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 notes that this motion will become moot should the Board deny Broad's Preliminary Motion No. 1 to change the Count.  Sigma-Aldrich also asserts 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 contends that Broad has not applied the one-way obviousness test and to address whether these claims 52-54 satisfy the written description requirement of 35 U.S.C. § 112(a).

With regard to the allowability vel non of these claims, Sigma-Aldrich sets forth the Board's conditions for granting Broad leave to file Contingent Motion No. 2 but then asserts that Broad has not fulfilled the condition that the claims be in condition for allowance, 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.  Sigma-Aldrich cites (and relies upon) its earlier-filed Opposition to Broad Motion No. 1 on why claims 52-54 of the '403 application were not allowed by the Examiner.

On the merits, Sigma-Aldrich cites the one-way obviousness test in support of its position that Claims 53 and 54 are not patentable over Proposed Count No. 3 (they would have been obvious) and thus the Board should not grant the Motion.  Finally, Sigma-Aldrich argues (as it has elsewhere) that the Broad P1 provisional application does not provide adequate written description support for Claims 52-54 of the '403 application.  In this regard Sigma-Aldrich argues that "the limited Section 112 analysis for a constructive reduction [to] practice is not the same as a full Section 112 analysis for compliance with the written description requirement," citing Google LLC v. Parus Holdings, Inc., 2021 Pat. App. LEXIS 6203 at *11 (PTAB Oct. 29, 2021) (the distinction being that satisfaction of the former requires disclosure of but a single embodiment within the scope of the Count while satisfaction of the written description requirement must show an adequate description throughout the full scope of the claims corresponding to the Count, citing Zynga, Inc. v. IGT, 2014 Par. App. LEXIS 753 at *24 (PTAB Feb. 14, 2014)).  Finally, Sigma-Aldrich argues that Broad did not even address whether Claims 52-54 of the '403 application were patentable in its Contingent Motion No. 2, nor that "Broad fails to address the fact that Broad's intervening AIA Application 61/842,322 disclosed and claimed 'wherein the gene product is luciferase,' which limitation was not disclosed or claimed in any of Broad's pre-AIA applications."  Once again, Sigma-Aldrich refers to and relies upon its Opposition to Broad Preliminary Motion No. 1 which addressed many of these same issues.