Method, system, and computer program product to assess properties of a chemical array

• US 20060078896A1
• Filed: 10/12/2004
• Published: 04/13/2006
• Est. Priority Date: 10/12/2004
• Status: Abandoned Application

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Peck, Bill J., Leproust, Eric M.
• Application Number:
  US10/964,063
• Publication Number:
  US 20060078896A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00693 Means for quality control
• CPC Class Codes: B01J 2219/00702 Processes involving means for analysing and characterising the products
• CPC Class Codes: C40B 40/08 Libraries containing RNA or DNA which encodes proteins, e.g. gene libraries
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression

Abstract

A method, a system, and a computer-readable medium storing a program for determining array quality during in-situ manufacturing of an array includes determining an average feature coverage fraction of the array, determining a background area fraction of the array, measuring a contact angle of the background, and determining the array quality based upon the measured, feature contact angle.

Claims

1. A method for evaluating a chemical array comprising a plurality of features, the method comprising:

determining an average feature coverage fraction on a chemical array;

measuring the contact angle of a drop covering a at least one feature;

determining a background area fraction of the array;

measuring a contact angle of the background;

obtaining an average of the measured contact angles weighted by the amount of surface area covered by features and background.

2. The method of claim 1, further comprising determining an average feature contact angle for the array.

3. The method of claim 1, wherein the average feature contact angle is correlated with polymer mass at a feature.

15. The method of claim 1, wherein the drop covering at least one feature is formed by a liquid dispensing system.

16. The method of claim 15, wherein the liquid dispensing system comprises an ink jet printer.

17. The method of claim 1, wherein the drop comprises water.

18. The method of claim 1, wherein the drop comprises propylene carbonate.

19. The method of claim 1, wherein the effective contact angle, θ

, determined by obtaining the weighted average of a feature contact angle and background contact angle, is determined by the equation;

cos (θ

)=ƒ

₁ cos (θ

₁)+ƒ

₂ cos (θ

₂), wherein

f₁ is the fraction of surface area covered by a feature that would make a contact angle of θ

₁ with a drop of liquid if the surface were homogeneously covered with that liquid,

f₂ is the surface coverage fraction of background regions of the array, and

θ

₂ is the contact angles of a drop of liquid contacting a background region.

20. The method of claim 1, wherein contact angle is measured using an imaging system in optical communication with the array.

21. A computer program product comprising a computer readable medium comprising a program for implementing a method of claim 1.

22. The computer program product of claim 21, wherein the program includes instructions for determining an average feature contact angle for a feature on a chemical array.

23. The computer program product of claim 21, wherein the program further comprises instructions for comparing an average feature contact angle to a feature contact angle determined for a validated chemical array.

24. The computer program product of claim 21, wherein the program further comprises instructions for correlating an average feature contact angle to polymer mass at features on the array.

4. The method of 3, wherein the polymer mass and/or average feature contact angle is compared to the polymer mass and/or average feature angle of a validated array which has been contacted with a sample comprising target molecules.

5. The method of claim 4, wherein binding of target molecules to one or more features of the validated array has been determined.

6. The method of claim 4, wherein the polymer comprises a polynucleotide.

7. The method of claim 6, wherein contact angles are measured after one or more steps of polymer synthesis at features on the array.

8. The method of claim 7, wherein contact angles are measured after each of a plurality of steps of polymer synthesis at features on the array.

9. The method of claim 7, wherein a decision to continue or discontinue polymer synthesis is made based on the determination of contact angles after one or more steps of polymer synthesis.

10. The method of claim 7, wherein a processor determines average feature contact angles after one or more steps of polymer synthesis.

11. The method of claim 10, wherein the processor instructs a polymer deposition system to continue or discontinue polymer deposition on a substrate on which a plurality of polymers is being synthesized at a plurality of locations, thereby forming features on the substrate at the locations.

12. The method of claim 11, wherein a user provides input to the processor regarding whether the deposition system should continue or discontinue polymer deposition.

13. The method of claim 11, wherein the processor automatically instructs the polymer deposition system based on a predetermined threshold for an average feature contact angle.

25. A system for performing a method according to claim 10, comprising a processor, a polymer deposition system, and a substrate comprising a chemical array.

26. The system of claim 25, further comprising a detector in optical communication with the array for determining a contact angle of a drop of liquid on the array.

27. The system of claim 25, wherein the processor is connectable to or comprises a memory comprising data relating to average feature contact angles for one or more arrays.

28. The system of claim 27, wherein the data further comprises data relating to one or more properties of the one or more arrays.

29. The system of claim 28, wherein the one or more properties comprise polymer mass at one or more features of the array.

30. The system of claim 28, wherein the one or more properties comprises target specificity of one or more features of the array.

31. The system of claim 25, wherein the array is associated with an identifier.

32. The system of claim 31, wherein the identifier is associated with data relating to average feature contact angle.

33. The system of claim 32, wherein the identifier is associated with data relating to polymer mass on the array.

34. The system of claim 25, wherein the processor receives information relating to the average feature size and number of features on the array and determines the average feature coverage fraction of the array.

35. The system of claim 34, wherein the information is provided by a user.

36. The system of claim 35, wherein the system further comprises a user interface in communication with the processor and the user inputs the information to the user interface.

37. The system of claim 34, wherein information is provided by a detector in optical communication with the array.

38. The system of claim 25, wherein the processor receives information relating to the background coverage fraction.

39. The system of claim 25, wherein processor provides instructions to the polymer deposition system based on an average feature contact angle determined for the array.

14. The method of 1, wherein the drop covering at least one feature covers a plurality of features.

40. A substrate comprising:

a chemical array comprising a plurality of addressable features, each feature comprising a probe for binding to a target in a sample;

a subarray for determining an average feature contact angle for features on the chemical array, comprising at least one feature and fewer features than those present in the chemical array.

41. The substrate of claim 40, further associated with an identifier, wherein the identifier is associated with data relating to the average feature coverage fraction and average background coverage fraction of the subarray.