the wedge domain. For examination purposes, it will be assumed that claim 49 is a duplicate of claim 47 as interpreted. Correction is required.
Claim 76 is indefinite in the recitation of “comprises a mutation in its nuclease active site that reduces nickase activity of the engineered Cas effector protein…” for the following reasons. A mutant of the nuclease domain of the heterologous polypeptide is not encompassed by the heterologous polypeptide of claim 1 because the nuclease domain of claim 1 lacks the mutation. It should also be noted that the nuclease domain of claim 1 is expected to have nuclease activity while the mutated nuclease domain of claim 76 can be one that lacks nuclease activity (reduced to zero nickase activity). Therefore, the scope of claim 76 is different from the scope of claim 1 in view of the fact that the heterologous polypeptide of claim 76 is a variant of the heterologous polypeptide of claim 76 by virtue of having different nuclease domains. For examination purposes, claim 76 will be interpreted as a duplicate of claim 1 as interpreted. Correction is required.
Claim 79 is indefinite in the recitation of “wherein the engineered Cas effector protein is a target strand and non-target strand nickase” for the following reasons. A protein that has target strand and non-target strand nickase activity can be interpreted as an endonuclease that cleaves double stranded nucleic acids. Therefore, it is unclear if the first nuclease domain of the heterologous polypeptide of claim 1 is required to have double strand nucleic acid cleaving activity. For examination purposes, it will be assumed that claim 79 is a duplicate of claim 1 as interpreted. Correction is required.
Claim 80 is indefinite in the recitation of “wherein the C-terminal amino acid residue of the first CRISPR-Cas effector polypeptide and the N-terminal amino acid residue of the second CRISPR-Cas effector polypeptide are two nonconsecutive amino acids in the same Cas12a protein and the heterologous polypeptide is between the two nonconsecutive amino acids” for the following reasons. It is unclear as to how this limitation further limits the engineered Cas effector protein because if the C-terminal amino acid of the first CRISPR-Cas effector polypeptide and the N-terminal amino acid of the second CRISPR-Cas effector protein together do not form a dipeptide found in the “same” Cas12a protein, the dipeptide formed by these two amino acids can be any dipeptide. In addition, if the heterologous polypeptide is linked to two nonconsecutive amino acids, is the heterologous polypeptide linked to the first and second CIRSPR-Cas effector polypeptides in a bridge configuration where the N-terminus of the heterologous polypeptide is linked to one of the two nonconsecutive amino acids and the C-terminus of the heterologous polypeptide is linked to the other of the two nonconsecutive amino acids? Is the heterologous polypeptide simply placed between the C-terminus of the first CRISPR-Cas effector polypeptide and the N-terminus of the second CRISPR-Cas effector polypeptide? For examination purposes, it will be assumed that claim 80 is a duplicate of claim 7. Correction is required.
When amending the claims, applicant is advised to carefully review all examined claims and make the necessary changes to ensure proper antecedent basis and dependency.
Claim Rejections - 35 USC § 112(a) or First Paragraph (pre-AIA )
Claims 1, 4-5, 7, 11-14, 16-17, 22-23, 47-49, 52-53, 76-80 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention. This rejection is necessitated by the introduction of new matter.
As set forth in MPEP 2163 (I)(B), new or amended claims which introduce elements or limitations that are not supported by the as-filed disclosure violate the written description requirement. See, e.g., In re Lukach, 442 F.2d 967, 169 USPQ 795 (CCPA 1971) (subgenus range was not supported by generic disclosure and specific example within the subgenus range); In re Smith, 458 F.2d 1389, 1395, 173 USPQ 679, 683 (CCPA 1972) (an adequate description of a genus may not support claims to a subgenus or species within the genus).
Claim 1 and dependent claims 4-5, 7, 11-14, 16-17, 22-23, 76-80 are now directed to an engineered Cas effector protein that comprises a second CRISPR-Cas effector polypeptide that comprises from the N- to C-terminus of said second CRISPR-Cas effector polypeptide a Rec2 domain, the PAM-interacting domain, a first portion of a RuvC domain, the bridge helix, a second portion of the RuvC domain, the Nuc domain and a third portion of the RuvC domain, wherein the first, second and third portions of the RuvC domain make up the RuvC domain. Claim 47 and dependent claims 48-49, 52-53 are now directed to an engineered Cas effector protein that comprises a second polypeptide that comprises the Rec2 domain, the PAM-interacting domain, the RuvC domain, the bridge helix, and the Nuc domain of a Cas12a protein. While the Examiner has found support for an engineered Cas effector protein that comprises a first polypeptide that comprises all or a portion of a wedge domain and/or a Rec1 domain of a Cas12a protein, and a second polypeptide that comprises all or a portion of a wedge domain, a Rec2 domain, a PAM-interacting domain, a RuvC domain, a bridge helix and a Nuc domain, the Examiner has been unable to locate support for (a) an engineered Cas effector protein that comprises a second CRISPR-Cas effector polypeptide that comprises from the N- to C-terminus of said second CRISPR-Cas effector polypeptide a Rec2 domain, the PAM-interacting domain, a first portion of a RuvC domain, the bridge helix, a second portion of the RuvC domain, the Nuc domain and a third portion of the RuvC domain, wherein the first, second and third portions of the RuvC domain make up the RuvC domain, or (b) an engineered Cas effector protein that comprises a second polypeptide that comprises the Rec2 domain, the PAM-interacting domain, the RuvC domain, the bridge helix, and the Nuc domain of a Cas12a protein.
Moreover, amended claim 14 further requires the heterologous polypeptide to comprise an amino acid sequence at least 90% identical to one or more of SEQ ID NO: 1 and 169-174. While the Examiner has found support for a heterologous polypeptide that comprises an amino acid sequence at least 90% identical to one of SEQ ID NO: 1, 169, 170, 171, 172, 173 or 174 (in the alternative), the Examiner has been unable to find support for a heterologous polypeptide that comprises at least 90% sequence identity to any combination of the sequences selected from the group consisting of SEQ ID NO: 1, 169, 170, 171, 172, 173 and 174. For example, claim 14 as currently amended requires the heterologous polypeptide to comprise an amino acid sequence that is at least 90% identical to SEQ ID NO: 1, SEQ ID NO: 169 and SEQ ID NO: 170.
In addition, while amended claim 16 now requires the first CRISPR-Cas effector polypeptide to have an amino acid sequence at least 90% identical to amino acids 1-250 of any one of SEQ ID NO: 50-66 or 151, the Examiner has been unable to find support for a polypeptide having an amino acid sequence at least 90% identical to amino acids 1-250 of any one of SEQ ID NO: 50-66 or 151. Furthermore, while 17 as amended now requires the second CRISPR-Cas effector polypeptide to have an amino acid sequence at least 90% identical to amino acid residue 350 to the C-terminus of any one of SEQ ID NO: 50-66, the Examiner has been unable to find support for a polypeptide that has an amino acid sequence identity of at least 90% to amino acid residue 350 to the C-terminus of any one of SEQ ID NO: 50-66.
There is no indication in the specification that (a) an engineered Cas effector protein that comprises a second CRISPR-Cas effector polypeptide that comprises from the N- to C-terminus of said second CRISPR-Cas effector polypeptide a Rec2 domain, the PAM-interacting domain, a first portion of a RuvC domain, the bridge helix, a second portion of the RuvC domain, the Nuc domain and a third portion of the RuvC domain, wherein the first, second and third portions of the RuvC domain make up the RuvC domain, (b) an engineered Cas effector protein that comprises a second polypeptide that comprises the Rec2 domain, the PAM-interacting domain, the RuvC domain, the bridge helix, and the Nuc domain of a Cas12a protein, (c) a polypeptide having an amino acid sequence at least 90% identical to amino acids 1-250 of any one of SEQ ID NO: 50-66 or 151, or (d) a polypeptide that has an amino acid sequence identity of at least 90% to amino acid residue 350 to the C-terminus of any one of SEQ ID NO: 50-66 were preferred embodiments of the invention. Thus, there is no indication that an engineered Cas effector protein that comprises (i) a second CRISPR-Cas effector polypeptide that comprises from the N- to C-terminus of said second CRISPR-Cas effector polypeptide a Rec2 domain, the PAM-interacting domain, a first portion of a RuvC domain, the bridge helix, a second portion of the RuvC domain, the Nuc domain and a third portion of the RuvC domain, wherein the first, second and third portions of the RuvC domain make up the RuvC domain, (ii) a second polypeptide that comprises the Rec2 domain, the PAM-interacting domain, the RuvC domain, the bridge helix, and the Nuc domain of a Cas12a protein, (iii) a polypeptide having an amino acid sequence at least 90% identical to amino acids 1-250 of any one of SEQ ID NO: 50-66 or 151, or (iv) a polypeptide that has an amino acid sequence identity of at least 90% to amino acid residue 350 to the C-terminus of any one of SEQ ID NO: 50-66 was within the scope of the invention as conceived by Applicant at the time of the invention. Accordingly, Applicant is required to cancel the new matter in the response to this Office Action.
Claims 1, 4-5, 7, 11-14, 16-17, 22-23, 47-49, 52-53, 76-79 remain rejected and new claim 80 is rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention. This rejection as it relates to claim 80 is necessitated by amendment.
This rejection has been discussed at length in the prior Office action. It is maintained and further applied to new claim 80 for the reasons of record and those set forth below.
Applicant argues that claims 1 and 47 have been amended to further define structural elements of the claimed invention. Applicant states that the application as originally filed clearly provides sufficient, relevant, identifying characteristics or properties of the claimed subject matter such that the skilled artisan would recognize that the inventors had possession of the claimed invention. Applicant states that claims 1 and 47 each include two polypeptides that comprise particular structural elements of a Cas12a protein, and that Cas12a proteins are well known in the art and described throughout the specification. Applicant submits that information which is well known in the art need not be described in detail in the specification. Applicant refers to Figure 4 of the specification as providing the crystal structure of a complex that includes a Cas12a protein and depicts various domains in a Cas12a protein. Applicant refers to the polypeptide of SEQ ID NO: 50 as a Cas12a protein from Lachnospiraceae bacterium. It is Applicant’s opinion that the engineered Cas effector protein of the claims is defined such that it conveys to one of skill in the art that the invention had possession of the claimed subject matter.
Applicant’s arguments have been fully considered but not deemed persuasive to overcome the instant rejection or avoid the rejection of claim 80. The Examiner acknowledges the amendments made to claims 1 and 47 as well as the teachings of the specification. However, the Examiner disagrees with Applicant’s contention that the claims provide structural elements for each of the recited polypeptides or that the specification provides adequate description of all the Cas12a proteins and all the heterologous proteins comprising a nuclease domain required by the claims.
With regard to the structural elements recited in claims 1 and 47, it is noted that while it is agreed that the claims refer to domains or fragments of domains of a Cas12a protein that are required in the claimed engineered CRISPR-Cas effector protein by name, the claims do not require any specific structural limitations regarding the domains or fragments thereof recited. Claims 1, 4-5, 7, 11-13, 47-49, 52-53, 76-80 require a genus of proteins that can comprise any amino acid sequence, thus having any structure.
With regard to claim 14, only a small fraction of the entire claimed protein is structurally defined since the entire protein, based on the length of the protein of SEQ ID NO: 131, is approximately 1400 amino acids long and the limitation of claim 14 only defines at most 130 amino acids (130 = 0.9x144; SEQ ID NO: 1 has 144 amino acids ). With regard to claims 16-17, it is noted that either the second CRISPR-Cas effector protein or the first CRISPR-Cas effector protein can have any amino acid sequence, thus being structurally undefined. Moreover, in the case of claim 17, there is a significant amount of structural variability with respect to the second CRISPR-Cas effector protein. For example, SEQ ID NO: 50 has 1227 amino acids. Therefore, a protein having at least 90% sequence identity to amino acids 350-1227 of the polypeptide of SEQ ID NO: 50 can have up to 89 amino acid modifications. With regard to claims 22-23, there is a significant amount of structural variability with respect to the members of the genus of proteins claimed. These claims encompass variants of the polypeptide of SEQ ID NO: 50 that can have up to 185 amino acid modifications (185 = 0.15x1227) when compared to the polypeptide of SEQ ID NO: 50, and variants of the polypeptide of SEQ ID NO: 131 that can have up to 69 amino acid modifications when compared to the polypeptide of SEQ ID NO: 131 (69 = 0.05x1377) .
With regard to the argument that Figure 4 of the specification provides the crystal structure of a complex that includes a Cas12a protein, and that the specification provides a Cas12a protein such that that of SEQ ID NO: 50, it is noted that that Figure 4 is merely a 3D model of how different domains in a generic Cas12a protein are located when complexed with a nucleic acid. There are no amino acid sequences or motifs required by each of the domains in the 3D model described in Figure 4. The Examiner acknowledges the disclosure of a limited number of Cas12a proteins, such as the protein of SEQ ID NO: 50. The Examiner also acknowledges that the prior art discloses a limited number of Cas12a proteins and their amino acid sequences. However, as previously indicated, neither the specification nor the prior art discloses the structural elements required in any Cas12a protein, any nuclease domain, any target strand nickase, any non-target strand nickase, or the structural elements within the polypeptide of SEQ ID NO: 131 that are required in any variant having the recited % sequence identity so that the resulting variant has the same function as that of the polypeptide of SEQ ID NO: 131. Neither the specification nor the prior art disclose the structural features of the Cas12a protein of SEQ ID NO: 50 required in any Cas12a protein. No disclosure of a structure/function correlation has been provided which would allow one of skill in the art to recognize which variants of the polypeptide of SEQ ID NO: 131 have the same nuclease activity as that of the polypeptide of SEQ ID NO: 131, or which proteins are Cas12a proteins, nucleases, target strand nickases, or non-target strand nickases.
It is reiterated herein that the claims encompass a large genus of proteins which are structurally unrelated or substantially unrelated. As previously indicated, the total number of variants of the protein of SEQ ID NO: 131 having 95% sequence identity with the polypeptide of SEQ ID NO: 131 is 6.83x10205 variants. See calculations previously provided. A sufficient written description of a genus of polypeptides may be achieved by a recitation of a representative number of polypeptides defined by their amino acid sequence or a recitation of structural features common to members of the genus, which features constitute a substantial portion of the genus. However, in the instant case, there is either no recited structural feature which is representative of all the members of the genus of engineered Cas effector proteins recited in the claims, or the recited structural feature, e.g., 95% sequence identity to SEQ ID NO: 131, is not representative of all the members of the genus of engineered Cas effectors recited since there is no information as to which are the structural elements within the polypeptide of SEQ ID NO: 131 that are essential for the desired activity, which are the remaining structural elements required in the recited polypeptides in addition to those recited in the claims such that the desired nuclease activity is displayed, or a correlation between structure and function which would provide those unknown structural features. While Applicant appears to argue that the few species disclosed are representative of the structure of all the members of the genus, it is noted that the art, as evidenced by Witkowski et al., Seffernick et al. and Tang et al., teaches how even highly structurally homologous polypeptides can have different enzymatic activities. Due to the fact that the specification only discloses a limited number of species of the genus of engineered Cas effector proteins required by the claims, and the lack of description of any additional species by any relevant, identifying characteristics or properties, one of skill in the art cannot reasonably conclude that the entire genus of proteins claimed is adequately described by the teachings of the specification and/or the prior art.
Claims 1, 4-5, 7, 11-14, 16-17, 22-23, 47-49, 52-53, 76-79 remain rejected and new claim 80 is rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for the protein of SEQ ID NO: 131, does not reasonably provide enablement for (I) an engineered Cas effector protein having any structure and function, wherein said engineered Cas effector protein comprises (a) two polypeptides (i.e., two CRISPR-Cas effector proteins) wherein each of these two polypeptides comprise fragments or domains of a Cas12a protein having any structure , and (b) a heterologous polypeptide that comprises a nuclease domain having any structure, or (II) variants of the polypeptide of SEQ ID NO: 131 or SEQ ID NO: 50. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention commensurate in scope with these claims. This rejection as it relates to claim 80 is necessitated by amendment.
This rejection has been discussed at length in the prior Office action. It is maintained and further applied to new claim 80 for the reasons of record and those set forth below.
Applicant argues that claims 1 and 47 have been amended to further define structural elements of the claimed invention. Applicant states that the claims recite specific structural elements suitable to allow the engineered Cas effector protein to cleave, cut, or nick a nucleic acid and/or bind to a polynucleotide. Applicant states that the specification provides ample guidance on the structure of the claimed proteins as well as working examples. Applicant states that the test for enablement is whether one of skill in the art could reproduce the claimed invention without undue experimentation. According to Applicant, with the teachings of the specification including the examples which describe the polypeptide of SEQ ID NO: 131 and other proteins, one of skill in the art could make and use the claimed invention without undue experimentation.
Applicant’s arguments have been fully considered but not deemed persuasive to overcome the instant rejection or avoid the rejection of claim 80. The Examiner acknowledges the amendments made to claims 1 and 47 as well as the teachings of the specification and the prior art. However, the Examiner disagrees with Applicant’s contention that the specification provides ample guidance on the structure of the claimed proteins as well as working examples such that one of skill in the art could make and use the claimed invention without undue experimentation.
As explained above, claims 1, 4-5, 7, 11-13, 47-49, 52-53, 76-80 require a genus of proteins that can comprise any amino acid sequence because the domains or fragments of domains recited in claims 1 and 47 are referred to by name only and do not require any specific structural limitation. As such, the proteins required by the claims can have any structure. In claim 14, only a small fraction of the entire claimed protein is structurally defined since the entire protein, based on the length of the protein of SEQ ID NO: 131, is approximately 1400 amino acids long and the limitation of claim 14 only defines at most 130 amino acids (130 = 0.9x144; SEQ ID NO: 1 has 144 amino acids ). With regard to claims 16-17, either the second CRISPR-Cas effector protein or the first CRISPR-Cas effector protein can have any amino acid sequence, thus being structurally undefined. In the case of claim 17, there is a significant amount of structural variability with respect to the second CRISPR-Cas effector protein. For example, a protein having at least 90% sequence identity to amino acids 350-1227 of the polypeptide of SEQ ID NO: 50 can have up to 89 amino acid modifications. In the case of claims 22-23, there is a significant amount of structural variability with respect to the members of the genus of proteins claimed. These claims encompass variants of the polypeptide of SEQ ID NO: 50 that can have up to 185 amino acid modifications (185 = 0.15x1227) when compared to the polypeptide of SEQ ID NO: 50, and variants of the polypeptide of SEQ ID NO: 131 that can have up to 69 amino acid modifications when compared to the polypeptide of SEQ ID NO: 131 (69 = 0.05x1377) .
It is reiterated herein that the specification discloses the amino acid sequence of a limited number of engineered Cas effector proteins, including the protein of SEQ ID NO: 131, and a limited number of Cas12a proteins, such as the protein of SEQ ID NO: 50, as working examples. However, the specification fails to provide any clue as to the structural elements required in any Cas12a protein, the structural elements required in any nuclease, the structural elements required in any target strand nickase or non-target strand nickase, the structural elements required in any protein to bind to a guide RNA, or the structural elements within the polypeptide of SEQ ID NO: 131 that are required in any variant having the recited % sequence identity so that the resulting variant has the same function as that of the polypeptide of SEQ ID NO: 131. No disclosure of a structure/function correlation has been provided which would allow one of skill in the art to recognize which proteins are Cas12a proteins, which proteins are nucleases, or which structural variants of the polypeptide of SEQ ID NO: 131 have the same nuclease activity as that of the polypeptide of SEQ ID NO: 131.
The art discloses a limited number of Cas12a proteins, a limited number of nucleases, a limited number of target strand nickases and non-target strand nickases, and a limited number of proteins that can bind to a guide RNA. However, neither the specification nor the art provide a correlation between structure and function such that one of skill in the art can envision the structure of any Cas12a protein, any nuclease, any nickase or any protein that can bind to a guide RNA. In addition, the art does not provide any teaching or guidance as to which changes can be made to the protein of SEQ ID NO: 131 such that the resulting variant would display the desired functional characteristics, or the general tolerance of nucleases to structural modifications and the extent of such tolerance. It is reiterated herein that there is a high level of unpredictability associated with accurate functional annotation of proteins based solely on structural homology, and that there is a high level of unpredictability with regard to the modification of a protein’s amino acid sequence to obtain the desired activity without any guidance/knowledge as to which amino acids in a protein are tolerant of modification and which ones are conserved. See teachings of Singh et al. and Sadowski et al. previously introduced.
At the time of the invention, it was not routine in the art to screen by a trial and error process for an essentially infinite number of proteins to find (i) Cas12a proteins, (ii) nucleases, (iii) target strand nickases or non-target strand nickases, or (iv) polypeptides having a nuclease domain that can be combined with any portion of any Cas12a protein and can have nuclease activity. In the absence of (a) a rational and predictable scheme for selecting those proteins most likely to have the desired functional features, and/or (b) a correlation between structure and function, one of skill in the art would have to test an essentially infinite number of proteins to determine which ones have the desired functional characteristics. While it is agreed that a considerable amount of experimentation is permissible if it is merely routine, in the instant case, testing an infinite number of proteins to find those having the desired function without a reasonable amount of guidance with respect to the direction in which the experimentation should process is not deemed routine experimentation. Therefore, contrary to Applicant’s assertions, neither the specification nor the prior art provides enablement to the full scope of the claimed invention.
Allowable Subject Matter
The protein of SEQ ID NO: 131 appears to be allowable over the prior art of record.
Conclusion
No claim is in condition for allowance.
Applicant is advised that any Internet email communication by the Examiner has to be authorized by Applicant in written form. See MPEP § 502.03 (II). Without a written authorization by Applicant in place, the USPTO will not respond via Internet email to any Internet correspondence which contains information subject to the confidentiality requirement as set forth in 35 U.S.C. 122. Sample written authorization language can be found in MPEP § 502.03 (II). An Authorization for Internet Communications in a Patent Application or Request to Withdraw Authorization for Internet Communications form (SB/439) can be found at https://www.uspto.gov/patent/forms/ forms-patent-applications-filed-or-after-september-16-2012, which can be electronically filed.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DELIA M RAMIREZ, Ph.D., whose telephone number is (571) 272-0938. The examiner can normally be reached on Monday-Friday from 8:30 AM to 5:00 PM. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Robert B. Mondesi, can be reached at (408) 918-7584. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
/DELIA M RAMIREZ/Primary Examiner, Art Unit 1652
DR
October 29, 2025