ASSAY FOR DETECTING NUCLEOTIDE SEQUENCES IN GENETICALLY MODIFIED CROPS AND PLANTS USING OPTICAL THIN-FILM BIOSENSOR CHIPS

• US 20090118136A1
• Filed: 12/29/2008
• Published: 05/07/2009
• Est. Priority Date: 06/28/2006
• Status: Abandoned Application

• Current Assignee: Xing Wang Deng
• Original Assignee: Xing Wang Deng
• Inventors: Deng, Xing Wang
• Application Number:
  US12/344,974
• Publication Number:
  US 20090118136A1
• Time in Patent Office: Days
• US Class Current: 506/9
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 1/6895 for plants, fungi or algae
• CPC Class Codes: C12Q 2563/131 the label being a member of a cognate binding pair, i.e. extends to antibodies, haptens, avidin
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

A process for detecting at least one DNA sequence using an optical thin-film biosensor chip includes the steps of placing a sample to be tested in contact with at least one capture probe attached to an optical thin-film biosensor chip; incubating the sample in the presence of an enzyme and a substrate; identifying a change in the color of the sample; and detecting the sample comprises at least one DNA sequence.

Claims

1. A process for detecting at least one DNA sequence using an optical thin-film biosensor chip, comprising:

placing a sample to be tested in contact with at least one capture probe attached to an optical thin-film biosensor chip;

incubating said sample in the presence of an enzyme and a substrate;

identifying a change in the color of said sample; and

detecting said sample comprises at least one DNA sequence.

2. The process of claim 1, wherein identifying comprises visualizing.

3. The process of claim 1, wherein identifying comprises producing a precipitate.

4. The process of claim 3, wherein producing comprises the steps of:

binding said enzyme to said substrate in the presence of said at least one DNA sequence matching said at least one capture probe; and

converting said substrate into a precipitable product.

5. The process of claim 1, wherein said at least one capture probe comprises an oligonucleotide probe having a nucleotide sequence that matches at least a portion of said at least one DNA sequence.

6. The process of claim 1, wherein placing said sample comprises the steps of:

hybridizing said at least one DNA sequence to said at least one capture probe in the presence of a ligase using a biotinylated polymerase chain reaction; and

washing said at least one DNA sequence attached to said at least one capture probe.

7. The process of claim 6, wherein said ligase comprises a thermostable DNA ligase.

8. The process of claim 1, further comprising the step of arraying and covalently attaching at least one capture probe to an optical thin-film biosensor chip prior to placing said sample in contact with said at least one capture probe.

9. The process of claim 8, wherein arraying and covalently attaching comprises the steps of:

arraying said at least one capture probe; and

covalently attaching said at least one capture probe to said optical thin-film biosensor chip.

10. The process of claim 9, wherein said at least one capture probe includes a forward strand sequence matching at least a portion of said at least one DNA sequence and a terminus covalently attached to a surface of said optical thin-film biosensor chip.

11. The process of claim 9, wherein said optical thin-film biosensor chip comprises a surface derivatized to form covalent bonds.

12. The process of claim 1, wherein said enzyme comprises an enzyme conjugate capable of detecting said at least one DNA sequence hybridized with said at least one capture probe.

13. The process of claim 1, wherein said substrate comprises a substrate capable of binding with said enzyme in the presence of at least one DNA sequence hybridized with said at least one capture probe.

14. The process of claim 1, wherein incubating comprises incubating said sample in the presence of said enzyme and said substrate for a period of time of about 5 minutes to about 30 minutes.

15. The process of claim 1, wherein said at least one DNA sequence is a transgene.

16. The process of claim 1, further comprising detecting the presence of a pathogen in said sample, said sample comprising a genetically modified crop, based upon the detection of said at least one DNA sequence.

17. The process of claim 1, further comprising mapping at least one trait of said sample, said sample comprising a genetically modified crop, based upon the detection of said at least one DNA sequence.

18. The process of claim 1, further comprising detecting at least one pathogen or at least one toxin in said sample, said sample comprising a genetically modified crop, based upon the detection of said at least one DNA sequence.

19. A process for detecting at least one SNP using an optical thin-film biosensor chip, comprising:

placing a sample to be tested in contact with at least one capture probe attached to an optical thin-film biosensor chip;

incubating said sample in the presence of an enzyme and a substrate;

identifying a change in the color of said sample; and

detecting said sample comprises at least one SNP.

20. The process of claim 19, wherein identifying comprises visualizing.

21. The process of claim 19, wherein detecting comprises producing a precipitate.

22. The process of claim 21, wherein producing comprises the steps of:

binding said enzyme to said substrate in the presence of said at least one SNP assay matching said at least one capture probe; and

converting said substrate into a precipitable product.

23. The process of claim 22, wherein said at least one capture probe comprises a first oligonucleotide probe and second oligonucleotide probe.

24. The process of claim 23, wherein said first oligonucleotide probe comprises a nucleotide sequence that compliments at least a portion of one side of said at least one SNP assay and said second oligonucleotide probe comprises a nucleotide sequence that compliments at least a portion of an opposing side adjacent to said at least one SNP assay.

25. The process of claim 23, wherein said first oligonucleotide probe includes a 3′

terminus having a reactive group for detecting said at least one SNP assay and a 5′

terminus covalently attached to a surface of said optical thin-film biosensor chip.

26. The process of claim 23, wherein said second oligonucleotide probe includes a 3′

terminus having a reactive group for detecting said at least one SNP assay and a 5′

terminus covalently attached to a surface of said optical thin-film biosensor chip.

27. The process of claim 19, further comprising the step of arraying and covalently attaching at least one capture probe to an optical thin-film biosensor chip prior to placing said sample in contact with said at least one capture probe.

28. The process of claim 27, wherein arraying and covalently attaching comprises the steps of:

arraying a first capture probe and a second capture probe;

covalently attaching said first capture probe and said second capture probe to a surface of said optical thin-film biosensor chip.

29. The process of claim 28, wherein said surface is derivatized to form covalent bonds.

30. The process of claim 19, wherein placing said sample comprises the steps of:

hybridizing said at least one SNP assay to said at least one capture probe in the presence of a ligase using a biotinylated polymerase chain reaction; and

washing said at least one SNP assay attached to said at least one capture probe.

31. The process of claim 30, wherein said ligase comprises a thermostable DNA ligase.

32. The process of claim 19, wherein said enzyme comprises an enzyme for detecting at least one SNP assay hybridized with said at least one capture probe.

33. The process of claim 19, wherein said substrate comprises a substrate for binding with said enzyme in the presence of at least one SNP assay hybridized with at least one capture probe.

34. The process of claim 19, wherein incubating comprises incubating said sample in the presence of said enzyme and said substrate for a period of time of about 10 minutes to about 30 minutes.

35. The process of claim 19, wherein said sample comprises a plant.

36. The process of claim 19, further comprising mapping a mutation in said sample, said sample comprising a plant, based upon the detection of said at least one SNP.

37. The process of claim 19, further comprising identifying a strain of said sample, said sample comprising a plant, based upon the detection of said at least one SNP.

38. The process of claim 19, further comprising detection a pathogen in said sample, said sample comprising a plant, based upon the detection of said at least one SNP.

39. The process of claim 19, further comprising mapping at least one trait of said sample, said sample comprises a plant, based upon the detection of said at least one SNP.

40. The process of claim 19, further comprising detecting at least one pathogen or at least one toxin in said sample, said sample comprising a plant, based upon the detection of said SNP.