Lab-on-chip system for analying nucleic acid

• US 20070042367A1
• Filed: 05/06/2003
• Published: 02/22/2007
• Est. Priority Date: 03/03/2003
• Status: Abandoned Application

• Current Assignee: CapitalBio Corporation, Tsinghua University
• Original Assignee: CapitalBio Corporation, Tsinghua University
• Inventors: Cheng, Jing, Zhang, Qiong, Ma, Xuemei, Zhou, Yuxiang, Tao, Shengce
• Application Number:
  US10/547,742
• Publication Number:
  US 20070042367A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: B01J 2219/00385 Printing
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/0063 Other, e.g. van der Waals forces, hydrogen bonding
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01L 2300/0636 Integrated biosensor, microarrays
• CPC Class Codes: B01L 2300/0822 Slides
• CPC Class Codes: B01L 2300/163 Biocompatibility
• CPC Class Codes: B01L 3/508 rigid containers not provided for above
• CPC Class Codes: B01L 7/52 with provision for submitting samples to a predetermined sequence of different temperatures, e.g. for treating nucleic acid samples amplification or hybridisation processes per se C12Q1/68; controlling sequential reactions for synthesis B01J19/0046
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2531/131 Inverse PCR
• CPC Class Codes: C12Q 2547/101 by confinement to a single tube/container
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 60/14 for creating libraries

Abstract

This invention relates generally to the field of nucleic acid detection. In particular, the invention provides a lab-on-chip system for analyzing a nucleic acid, which system comprises, inter alia, controllably closed space, and a target nucleic acid can be prepared and/or amplified, and hybridized to a nucleic acid probe, and the hybridization signal can be acquired if desirable, in the controllably closed space without any material exchange between the controllably closed space and the outside environment. Methods for analyzing a nucleic acid using the lab-on-chip system is also provided.

Claims

1. A lab-on-chip system for analyzing a nucleic acid, which system comprises a controllably closed space enclosed by a suitable material on a substrate, wherein said suitable material is thermoconductive, biocompatible and does not inhibit nucleic acid amplification or hybridization, and said controllably closed space comprising, on the surface of said substrate, a nucleic acid probe complementary to a target nucleic acid and, on or off the surface of said substrate, other reagents suitable for preparation of said target nucleic acid from a sample, amplification of said target nucleic acid, hybridization between said nucleic acid probe and said target nucleic acid, and/or means for detecting hybridization between said nucleic acid probe and said target nucleic acid, and wherein addition of a sample comprising said target nucleic acid into said controllably closed space, under suitable conditions, results in continuous sample preparation from said sample and/or amplification of said prepared target nucleic acid, and hybridization between said nucleic acid probe and said target nucleic acid, and preferably detection of the hybridization signal, in said controllably closed space without any material exchange between said controllably closed space and the outside environment.

2. The lab-on-chip system of claim 1, wherein the suitable material is an air-tight material.

3. The lab-on-chip system of claim 1, wherein the suitable material is glued on the substrate to form the controllably closed space.

4. The lab-on-chip system of claim 1, wherein the suitable material is microfabricated on the substrate to form the controllably closed space.

5. The lab-on-chip system of claim 1, wherein the substrate comprises a material selected from the group consisting of a silicon, a plastic, a glass, a quartz glass, a ceramic, a rubber, a metal, a polymer and a combination thereof.

6. The lab-on-chip system of claim 1, which comprises a single nucleic acid probe on the substrate.

7. The lab-on-chip system of claim 1, which comprises a plurality of nucleic acid probes on the substrate.

8. The lab-on-chip system of claim 1, wherein the nucleic acid probe has a length ranging from about 5 basepairs to about 100 basepairs or a length ranging from about 5 nucleotide (nt) to about 100 nt.

9. The lab-on-chip system of claim 1, wherein the nucleic acid probe is labeled.

10. The lab-on-chip system of claim 9, wherein the label is selected from the group consisting of a radioactive label, a fluorescent label, a chemical label, an enzymatic label, a luminescent label, a fluorescence resonance energy transfer (FRET) label and a molecular beacon.

11. The lab-on-chip system of claim 1, wherein the nucleic acid probe is modified to facilitate its attachment to the substrate.

12. The lab-on-chip system of claim 1, wherein the nucleic acid probe is attached to the substrate via a functional group on the substrate.

13. The lab-on-chip system of claim 12, wherein the functional group is selected from the group consisting of —

CHO, —

NH₂, —

SH and —

S—

S—

.

14. The lab-on-chip system of claim 1, wherein the nucleic acid probe is attached to the substrate via a binding pair.

15. The lab-on-chip system of claim 14, wherein the binding pair is biotin/avidin pair or biotin/streptavidin pair.

16. The lab-on-chip system of claim 1, wherein the nucleic acid probe is attached to the substrate via ultraviolet-activated crosslinking, heat-activated crosslinking, an interaction between NH₂ and —

CHO, an interaction between —

SH and —

SH, an interaction between biotin and avidin and an interaction between biotin and streptavidin.

17. The lab-on-chip system of claim 1, wherein the nucleic acid probe is a specific or degenerate probe.

18. The lab-on-chip system of claim 1, wherein the nucleic acid probe is DNA, RNA, PNA, LNA or a combination thereof.

19. The lab-on-chip system of claim 1, which, for a detecting position, comprises two nucleic acid probes, wherein a first probe comprises a first FRET label and is attached to the substrate and a second probe comprises a second FRET label in liquid, and hybridization of both the first and the second probes to a target nucleic acid brings the two probes into close proximity to allow fluorescence resonance energy transfer between the two probes to generate a detectable signal.

20. The lab-on-chip system of claim 19, wherein the two FRET labels are a combination of Fluroscein and TAMRA, TAMRA and Cy5, ROX and Cy5, IAEDNS and Fluroscein, or Fluroscein and QSY-7.

21. The lab-on-chip system of claim 1, which, for a detecting position, comprises two nucleic acid probes, wherein the first probe is attached to the substrate and the second probe is in a liquid, the two probes are complementary to each other and the first probe is complementary to a target nucleic acid, the Tm of a hybrid of the two probes is about 5°

C. to about 30°

C. lower than that of a hybrid of the target nucleic acid and the first probe, the first probe comprises a fluorescent label and the second probe comprises a quencher for the fluorescent label, and wherein in the absence of the target nucleic acid, the two probes are hybridized and the fluorescent label is quenched by the quencher, and in the presence of a target nucleic acid, the probes are separated by the hybridization of the first probe to the target nucleic acid, and the fluorescent label is no longer quenched by the quencher to generate a detectable signal.

22. The lab-on-chip system of claim 21, wherein the fluorescent label is selected from the group consisting of 6-FAM, TET, HEX, Cy3, Cy5, Texas Red, ROX, Fluroscein and TAMRA and the quencher for the fluorescent label is selected from the group consisting of Dacyl, Black Hole-1, Black Hole-2 and a gold particle with a diameter from about 0.1 nm to about 10 nm.

23. The lab-on-chip system of claim 1, wherein the nucleic acid probe is substantially complementary to the target nucleic acid.

24. The lab-on-chip system of claim 1, wherein the target nucleic acid amplification is effected via polymerase chain reaction (PCR), ligase chain reaction (LCR), nucleic acid sequence-based amplification (NASBA), strand displacement amplification (SDA), transcription-medicated amplification (TMA) and rolling cycle amplification (RCA).

25. The lab-on-chip system of claim 24, which comprises a buffer suitable for at least one of the target nucleic acid amplification methods.

26. The lab-on-chip system of claim 1, which comprises reagents suitable for amplification of the target nucleic acid and hybridization between a nucleic acid probe and the target nucleic acid.

27. The lab-on-chip system of claim 1, which comprises reagents suitable for preparation of the target nucleic acid from a sample, amplification of the target nucleic acid, and hybridization between said nucleic acid probe and the target nucleic acid.

28. The lab-on-chip system of claim 1, which further comprises a temperature controlling device.

29. The lab-on-chip system of claim 28, wherein the temperature controlling device comprises a temperature controlling unit of a commercially available PCR machine or a water bath.

30. The lab-on-chip system of claim 1, which farther comprises a signal detecting device.

31. The lab-on-chip system of claim 30, wherein the signal detecting device comprises a fluorescent imaging device.

32. The lab-on-chip system of claim 1, which is used for continuous sample preparation of the target nucleic acid from the sample and hybridization between the nucleic acid probe and the prepared target nucleic acid in the controllably closed space.

33. The lab-on-chip system of claim 1, which is used for continuous hybridization between the nucleic acid probe and a prepared target nucleic acid and hybridization signal analysis in the controllably closed space.

34. The lab-on-chip system of claim 1, which further comprises an instruction for preparing, amplifying and/or hybridizing a target nucleic acid in a sample using the system.

35. The lab-on-chip system of claim 1, which is used for continuous amplification of the target nucleic acid from the sample, hybridization between the nucleic acid probe and the amplified target nucleic acid, and hybridization signal analysis in the controllably closed space.

36. The lab-on-chip system of claim 1, which is used for continuous sample preparation of the target nucleic acid from the sample, amplification of the target nucleic acid from the prepared target nucleic acid, hybridization between the nucleic acid probe and the amplified target nucleic acid, and hybridization signal analysis in the controllably closed space.

37. A method for analyzing a nucleic acid, which method comprises:

a) providing an above-described lab-on-chip system;

b) adding a sample containing or suspected of containing a target nucleic acid into said controllably closed space of said system provided in a); and

c) allowing continuous sample preparation of said target nucleic acid from said sample and/or amplification of said prepared target nucleic acid, and hybridization between said nucleic acid probe and said prepared target nucleic acid, and preferably detection of the hybridization signal, in said controllably closed space.

38. The method of claim 37, which further comprises amplifying the target nucleic acid in the controllably closed space.

39. The method of claim 37, which further comprises analyzing hybridization between the nucleic acid probe and the prepared target nucleic acid in the controllably closed space.