Apparatus and methods for sequencing nucleic acids in microfluidic systems

• US 6,316,201 B1
• Filed: 06/21/2000
• Issued: 11/13/2001
• Est. Priority Date: 10/16/1997
• Status: Expired due to Term

• Current Assignee: Caliper Holdings Incorporated
• Original Assignee: Caliper Holdings Incorporated
• Inventors: Nikiforov, Theo T.
• Primary Examiner(s): Houtteman, Scott W.
• Application Number:
  US09/598,807
• Time in Patent Office: 510 Days
• Field of Search: 435/6, 435/91.1, 216/35, 356/344
• US Class Current: 435/6.12
• CPC Class Codes: B01L 3/5027 by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip B01L3/5023 takes precedence; micromixers B01F33/30; microreactors for synthesis B01J19/0093; microcapillary devices in general B81B1/00
• CPC Class Codes: G01N 27/44791 Microapparatus sample containers with integrated microfluidic structures B01L3/5027

Abstract

The present invention is generally directed to microfluidic systems and methods of using such systems in the determination of the nucleotide sequence of target nucleic acid sequences (referred to herein as the “target”). In particular, the present invention provides methods and systems for determining the relative positions within a target nucleic acid sequence that are occupied by a given nucleotide, e.g., A, T, G or C, by separating mixtures of nested sets of fragments of the target nucleic acid, which sets each include fragments that terminate in a different given nucleotide.

Claims

1. A method of analyzing a first material, comprising:

providing a microfluidic device having disposed therein;

a separation channel;

an injection channel that intersects and is in fluid communication with the separation channel;

a source of a first material in fluid communication with the injection channel; and

a source of a second material in fluid communication with the injection channel;

transporting an amount of the first material and an amount of the second material into the injection channel whereby the first and second material mix to form a first mixture;

injecting an amount of the first mixture into the separation channel;

separating the first and second material by size; and

determining a size of the first material relative to the second material.

2. The method of claim 1, wherein the first material comprises a nucleic acid.

3. The method of claim 1, wherein the second material comprises a nucleic acid.

4. The method of claim 1, wherein the second material comprises nucleic acid fragments that terminate in a given nucleotide.

5. The method of claim 1, wherein the source of second material comprises a reservoir disposed in the microfluidic device, the reservoir containing the second material.

6. The method of claim 1, wherein the separating step comprises electrophoretically separating the first and second materials in the separation channel.

7. The method of claim 1, wherein the transporting step comprises electrokinetically transporting the first and second materials from the sources of first and second materials, respectively, into the injection channel.

8. The method of claim 1, wherein the injecting step comprises electrokinetically injecting the first mixture into the separation channel.

9. The method of claim 1, wherein:

the source of the first material comprises a first reservoir disposed in the microfluidic device having the first material disposed therein; and

the source of the second material comprises a second reservoir disposed in the microfluidic device having the second material disposed therein.

10. The method of claim 1, wherein:

the providing step further comprises providing a source of a third material in fluid communication with the injection channel;

the transporting step comprises transporting an amount of the third material from the source of the third material into the injection channel whereby the first, second and third material are mixed in the first mixture;

the separating step comprises separating the first, second and third materials by size; and

the determining step comprises determining a size of the first material relative to the second and third material.

11. The method of claim 10, wherein each of the first, second and third materials comprise nucleic acids.

12. The method of claim 10, wherein:

the providing step further comprises providing a source of a fourth material in fluid communication with the injection channel;

the transporting step comprises transporting an amount of the fourth material from the source of the fourth material into the injection channel whereby the first, second, third and fourth material are mixed in the first mixture;

the separating step comprises separating the first, second, third and fourth materials by size; and

the determining step comprises determining a size of the first material relative to the second, third and fourth material.

13. The method of claim 12, wherein each of the first, second, third and fourth materials comprise nucleic acids.

14. The method of claim 12, wherein the first, second, third and fourth materials comprise nested sets of fragments of a nucleic acid sequence of interest.

15. The method of claim 14, wherein each of the nested sets of fragments ends in a different nucleotide.

16. A microfluidic system, comprising:

a microfluidic device having disposed therein;

a separation channel;

an injection channel that intersects and is in fluid communication with the separation channel;

a source of a first material in fluid communication with the injection channel; and

a source of a second material in fluid communication with the injection channel;

a flow controller operably coupled to the microfluidic device for directing flow of the first and second materials within the microfluidic device; and

a computer operably coupled to the flow controller, the computer comprising programming for instructing the flow controller to transport an amount of the first and second material into the injection channel, whereby the first and second material mix to form a first mixture, injecting an amount of the first mixture into the separation channel, and separating the first and second material by size within the separation channel.

17. A microfluidic system, comprising:

a microfluidic device that comprises a separation channel having first and second materials disposed therein, the first and second materials being separated by size;

a detector disposed in sensory communication with the separation channel to detect the first and second materials; and

a computer operably coupled to the detector and being appropriately programmed to determine a size of the first material relative to a size of the second material based upon the detected first and second materials.

18. The microfluidic system of claim 17, wherein the first material comprises a nucleic acid.