DETECTION OLIGOMER AND METHOD FOR CONTROLLING QUALITY OF BIOCHIP USING DETECTION OLIGOMER

• US 20090239770A1
• Filed: 01/23/2009
• Published: 09/24/2009
• Est. Priority Date: 01/24/2008
• Status: Active Grant

• Current Assignee: Samsung Electronics Co. Ltd.
• Original Assignee: Samsung Electronics Co. Ltd.
• Inventors: Cho, Seung-Hei, RHEE, Joo-Won, Kim, Byung-chul, Jung, Sun-Ok
• Granted Patent: US 8,313,905 B2
• Time in Patent Office: Days
• US Class Current: 506/42
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2521/501 Ligase
• CPC Class Codes: C12Q 2525/131 incorporating a restriction site
• CPC Class Codes: C12Q 2525/301 Hairpin oligonucleotides

Abstract

A detection oligomer and method for controlling the quality of a biochip using the detection oligomer are provided. The detection oligomer includes a template having a first and second end and having a sequence that is complementary to a specific sequence of an oligomer, and a hairpin connected to the first end of the template.

Claims

1. A detection oligomer comprising:

a template having a first and second end and having a sequence that is complementary to a sequence of an oligomer; and

a hairpin connected to the first end of the template.

2. The oligomer of claim 1, wherein the hairpin comprises a stem including first and second single strands that hybridize to each other and a loop, the first single strand has a first end coupled with the loop and a second end coupled with the first end of the template and having a sequence corresponding to a nuclease, and the second single strand has a first end coupled with the loop and a second end having a sequence corresponding to the nuclease.

3. The oligomer of claim 1, further comprising:

a label coupled to the template and/or the hairpin.

4. The oligomer of claim 3, wherein the second end of the template is a 5′

-terminus and the label is coupled to the second end of the template.

5. A detection oligomer comprising:

a first single-stranded oligomer having a sequence complementary to an oligomer having a sequence; and

a second single-stranded oligomer connected to a first end of the first oligomer and having a sequence that can form a hairpin structure.

6. The oligomer of claim 5, wherein a free energy change induced when the second single-stranded oligomer forms the hairpin structure at room temperature is less than about −

20 kcal/mol.

7. The oligomer of claim 5, wherein two ends, including the first end and a second end, of the second single-stranded oligomer contain sequences which correspond to nuclease.

8. The oligomer of claim 5, further comprising a label coupled to one of the first and second single-stranded oligomers.

9. The oligomer of claim 8, wherein the second end of the first oligomer is a 5′

-terminus and the label is coupled to the second end of the first oligomer.

10. A method for controlling a quality of a biochip, the method comprising:

providing a biochip including a plurality of probes, each of which has a first end coupled to an immobilization layer, wherein the plurality of probes include a first probe having a desired number of monomers and a second probe having an undesired number of monomers;

hybridizing a Quality Control probe to the first and second probes coupled to the immobilization layer;

connecting the Quality Control probe with the first probe; and

removing the hybridization coupling between each of the first and second probes and the Quality Control probe,

wherein the Quality Control probe includes a template having a sequence complementary to a base sequence of the first probe and a hairpin connected to a first end of the template.

11. The method of claim 10, further comprising:

phosphorylating second ends of each of the first and second probes before the hybridizing of the Quality Control probe to the first and second probes.

12. The method of claim 10, wherein the hairpin in the Quality Control probe includes a stem having first and second single strands that hybridize to each other and a loop,

wherein the first single strand has a first end coupled with the loop and a second end coupled with the first end of the template and the second single strand has a first end coupled with the loop and a second end coupled with the second end of the first probe, and

wherein in the connecting of the Quality Control probe with the first probe, the second end of the second single strand in the Quality Control probe is coupled with the second end of the first probe.

13. The method of claim 10, wherein:

the hairpin in the Quality Control probe includes a stem having first and second single strands that hybridize to each other and a loop; and

in the connecting of the Quality Control probe with the second probe, the second end of the second single strand in the Quality Control probe is spaced apart from the second end of the second probe.

14. The method of claim 10, further comprising:

after the removing of the hybridization coupling, hybridizing the first probe to the template of the Quality Control probe to form a double strand, coupling a label to the double strand, and detecting a signal provided by the label.

15. The method of claim 10, wherein the Quality Control probe further includes a label coupled to one of the template and the hairpin, and after the removing of the hybridization coupling, further comprising detecting a signal provided by the label in the Quality Control probe coupled to the first probe.

16. The method of claim 14, further comprising:

decoupling the Quality Control probe from the first probe after the detecting of the signal.

17. The method of claim 16, wherein the hairpin comprises a stem including first and second single strands that hybridize to each other and a loop, the first single strand has a first end coupled with the loop and a second end coupled with a first end of the template and has a sequence specific to a nuclease, the second single strand has a first end coupled with the loop and a second end having a sequence specific to a nuclease, and the decoupling of the Quality Control probe is performed using nuclease reacting to the specific sequences.