Biopolymer array inspection

• US 6,232,072 B1
• Filed: 10/15/1999
• Issued: 05/15/2001
• Est. Priority Date: 10/15/1999
• Status: Expired due to Fees

• Current Assignee: Agilent Technologies Europe BV (Agilent Technologies, Inc.)
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Fisher, William D.
• Primary Examiner(s): Brusca, John S.
• Assistant Examiner(s): KIM, YOUNG J
• Application Number:
  US09/419,447
• Time in Patent Office: 578 Days
• Field of Search: 435/6, 436/518, 356/364, 356/369, 422/82.05
• US Class Current: 435/6.11
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00351 Means for dispensing and evacuation of reagents
• CPC Class Codes: B01J 2219/00378 Piezoelectric or ink jet dispensers
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00704 integrated with the reactor apparatus
• CPC Class Codes: B01J 2219/00707 separated from the reactor apparatus
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof

Abstract

A method of fabricating a biopolymer array, and an apparatus which can execute the method. droplets of fluid carrying the biopolymer or a biomonomer are deposited onto a front side of a transparent substrate. Light is directed through the substrate from the front side, back through a substrate back side and a first set of deposited droplets on the first side to an image sensor. The substrate may be mounted by means of a chuck with parallel channels, and a scanning operation of a droplet dispensing head, light source, and sensor conducted in unison in the direction of the channels.

Claims

1. A method comprising:

(a) depositing droplets of fluid carrying a biopolymer or a biomonomer onto a front side of a transparent substrate so as to fabricate a biopolymer array; and

(b) directing light through the substrate from the front side then backward through the substrate and a first set of deposited droplets on the substrate front side, to an image sensor.

2. A method according to claim 1 wherein the biopolymer is a polynucleotide.

3. A method according to claim 2 wherein the polynucleotide is a DNA.

4. A method according to claim 1 wherein the light passes through the substrate from the front side at a position other than the first droplet set before being reflected to pass backward through the substrate and first droplet set, and wherein the light is reflected at a position spaced from a back side of the substrate so as to reduce at the sensor any shadow from any non first set droplets on the front side through which the light may initially pass before being reflected.

5. A method according to claim 4 wherein the light passes through the substrate from the front side at an angle to a normal of the front side, and passes backward through the back side and first droplet set at a complementary angle to the normal.

6. A method according to claim 1 wherein light passes through the first droplet set when passing through the substrate from the front side, before being reflected to again pass through the first droplet set.

7. A method according to claim 6 wherein the light is reflected at a position spaced from a back side of the substrate.

8. A method according to claim 1 additionally comprising:

repeating step (b) for additional sets of the deposited droplets by scanning the directed and reflected light across the front side.

9. A method according to claim 8 wherein both a light source of the directed light and the image sensor are scanned in unison across the front side.

10. A method according to claim 8 wherein the droplets are deposited as droplet sets by a deposition head, and wherein multiple droplet sets are deposited by scanning the deposition head across the front side.

11. A method according to claim 10 wherein the light source, image sensor and deposition head are physically interconnected and are scanned in unison across the front side.

12. A method according to claim 8 wherein the light is reflected from a mirror which faces at least an area on a back side of the substrate corresponding to an area on the front side across which droplet sets are deposited.

13. A method according to claim 10 wherein:

the substrate is held in a chuck having multiple upstanding ribs to support a back side of the substrate;

light is reflected from a mirror comprising multiple mirror segments extending along channels defined between the ribs; and

the deposition head is scanned across the front side of the substrate by scanning along the channels in turn.

14. A method according to claim 13 wherein:

a light source of the directed light and a camera which includes the sensor, are positioned so as to direct and receive the reflected light at complementary angles to a normal of the front side such that light from the source initially passes through the front side of the substrate at a position other than the first droplet set before being reflected to pass through the first droplet set;

the direction of light from the source to the sensor being on a plane oriented in the direction of the channels; and

the source and sensor are scanned in a direction along the channels in turn.

15. A method according to claim 14 wherein the plane is parallel to the direction of the channels.

16. A method according to claim 10 wherein the deposition head is adjusted toward or away from the front side of the substrate independently of the sensor.

17. A method according to claim 10 additionally comprising, after depositing droplets of at least the first droplet set, re-positioning the substrate with respect to the light source and image sensor such that the reflected light is received at the image sensor after it has passed back through the first droplet set.

18. A method according to claim 1 additionally comprising exposing the array to a sample to be tested, and interrogating the array following exposure.

19. A method according to claim 1 additionally comprising exposing the array to a sample to be tested at a first location, interrogating the array, and communicating the result or a conclusion based on the result to a location remote from the first location.

20. A method according to claim 19 wherein the sample was obtained from a remote location.

21. An apparatus for fabricating a biopolymer array, comprising:

(a) a mount on which a transparent substrate can be mounted;

(b) a deposition head to deposit droplets of a fluid carrying the biopolymer or a biomonomer onto a front side of the mounted substrate;

(c) a light source to direct light through the mounted substrate from the front side;

(d) a reflector to reflect light from the source which has passed through the mounted substrate backward through the mounted substrate and a first set of deposited droplets on the front side; and

(e) an image sensor facing a front side of the mounted substrate to receive the reflected light after it has passed back through the first droplet set.

22. An apparatus according to claim 21 wherein the reflector comprises a mirror facing a back side of the mounted substrate.

23. An apparatus according to claim 22 wherein the deposition head comprises multiple pulse jets each of which can be electrically activated to deposit a droplet.

24. An apparatus according to claim 23 wherein the volume of a droplet delivered by a pulse jet on a single activation is between 0.1 to 1000 pL.

25. An apparatus according to claim 21 wherein the light source and the image sensor, are positioned such that light from the source initially passes through the front side of the substrate at a position other than the first droplet set before being reflected to pass backward through the substrate and first droplet set.

26. An apparatus according to claim 25 wherein the mirror is spaced from the back side of the mounted substrate so as to reduce at the sensor any shadow from any droplets on the front side through which the light may initially pass before being reflected from the mirror.

27. An apparatus according to claim 25 wherein the light source is positioned to direct light through the substrate at an angle to a normal of the front side, and the image sensor is positioned to receive the light which has passed back through the first droplet set at a complementary angle to the normal.

28. An apparatus according to claim 21 wherein the light source and image sensor are positioned such that light from the source initially passes through the front side of the mounted substrate at the position of the first droplet set before being reflected to again pass through the first droplet set.

29. An apparatus according to claim 28 wherein the mirror is spaced from the back side of the substrate.

30. An apparatus according to claim 22 additionally comprising:

a transport system to scan at least one of the deposition head and substrate across the other.

31. An apparatus according to claim 30 additionally comprising a processor to control the transport system and cause the deposition head to dispense multiple droplet sets in co-ordination with relative movement of the deposition head and substrate.

32. An apparatus according to claim 22 additionally comprising a transport system to scan both the light source and image sensor in unison across the front side so that the reflected light can be received at the sensor from additional sets of the deposited droplets.

33. An apparatus according to claim 32 wherein the light source, image sensor and deposition head are physically interconnected, and the transport system scans the light source, image sensor and deposition head in unison across the front side.

34. An apparatus according to claim 30 wherein:

the substrate mount comprises a chuck having multiple upstanding ribs to support the back side of the substrate;

the mirror comprises multiple mirror segments extending along channels defined between the ribs; and

the transport system scans the deposition head across the front side of the substrate by scanning along the channels in turn.

35. An apparatus according to claim 34 wherein:

the light source and a camera which includes the image sensor, are positioned so as to direct and receive the reflected light at complementary angles to a normal of the front side such that light from the source initially passes through the front side of the substrate at a position other than the first droplet set before being reflected to pass through the first droplet set;

the direction of light from the source to the sensor being on a plane oriented in the direction of the channels; and

the source and sensor are scanned in a direction along the channels in turn.

36. An apparatus according to claim 35 wherein the plane is parallel to the direction of the channels.

37. An apparatus according to claim 22, wherein the light source, image sensor and deposition head are physically interconnected, the apparatus additionally comprising a transport system to scan the light source, image sensor and deposition head in unison across the front side.

38. An apparatus according to claim 37 wherein the transport system adjusts the deposition head toward or away from the front side of the mounted substrate independently of the sensor.