Nautilus Biotechnology Inc v. Somalogic Inc

I. Executive Summary and Procedural Information

• Parties & Counsel:
  • Plaintiff: Nautilus Biotechnology, Inc. (Delaware)
  • Defendant: SomaLogic, Inc. (Delaware); Panther Merger Subsidiary II, LLC (Delaware); California Institute of Technology (California)
  • Plaintiff's Counsel: Weil, Gotshal & Manges LLP
• Case Identification: 5:23-cv-06440, N.D. Cal., 04/19/2024
• Venue Allegations: Venue is asserted in the Northern District of California because a substantial part of the events, including the creation and development of Plaintiff's accused technology, allegedly occurred in the district.
• Core Dispute: Plaintiff seeks a declaratory judgment that its Proteome Analysis Platform does not infringe Defendant Caltech's U.S. Patent No. 7,842,793, which Plaintiff alleges was asserted against it by Defendant SomaLogic.
• Technical Context: The technology is in the field of proteomics and involves methods of creating complex, self-assembling nanoscale structures from nucleic acids, a technique commonly known as "DNA Origami."
• Key Procedural History: The dispute stems from pre-suit correspondence in which Defendant SomaLogic allegedly accused Plaintiff Nautilus of infringing the patent-in-suit and demanded that Nautilus cease and desist its activities. The complaint also raises issues regarding the corporate relationship between SomaLogic and Panther Merger Subsidiary II, alleging they are alter egos and questioning which entity is the proper exclusive licensee.

Case Timeline

Date	Event
2005-06-14	'793 Patent Priority Date
2010-11-30	'793 Patent Issue Date
2022-07-01	Approximate date SomaLogic acquired Palamedrix Inc.
2023-07-05	SomaLogic sends letter to Nautilus alleging potential infringement
2023-08-01	Nautilus sends responsive letter to SomaLogic denying need for a license
2023-12-08	SomaLogic, through outside counsel, sends letter alleging infringement and demanding cessation
2024-04-19	First Amended Complaint for Declaratory Judgment filed

II. Technology and Patent(s)-in-Suit Analysis

U.S. Patent No. 7,842,793 - Methods of Making Nucleic Acid Nanostructures (issued Nov. 30, 2010)

The Invention Explained

• Problem Addressed: The patent background describes a demand for "ever-shrinking devices of ever-increasing complexity" and notes the difficulty of manufacturing such structures with high resolution and ease '793 Patent, background section Existing methods for creating DNA nanostructures were often complicated, low-yield, and highly sensitive to the precise ratios of component strands '793 Patent, col. 5:50-65
• The Patented Solution: The invention, termed "scaffolded nucleic acid origami," provides a method for folding a long, single-stranded polynucleotide (a "scaffold") into a predetermined arbitrary shape using hundreds of short "helper/staple" strands '793 Patent, abstract '793 Patent, col. 5:20-29 These staples act like glue, binding to different segments of the scaffold to guide its self-assembly into a complex 2D or 3D structure, as depicted in the design process flow of Figure 1 '793 Patent, FIG. 1 This use of a single, long scaffold strand makes the process robust, high-yield, and less sensitive to stoichiometry than previous methods '793 Patent, col. 7:56-62
• Technical Importance: This method enables the reliable, high-yield creation of arbitrary and complex nanoscale shapes, serving as a "nanobreadboard" for arranging other components like proteins or nanoparticles with approximately 6-nanometer precision '793 Patent, col. 14:35-42

Key Claims at a Glance

• The complaint seeks a declaratory judgment of non-infringement of "any valid claim of the Asserted Patent" Compl. ¶35 but focuses its non-infringement argument on a limitation present in independent claim 1.
• Independent Claim 1 includes the following essential elements:
  • A method for the ex-vivo production of a non-naturally occurring nucleic acid nanostructure of an arbitrary 2D or 3D shape.
  • The method involves selecting a shape, providing a single-stranded DNA scaffold, designing a folding path for the scaffold, and designing a plurality of helper/staple strands.
  • The nanostructure is produced by allowing the scaffold and helper strands to anneal.
  • The helper strands bind the scaffold to form a desired bend or angle, producing "parallel helices held together by a periodic pattern of crossovers spaced so that the distance between crossovers formed by two consecutive oligonucleotide helper/staple strands is an odd number of half turns apart." '793 Patent, claim 1
• The complaint does not reserve the right to assert arguments against specific dependent claims.

III. The Accused Instrumentality

Product Identification

• The "Nautilus's Proteome Analysis Platform" is the instrumentality at issue Compl. ¶9

Functionality and Market Context

• The complaint describes the platform as a technology for "quantifying and unlocking the complexity of the proteome," which is the set of all proteins in a biological sample Compl. ¶3
• It is alleged to be a "new proteomic analysis technology that is scalable and reliable" and capable of identifying roughly 95% of proteins in a sample, overcoming limitations of prior platforms by enabling "deep characterization of the proteome with high throughput, sensitivity and ease" Compl. ¶4 The complaint alleges that the platform does not use the specific structural configuration required by the patent's claims Compl. ¶¶36-37

IV. Analysis of Infringement Allegations

The complaint seeks a declaratory judgment of non-infringement. The following table summarizes the Plaintiff's primary argument for why its product does not meet a key limitation of the patent's claims.

'793 Patent Infringement Allegations

Claim Element (from Independent Claim 1)	Alleged Non-Infringing Functionality	Complaint Citation	Patent Citation
parallel helices held together by a periodic pattern of crossovers spaced so that the distance between crossovers formed by two consecutive oligonucleotide helper/staple strands is an odd number of half turns apart	The Nautilus Proteome Analysis Platform "does not utilize a structure wherein 'the distance between crossovers formed by two consecutive oligonucleotide helper/staple strands is an odd number of half turns apart.'" Compl. ¶36 Instead, it allegedly uses a different structure that does not result in a "flat or square lattice structure."	¶36; ¶37	col. 2:63-68

• Visual Evidence: A large redacted visual on page 15 is presented to illustrate the specific structure Nautilus's platform allegedly uses, which is contrasted with the claimed structure Compl. ¶37
• Identified Points of Contention:
  • Technical Question: A central factual dispute will be whether the Nautilus Proteome Analysis Platform, as a matter of technical reality, employs a structure where consecutive staple-strand crossovers are separated by a distance equivalent to an "odd number of half turns." The complaint denies this but redacts the details of its alternative structure Compl. ¶37
  • Scope Questions: The case raises the question of whether the claim term "odd number of half turns apart" is functionally tied to a specific geometric outcome. The patent specification suggests this spacing results in a "flat conformation" '793 Patent, col. 2:1-3, a point Nautilus leverages by arguing its structure is not a "flat or square lattice" Compl. ¶37 The dispute may turn on whether any structure using this crossover spacing principle is covered, or only those that result in a demonstrably flat lattice.

V. Key Claim Terms for Construction

• The Term: "the distance between crossovers formed by two consecutive oligonucleotide helper/staple strands is an odd number of half turns apart"
• Context and Importance: This term is the core of Nautilus's non-infringement argument Compl. ¶¶36-37 The interpretation of this phrase-specifically, whether it dictates a resulting physical geometry (e.g., flatness) or merely a method of design-will be critical to determining infringement. Practitioners may focus on this term because Nautilus has staked its non-infringement position on its platform not creating the "flat or square lattice structure" associated with this claim language Compl. ¶37
• Intrinsic Evidence for Interpretation:
  • Evidence for a Broader Interpretation: The plain language of claim 1 describes the spacing of crossovers but does not explicitly require a "flat" or "180 degree" angular outcome within the claim itself '793 Patent, claim 1 A patentee might argue that the claim covers any structure made using this crossover rule, regardless of minor variations or curvatures that deviate from perfect flatness.
  • Evidence for a Narrower Interpretation: The patent's summary explicitly links this limitation to a specific physical result, stating that with this spacing, "three adjacent parallel helices of a domain of the polynucleotide scaffold form an angle of 180 degrees and structural unit assumes a flat conformation" '793 Patent, col. 2:1-3 This passage may support an argument that the claim term is defined by its function of creating a flat structure, and a non-flat structure would not infringe.

VI. Other Allegations

• Indirect Infringement: The complaint seeks a declaratory judgment of non-infringement "directly or indirectly" Compl. ¶35, but provides no specific facts for analysis regarding inducement or contributory infringement theories.
• Willful Infringement: As this is a declaratory judgment action filed by the accused infringer, willfulness is not formally alleged by the patentee. However, the complaint documents pre-suit notice of infringement via letters from SomaLogic dated July 5, 2023, and December 8, 2023 Compl. ¶27 Compl. ¶29 This correspondence would likely form the basis for a future willfulness claim by SomaLogic if it were to file counterclaims.
• Unfair Competition and Fraud: Nautilus has also brought claims against SomaLogic for unfair competition and actual fraud under California law Compl. ¶¶39-52 These claims are based on SomaLogic's alleged misrepresentations regarding its status as the "exclusive licensee," where in one communication it claimed to be the exclusive licensee Compl. ¶42 and in a later court filing contended that its subsidiary, Panther Merger Subsidiary II, was the exclusive licensee Compl. ¶41

VII. Analyst's Conclusion: Key Questions for the Case

• A primary issue will be one of claim construction: does the claim term "distance between crossovers... is an odd number of half turns apart" require the creation of a geometrically "flat" structure, as suggested by the patent's specification, or does it more broadly describe a design rule whose infringement is independent of the final structure's flatness?
• The case will also present a critical evidentiary question: what is the actual nanostructure used by the Nautilus Proteome Analysis Platform? The resolution of the case will depend on technical evidence, currently redacted in the complaint, demonstrating whether or not that structure meets the limitations of the patent's claims as construed by the court.
• A procedural and ancillary question concerns standing and proper parties: the dispute over whether SomaLogic or its subsidiary is the true exclusive licensee, which forms the basis for Nautilus's fraud and unfair competition claims, may impact which defendant has the right to enforce the patent and defend this declaratory judgment action.