DCT
5:23-cv-06440
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 alleged to be proper in the Northern District of California because a substantial part of the events giving rise to the claim occurred there, specifically the creation and development of Plaintiff's accused technology in San Carlos, California.
- Core Dispute: Plaintiff seeks a declaratory judgment that its Proteome Analysis Platform does not infringe a patent owned by Defendant California Institute of Technology and exclusively licensed to Defendants SomaLogic and/or Panther Merger Subsidiary II.
- Technical Context: The case involves "DNA origami," a technology for folding long strands of DNA into precise, predetermined nanostructures, and its alleged application in the field of proteomics, the large-scale study of proteins.
- Key Procedural History: This action was prompted by letters from SomaLogic to Nautilus, dated July 5, 2023, and December 8, 2023, alleging that the Nautilus Proteome Analysis Platform infringes the patent-in-suit. The complaint also raises allegations of unfair competition and fraud, stemming from a dispute over whether SomaLogic or its subsidiary, Panther Merger, is the true exclusive licensee of the patent.
Case Timeline
| Date | Event |
|---|---|
| 2005-06-14 | ’793 Patent Priority Date |
| 2010-11-30 | ’793 Patent Issue Date |
| 2023-07-05 | SomaLogic sends first letter to Nautilus alleging infringement |
| 2023-08-01 | Nautilus responds to SomaLogic denying need for a license |
| 2023-12-08 | SomaLogic, through counsel, sends second letter alleging infringement |
| 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”
- Patent Identification: U.S. Patent No. 7,842,793, “Methods of Making Nucleic Acid Nanostructures,” issued November 30, 2010.
The Invention Explained
- Problem Addressed: Prior methods for creating complex nanostructures from DNA were often complicated, required extensive purification, were sensitive to the precise ratio of components, and resulted in low yields of the desired structure (’793 Patent, col. 6:41-57).
- The Patented Solution: The patent discloses a method termed "scaffolded DNA origami." This technique uses a long, single strand of a known polynucleotide (the "scaffold") and a multitude of short "helper" or "staple" strands. These staples are designed to bind to specific, non-contiguous regions of the scaffold, effectively folding the long scaffold strand upon itself to form a predetermined two- or three-dimensional shape, much like staples holding a folded piece of paper in place (’793 Patent, Abstract; col. 7:12-25; Fig. 2B-C).
- Technical Importance: This "scaffolded" approach enabled the creation of significantly larger and more complex arbitrary patterns and shapes at the nanoscale with higher yields and greater simplicity than previously possible (’793 Patent, col. 6:21-30).
Key Claims at a Glance
- The complaint seeks a declaratory judgment of non-infringement of any valid claim of the ’793 Patent (Compl. ¶35). The non-infringement arguments focus on a central limitation found in independent claim 1.
- Independent Claim 1 requires, among other elements:
- A method for the ex-vivo production of a non-naturally occurring nucleic acid nanostructure of a desired shape.
- The method involves providing a long "single stranded DNA polynucleotide scaffold" and designing a plurality of shorter "helper/staple strands."
- The helper/staple strands anneal to the scaffold, causing it to fold into the desired shape.
- A key structural requirement is the production of "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."
III. The Accused Instrumentality
Product Identification
- The "Nautilus Proteome Analysis Platform" (Compl. ¶1, ¶9).
Functionality and Market Context
- The complaint describes the accused instrumentality as a platform 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 designed to be a scalable and reliable technology capable of identifying approximately 95% of proteins in a sample, thereby overcoming limitations of existing proteomics platforms by enabling deeper characterization with high throughput and sensitivity (Compl. ¶4). The complaint alleges the platform was created and developed in San Carlos, California (Compl. ¶24).
IV. Analysis of Infringement Allegations
No probative visual evidence provided in complaint.
The core of Nautilus’s request for a declaratory judgment of non-infringement rests on the assertion that its platform does not meet a key structural limitation of the patent’s claims. The infringement allegations from SomaLogic are detailed in letters referenced by the complaint (Compl. ¶27, ¶29).
’793 Patent Infringement Allegations
| Claim Element (from Independent Claim 1) | Alleged Infringing Functionality | Complaint Citation | Patent Citation |
|---|---|---|---|
| ...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. | The complaint asserts that the Nautilus Proteome Analysis Platform does not utilize a structure with this specific crossover spacing and therefore does not infringe. | ¶36, ¶37 | col. 15:60-68 |
- Identified Points of Contention:
- Technical Question: The central factual dispute will be whether the Nautilus Proteome Analysis Platform, in its actual operation, employs a DNA nanostructure that meets the claim limitation of having crossovers spaced by an "odd number of half turns." The complaint categorically denies this (Compl. ¶37), making this a key evidentiary question for the court.
- Scope Questions: Does the term "nanostructure" as used and described in the patent, which focuses heavily on creating arbitrary geometric shapes and patterns (e.g., squares, stars, smiley faces), read on the functional components of a protein analysis platform? This raises the question of whether the patent's scope, when read in light of its specification, is limited to such geometric constructions or extends to different technical applications like proteomics.
V. Key Claim Terms for Construction
The Term: "an odd number of half turns apart"
- Context and Importance: This term defines the specific geometry of the crossovers that hold the nanostructure together. Its construction is critical because Nautilus’s primary non-infringement argument is that its platform does not use a structure meeting this precise requirement (Compl. ¶36, ¶37). The outcome of the case may hinge on the precise technical meaning of this phrase.
- Intrinsic Evidence for Interpretation:
- Evidence for a Broader Interpretation: The patent summary suggests the method is broadly applicable for generating a wide array of devices and systems (’793 Patent, col. 2:25-29). A party might argue the "odd number of half turns" is a general principle for achieving parallel helices, not strictly tied to the examples.
- Evidence for a Narrower Interpretation: The specification repeatedly links this spacing to specific structural outcomes, such as creating a "flat conformation" or a "flat or square lattice structure" (’793 Patent, col. 15:1-3; Compl. ¶37). The patent also provides specific numerical examples, such as 1.5 turns, which may be used to argue for a narrower construction tied to the disclosed embodiments (’793 Patent, col. 8:20-24).
The Term: "nanostructure"
- Context and Importance: This term defines the ultimate product of the claimed method. Practitioners may focus on this term because the ’793 patent’s disclosure is replete with examples of creating arbitrary, pre-designed visual shapes and patterns (’793 Patent, Fig. 3, Fig. 4). The dispute raises the question of whether the functional components of Nautilus's protein analysis system constitute the type of "nanostructure" contemplated and enabled by the patent.
- Intrinsic Evidence for Interpretation:
- Evidence for a Broader Interpretation: The patent’s "Technical Field" and "Summary" sections describe the invention in broad terms, including its use for "nanoscale devices, systems, delivery compositions and nanoscale protein factories," which could support a reading beyond simple geometric shapes (’793 Patent, col. 2:25-29).
- Evidence for a Narrower Interpretation: The detailed description, figures, and examples overwhelmingly focus on the visual and structural "shape" of the resulting object (e.g., "square," "star," "disk with three holes") (’793 Patent, Fig. 3). This may support an argument that the term is limited to structures whose primary inventive characteristic is their predetermined geometry, rather than an unrelated technical function.
VI. Other Allegations
- Indirect Infringement: The complaint seeks a declaration of non-infringement for both direct and indirect infringement (Compl. ¶35; Prayer for Relief ¶1). However, the complaint does not provide specific facts for analysis of any indirect infringement theory that SomaLogic may have asserted.
- Willful Infringement: As a declaratory judgment action brought by the accused infringer, there is no claim for willful infringement. The complaint does, however, establish that SomaLogic had pre-suit knowledge of Nautilus's platform and accused it of infringement in letters dated July 5, 2023, and December 8, 2023, which forms the basis for the existence of an "actual controversy" justifying the suit (Compl. ¶27, ¶29).
VII. Analyst’s Conclusion: Key Questions for the Case
- A central issue will be one of technical fact: Does the Nautilus Proteome Analysis Platform actually utilize DNA nanostructures with the specific crossover geometry—"an odd number of half turns apart"—required by the asserted patent's independent claim, or is there a fundamental mismatch in the technology's physical structure?
- The case will also turn on a question of claim scope: Will the term "nanostructure", as defined and enabled by a patent focused on creating arbitrary geometric shapes, be construed broadly enough to cover the functional components within a complex proteomics analysis platform, or is the accused technology outside the patent's intended field of invention?
- A significant procedural question concerns corporate identity and standing: The complaint alleges that SomaLogic and its subsidiary have provided conflicting statements about which entity is the exclusive licensee of the ’793 patent. This raises threshold questions about which defendant is a proper party to the action and whether their pre-suit conduct constitutes unfair competition or fraud under California law.