Flexible tape-based chemistry apparatus

• US 10,351,846 B2
• Filed: 09/11/2015
• Issued: 07/16/2019
• Est. Priority Date: 09/17/2014
• Status: Active Grant

• Current Assignee: Illumina Cambridge Limited (Illumina Incorporated)
• Original Assignee: Illumina Cambridge Limited (Illumina Incorporated)
• Inventors: Boutell, Jonathan Mark, Skinner, Gary Mark, Jenkins, Gareth
• Primary Examiner(s): Vivlemore, Tracy
• Assistant Examiner(s): Kaup, Sahana S
• Application Number:
  US14/851,090
• Publication Number:
  US 20160076025A1
• Time in Patent Office: 1,404 Days
• Field of Search: None
• CPC Class Codes: C12N 15/1013 by using magnetic beads
• CPC Class Codes: C12N 15/1068 Template (nucleic acid) mediated chemical library synthesis, e.g. chemical and enzymatical DNA-templated organic molecule synthesis, libraries prepared by non ribosomal polypeptide synthesis [NRPS], DNA/RNA-polymerase mediated polypeptide synthesis
• CPC Class Codes: G01N 33/48764 Test tape taken off a spool

Abstract

An apparatus and method for applying a chemistry to samples of interest are provided. The apparatus and method include a flexible tape mounted on an arrangement of guide rollers. Samples of interest (e.g., clusters of DNA templates) are bound to at least one surface of the flexible tape. The method and apparatus further comprise one or more read heads in relation to the flexible tape and a plurality of reservoirs along a path of the flexible tape. The reservoirs comprise liquids comprising chemical reagents for performing the chemistry on the samples of interest bound to the at least one surface of the flexible tape. The method and apparatus further comprise a drive system for driving at least one of the guide rollers to advance the flexible tape into and out of the reservoirs.

Claims

1. An apparatus for applying a chemistry to samples of interest, comprising:

a flexible tape mounted on an arrangement of guide rollers, wherein samples of interest are immobilized to respective local areas along a common solid surface of at least one side of the flexible tape;

one or more read heads in relation to the flexible tape;

a plurality of reservoirs along a path of the flexible tape, wherein the reservoirs comprise liquids comprising chemical reagents for performing a select chemistry on the samples of interest immobilized to the respective local areas along the common solid surface of the flexible tape; and

a drive system for driving at least one of the guide rollers to advance the flexible tape into and out of the reservoirs.

2. The apparatus of claim 1, wherein the flexible tape mounted on the arrangement of guide rollers comprises a continuous loop configuration.

3. The apparatus of claim 1, wherein the flexible tape mounted on the arrangement of guide rollers comprises a reel-to-reel configuration.

4. The apparatus of claim 1, wherein the at least one side of the flexible tape is in direct contact with a flat surface of each of the guide rollers.

5. The apparatus of claim 1, wherein the guide rollers comprise sprockets, and wherein the flexible tape comprises sprocket holes along edges of the flexible tape.

6. The apparatus of claim 1, wherein the one or more read heads are positioned such that the flexible tape is within a field of view of the corresponding read head and such that a plane of the flexible tape is substantially at a focal plane of the corresponding read head.

7. The apparatus of claim 1, wherein the one or more read heads comprise a digital imaging device.

8. The apparatus of claim 7, wherein the digital imaging device comprises a charge-coupled device (CCD) image sensor.

9. The apparatus of claim 1, wherein at least one of the plurality of reservoirs comprises a liquid comprising an incorporation mix.

10. The apparatus of claim 1, wherein at least one of the plurality of reservoirs comprises a liquid comprising a wash buffer.

11. The apparatus of claim 1, wherein at least one of the plurality of reservoirs comprises a liquid comprising a cleavage mix.

12. The apparatus of claim 1, wherein the samples of interest represent clusters of DNA templates, and at least one of the plurality of reservoirs comprises a liquid comprising sample DNA and reagents suitable for conducting kinetic exclusion amplification.

13. The apparatus of claim 1, wherein at least one of the plurality of reservoirs comprises a liquid comprising a linearization mix.

14. The apparatus of claim 1, wherein at least one of the plurality of reservoirs comprises a liquid comprising a linearization denaturation reagent.

15. The apparatus of claim 1, wherein at least one of the plurality of reservoirs comprises a liquid comprising a sequencing primer.

16. The apparatus of claim 1, wherein the reservoirs are moveable and capable of being individually controlled.

17. The apparatus of claim 1, wherein the guide rollers are moveable and capable of being individually controlled.

18. The apparatus of claim 1, wherein at least one read head is arranged downstream of the reservoirs comprising sequencing reagents.

19. The apparatus of claim 1, wherein the flexible tape comprises magnetic tape, plastic tape, or glass.

20. The apparatus of claim 19, wherein the flexible tape comprises magnetic tape and wherein at least one read head is a magnetic read head for at least one of writing information to or reading information from the flexible tape.

21. The apparatus of claim 1, wherein the samples of interest are bound to both sides of the flexible tape, further wherein the apparatus comprises two read heads in which one read head is positioned in relation to one side of the flexible tape and another read head is positioned in relation to another side of the flexible tape.

22. The apparatus of claim 1, wherein samples of interest are bound to one side of the flexible tape, and wherein the flexible tape comprises a Mö

bius strip.

23. The apparatus of claim 1, wherein the plurality of reservoirs comprises a carousel of reservoirs capable of rotating from one to another at a given location.

24. The apparatus of claim 1, wherein at least one of the plurality of reservoirs comprises an independently controlled heating element.

25. A method of DNA template cluster generation using the apparatus of claim 1 comprising:

providing the flexible tape mounted on the arrangement of guide rollers, wherein the samples of interest include clusters of DNA;

arranging the reservoirs along the path of the flexible tape, wherein the chemical reagents are selected for performing DNA sequencing on the DNA templates; and

selectively advancing a portion of the flexible tape into one or more of the reservoirs;

wherein DNA templates are clustered on the flexible tape.

26. A method of DNA template linearization using the apparatus of claim 1 comprising:

providing the flexible tape mounted on the arrangement of guide rollers, wherein the samples of interest include clusters of DNA templates;

arranging the reservoirs along the path of the flexible tape, wherein the chemical reagents for performing DNA sequencing on the DNA templates; and

selectively advancing a portion of the flexible tape into reservoirs, wherein the portion of the flexible tape is advanced sequentially into reservoirs comprising;

a linearization mix;

a linearization denaturation reagent; and

a sequencing primer;

wherein DNA templates on a surface of the portion of the flexible tape are linearized.

27. A method of applying a chemistry to samples of interest using the apparatus of claim 1 comprising:

providing the flexible tape mounted on the arrangement of guide rollers;

arranging the reservoirs along the path of the flexible tape, wherein the chemical reagents are configured for performing a select chemistry on the samples of interest; and

selectively advancing a portion of the flexible tape of the apparatus comprising the samples of interest into reservoirs, wherein the portion of the flexible tape is advanced sequentially into reservoirs comprising;

an incorporation mix;

a wash buffer;

a cleavage mix; and

a wash buffer;

wherein the portion of the flexible tape comprising the samples of interest is passed by a field of view of a read head, wherein images of the samples of interest are captured.

28. The apparatus of claim 1, wherein the select chemistry constitutes a sequencing-by-synthesis (SBS) chemistry.

29. The apparatus of claim 1, wherein the flexible tape is configured to be at least one of submerged and advanced through at least one of the reservoirs at a designated speed or submerged and dwell within at least one of the reservoirs for a designated period of time.

30. An apparatus for applying a chemistry to samples of interest, comprising:

a flexible tape mounted on an arrangement of guide rollers, wherein samples of interest are immobilized to respective local areas along a common solid surface of at least one side of the flexible tape;

one or more read heads in relation to the flexible tape;

a plurality of reservoirs along a path of the flexible tape, wherein the reservoirs comprise liquids comprising chemical reagents for performing a select chemistry on the samples of interest immobilized to the respective local areas along the common solid surface of the flexible tape; and

a drive system for driving at least one of the guide rollers to advance the flexible tape into and out of the reservoirs;

wherein at least one of the guide rollers is configured to be submerged within one of the reservoirs as the flexible tape is advanced through the one reservoir.