The claims that were the subject of Broad's Motion recite a CRISPR method in eukaryotic cells that cleaves both strands and repairs the break by integration of a template polynucleotide.  Claim 52 is generic with regard to the guide RNA species, comprising dual-molecule and single-molecule (sgRNA) species:

52.  A method comprising: introducing into, or expressing in, a eukaryotic cell having a DNA molecule,
    (I) a Cas9 protein or one or more nucleotide sequences encoding the Cas9 protein,
    (II) an RNA or one or more nucleotide sequences encoding the RNA, the RNA comprising:
        (a) a first RNA comprising a first ribonucleotide sequence and a second ribonucleotide sequence, and
        (b) a second RNA, and
    (III) a template polynucleotide,
    wherein, the second RNA forms an RNA duplex with the second ribonucleotide sequence, and wherein, in the eukaryotic cell, the first ribonucleotide sequence directs the Cas9 protein to a target sequence of the DNA molecule, whereby the Cas9 cleaves both strands of the DNA molecule and the cleavage is repaired by integration of the template polynucleotide into  the DNA molecule in the eukaryotic cell.

Claim 53 (dual molecule RNA species) and claim 54 (single-molecule RNA species) recite the two alternative species.  Broad asserted that these claims were deemed allowable by the U.S. Patent and Trademark Office Examiner on November 15, 2021.

Sigma-Aldrich's Opposition noted that this motion will become moot should the Board deny Broad's Preliminary Motion No. 1 to change the Count.  Sigma-Aldrich also asserted that none of the claims in the '403 application have been allowed (or considered in condition for allowance) by the Examiner, prosecution of that application having been suspended with the Declaration of this Interference.  Should the Board reach the merits, Sigma-Aldrich contended that Broad has not applied the one-way obviousness test to address whether these claims 52-54 satisfy the written description requirement of 35 U.S.C. § 112(a).  Sigma-Aldrich also accused Broad of not satisfying the Board's requirements for leave to file Contingent Motion No. 2, characterizing Broad's position as being "misleading" and citing several assertions from the Contingent Motion that state or imply that the Examiner has made an allowability determination.  And on the merits Sigma-Aldrich asserted that under the one-way test for obviousness Claims 53 and 54 are not patentable over Proposed Count 3.

In its Reply, Broad first addresses Sigma-Aldrich's incorporation by reference of what Broad states is over 25 pages from its Opposition to Broad's Preliminary Motion No. 1, which besides being improper under Standing Order ¶ 106.2 was the only basis for several arguments.  Accordingly, Broad states that these arguments should be considered waived.  Broad also argues that Claim 52 "was and is allowable" because the Examiner sua sponte indicated these claims were allowable (and remained so upon entry of further amendments).  Allowability follows for dependent claims 53 and 54, which recite species of the RNA component of the claimed CRISPR-Cas9 complexes recited in Claim 52.  Broad further sets forth the basis for adequate written description of Claims 52-54 in the Zhang B1 priority document, because the disclosure in that document is identical in the specification of the '403 application (which incorporates the B1 application by reference, providing "an unbroken chain of identical disclosures supporting the subject matter of claims 52-54").

As in other Replies, Broad sets forth the basis for the Board to find claims 52-54 to be patentable over Sigma-Aldrich's earliest priority disclosure and why the '403 application is entitled to the benefit of pre-AIA status.  Regarding the latter argument, Broad argues that AIA §§ 3(n)(1) and 3(n)(2) (the statutory basis for Sigma-Aldrich's argument) do not apply to priority claims to a provisional application under 35 U.S.C. § 119(e) (although a fair reading of the statute would appreciate that the basis for the distinctions under the AIA relate to the claims in a pre-AIA priority application and provisional applications have no claims, at least not formally).  And Broad reminds the Board that Sigma-Aldrich attempted to broach this issue in its own Preliminary Motion but the Board denied that request.  On the merits, Broad also contends that any differences between what is disclosed in the '403 application and the priority applications, including the Zhang application, do not satisfy the standard to qualify as new matter and hence prohibit pre-AIA status.

For all these reasons, Broad asks the Board to grant this Motion if it grants Broad's Preliminary Motion No. 1.