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US-12616949-B2 - Row-independent oligonucleotide synthesis

US12616949B2US 12616949 B2US12616949 B2US 12616949B2US-12616949-B2

Abstract

Apparatuses and a method for plate-based oligonucleotide synthesis are disclosed. In one example, an apparatus used in oligonucleotide synthesis includes a synthesis adapter base to receive a commercially available synthesis plate. A keeper is used to apply pressure to the commercially available synthesis plate, and a sealing element is used to seal the commercially-available synthesis plate to the system adapter base. Other methods and apparatuses are disclosed.

Inventors

  • Bruce Erickson
  • Marshall Henry

Assignees

  • SIERRA BIOSYSTEMS, INC.

Dates

Publication Date
20260505
Application Date
20250729

Claims (20)

  1. 1 . An apparatus comprising: one or more synthesis plates, each of the one or more synthesis plates having a plurality of rows, each row of the plurality of rows comprising a plurality of wells and each well of the plurality of wells comprising a waste tip; a synthesis adapter base; the system adapter base located beneath the one or more synthesis plates, wherein the synthesis adapter base is operably coupled to the synthesis plates by one or more fasteners; and a keeper located on top of the one or more synthesis plates, the keeper applying pressure to the one or more synthesis plates, thereby forming a seal around one or both of (i) each of the plurality of rows and (ii) each of the plurality of wells of the one or more synthesis plates.
  2. 2 . The apparatus of claim 1 , wherein the synthesis adapter base comprises one or more adapter base plates.
  3. 3 . The apparatus of claim 2 , wherein the one or more adapter base plates further comprises one or more waste channels, the one or more waste channels dispensing reagents through one or more outlet holes located on the sides of each one of the one or more adapter base plates.
  4. 4 . The apparatus of claim 2 , wherein the one or more adapter plates further comprises a plurality of waste pass-through holes, each of the one or more waste pass-through holes leading to one or more waste channel on another one of the one or more adapter base plates within the synthesis adapter base.
  5. 5 . The apparatus of claim 2 , wherein the one or more adapter plates further comprises a plurality of waste pass-through holes, each of the one or more waste pass-through holes leading to one or more waste pass-through holes on another one of the one or more adapter plates within the synthesis adapter base.
  6. 6 . The apparatus of claim 2 , wherein the one or more adapter base plates further comprises one or more machined O-ring grooves.
  7. 7 . The apparatus of claim 1 , further comprising a chamber surrounding the one or more synthesis plates and a vacuum pump operably connected to a chamber via one or more tubes, where the vacuum pump creates a negative pressure inside the chamber.
  8. 8 . The apparatus of claim 1 , further comprising a chamber surrounding the one or more synthesis plates and a gas source operably coupled to the chamber via one or more tubes, where the gas source creates a positive pressure inside the chamber.
  9. 9 . The apparatus of claim 1 , further comprising a dispense-tip assembly.
  10. 10 . The apparatus of claim 1 , further comprising a dispense nozzle.
  11. 11 . An apparatus comprising: a chamber; one or more synthesis plates inside the chamber, each of the one or more synthesis plates having a plurality of rows, each row of the plurality of rows comprising a plurality of wells and each well of the plurality of wells comprising a waste tip; a synthesis adapter base having one or more adapter plates; the system adapter base located beneath the one or more synthesis plates; a synthesizer frame; wherein the synthesizer frame interfaces with the synthesis adapter base to provide structural support and alignment for the one or more synthesis plates; a keeper located on top of the one or more synthesis plates, the keeper applying pressure to the one or more synthesis plates, thereby forming a seal around one or both of (i) each of the plurality of rows and (ii) each of the plurality of wells of the one or more synthesis plates; and one or more waste channels, the one or more waste channels dispensing reagents through the chamber to one or more outlets of the one or more adapter plates.
  12. 12 . The apparatus of claim 11 , further comprising one or more waste pass-through holes, each of the one or more pass waste pass-through holes operably aligned to the one or more waste channels of the one or more synthesis adapter plates.
  13. 13 . The apparatus of claim 11 , wherein the one or more synthesis adapter plate further comprising one or more receiving threads attaching the one or more synthesis plates to the synthesis adapter base.
  14. 14 . The apparatus of claim 11 , wherein an interior pressure of the chamber is a positive pressure.
  15. 15 . The apparatus of claim 11 , further comprising a vacuum pump operably connected to the chamber via one or more tubes.
  16. 16 . The apparatus of claim 11 , wherein an interior pressure of the chamber is a negative pressure.
  17. 17 . The apparatus of claim 11 , wherein an interior pressure of the chamber is a hybridization of a positive pressure and a negative pressure.
  18. 18 . An apparatus comprising: a chamber comprising a lid; one or more synthesis plates inside the chamber, each of the one or more synthesis plates having a plurality of rows, each row of the plurality of rows comprising a plurality of wells and each well of the plurality of wells comprising a waste tip; a synthesis adapter base, the synthesis adapter base located beneath the one or more synthesis plates; and a keeper located on top of the one or more synthesis plates, the keeper applying pressure to the one or more synthesis plates, thereby forming a seal around one or both of (i) each of the plurality of rows and (ii) each of the plurality of wells of the one or more synthesis plates.
  19. 19 . The apparatus of claim 18 , where the lid comprises a cavity with a plurality of bottles containing reagents inside the cavity.
  20. 20 . The apparatus of claim 18 , further comprising an opening in the lid, the opening containing a valve array, the valve array dispensing the reagents from the plurality of bottles to the plurality of wells of the one or more synthesis plates.

Description

CLAIM OF PRIORITY This patent application claims priority to and is a continuation-in-part of U.S. patent application Ser. No. 18/385,857, filed Oct. 31, 2023, which issued as U.S. Pat. No. 12,370,521, on Jul. 29, 2025, which is a continuation of U.S. patent application Ser. No. 18/118,032, filed Mar. 6, 2023, which issues as U.S. Pat. No. 11,856,177, which is a continuation of U.S. patent application Ser. No. 17/250,642, filed Feb. 15, 2021, which issued as U.S. Pat. No. 11,596,919 on Mar. 7, 2023, which, pursuant to 35 U.S.C. § 371, is a U.S. National Phase application of and claims priority to PCT/US2019/046802, now WO 2020/037194, filed Aug. 16, 2019, which claims priority pursuant to 35 U.S.C. § 119 (e) to U.S. Provisional Application Ser. No. 62/719,487, filed Aug. 17, 2018. The text and contents of each of these patent applications are hereby incorporated into this application by reference as though fully set forth herein. TECHNOLOGY FIELD The disclosed subject matter is generally related to the field of biotechnology. More specifically, the disclosed subject matter is related to the de novo synthesis of DNA, RNA, synthons, and full genes-frequently generically referred to as oligonucleotide synthesis. BACKGROUND Since the release of the seminal paper on tRNA synthesis in 1972 by H. G. Khorana et al., the field of gene synthesis has experienced steady growth. With its use in generating novel therapeutics and biomaterials, academic and industrial researchers frequently require more exogenous DNA sequences than a standard laboratory can produce. To fill this need, automated oligonucleotide synthesis systems have been developed to generate oligonucleotides in hours, in quantities and varieties that a single laboratory technician would have otherwise needed weeks or months to complete. As the demand for synthetic oligonucleotides increases, these high-throughput systems must experience continual refinement to meet the needs of the marketplace. The information described in this section is provided to offer the skilled artisan a context for the following disclosed subject matter and should not be considered as admitted prior art. SUMMARY Devices, mechanisms, and design elements are disclosed herein that reduce reagent consumption, increase throughput, and shorten cycle times on an oligonucleotide synthesis apparatus. In an embodiment, a mechanism for these improvements includes, in various embodiments, a machined block that can receive commercially-available synthesis plates and synthesize unique genetic material in each well, while allowing self-contained rows of each of the plates to retain full autonomy with respect to one another. This autonomy not only increases the versatility of the plates, but also allows a user to conduct synthesis in a continuum or gradient, thereby decreasing cycle times. Various embodiments presented herein offer an end user processes for generating oligonucleotides at a significantly reduced cost with significantly higher production rates. In an embodiment, the disclosed subject matter includes an apparatus used for oligonucleotide synthesis. The apparatus includes a machined block configured to receive a commercially-available synthesis plate, a keeper to apply pressure to the commercially-available synthesis plate, and a sealing element to seal the commercially-available synthesis plate to the machined block. In another embodiment, the disclosed subject matter includes an apparatus with an “All Plate” system that provides a modular platform or a System Adapter Base which allows an user to interchange among multiple synthesis vessel configurations with minimal effort. The modular platform or Synthesis Adapter Base interfaces with a synthesizer frame and row-independent oligonucleotide (RIOS) system. Various adapter plates can be mounted to the Synthesis Adapter Base using one or more fasteners. Each adapter plate is configured to receive and seal a specific vessel format or layout while maintaining the RIOS retention and alignment requirements. The Synthesis Adapter Base further comprises a planar mounting interface configured to receive interchangeable adapter plates. The Base does not directly contact or seal the synthesis vessels and instead provides structural support and alignment for the RIOS system. BRIEF DESCRIPTION OF THE DRAWINGS FIG. 1 shows a high-level, exemplary embodiment of a RIOS system; FIG. 2A shows an exemplary embodiment of a broken-out, disassembled draining apparatus comprising a drain block, a sealing element, a synthesis plate, and a keeper in accordance with various embodiments of the disclosed subject matter; FIG. 2B shows a top view of the synthesis plate of FIG. 2A; FIG. 2C shows a side view of the synthesis plate of FIG. 2A; FIG. 2D shows an enlarged view of waste tips of the synthesis plate of FIG. 2A; FIG. 3 shows an exemplary embodiment of an assembled draining apparatus in accordance with various embodiments of the disclosed subject matter; F