Methods and apparatuses for stretching polymers

• US 8,518,705 B2
• Filed: 02/10/2004
• Issued: 08/27/2013
• Est. Priority Date: 08/13/1999
• Status: Expired due to Fees

• Current Assignee: PathoGenetix, Inc. (Toxic Reports LLC)
• Original Assignee: PathoGenetix, Inc. (Toxic Reports LLC)
• Inventors: Chan, Eugene Y., Gleich, Lance C., Wellman, Parris S.
• Primary Examiner(s): LUDLOW, JAN M
• Application Number:
  US10/775,599
• Publication Number:
  US 20040166025A1
• Time in Patent Office: 3,486 Days
• Field of Search: 422/99, 422/82.05, 422/101, 422/102, 422/68.1, 422/502, 422/503, 436/86, 436/94
• US Class Current: 436/94
• CPC Class Codes: B01F 25/431 Straight mixing tubes with baffles or obstructions that do not cause substantial pressure drop; Baffles therefor
• CPC Class Codes: B01F 25/432 with means for dividing the material flow into separate sub-flows and for repositioning and recombining these sub-flows; Cross-mixing, e.g. conducting the outer layer of the material nearer to the axis of the tube or vice-versa
• CPC Class Codes: B01F 25/433 Mixing tubes wherein the shape of the tube influences the mixing, e.g. mixing tubes with varying cross-section or provided with inwardly extending profiles
• CPC Class Codes: B01F 33/30 Micromixers
• CPC Class Codes: B01L 2200/0647 Handling flowable solids, e.g. microscopic beads, cells, particles
• CPC Class Codes: B01L 2200/0663 Stretching or orienting elongated molecules or particles
• CPC Class Codes: B01L 2300/0816 Cards, e.g. flat sample carriers usually with flow in two horizontal directions
• CPC Class Codes: B01L 2300/0883 Serpentine channels
• CPC Class Codes: B01L 2400/086 using baffles or other fixed flow obstructions
• CPC Class Codes: B01L 3/50273 characterised by the means or forces applied to move the fluids micropumps F04B19/006, of the membrane type F04B43/043
• CPC Class Codes: B01L 3/502746 characterised by the means for controlling flow resistance, e.g. flow controllers, baffles B01L3/502738 takes precedence
• CPC Class Codes: B01L 3/502761 specially adapted for handling suspended solids or molecules independently from the bulk fluid flow, e.g. for trapping or sorting beads, for physically stretching molecules investigating characteristics of particles G01N15/00
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: G01N 1/286 involving mechanical work, e.g. chopping, disintegrating, compacting, homogenising microtomes G01N1/06; pulverising in general B02C; mixing in general B01F
• CPC Class Codes: G01N 15/1456 without spatial resolution of the texture or inner structure of the particle, e.g. processing of pulse signals
• CPC Class Codes: G01N 15/1459 the analysis being performed on a sample stream
• CPC Class Codes: G01N 2015/1493 Particle size
• CPC Class Codes: G01N 2015/1495 Deformation of particles
• CPC Class Codes: G01N 33/442 Resins; Plastics
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

The present invention provides structures and methods that allow polymers of any length, including nucleic acids containing entire genomes, to be stretched into a long, linear conformation for further analysis. The present invention also provides structures and methods for selecting and stretching polymers based on their lengths. Polymers are loaded into a device and run through the structures. Stretching is achieved by, e.g., applying shear forces as the polymer passes through the structures, placing obstacles in the path of the polymer, or a combination thereof. Since multiple molecules may be stretched in succession, extremely high throughput screening, e.g., screening of more than one molecule per second, is achieved.

Claims

1. An apparatus for stretching at least one polymer in a fluid sample, comprising:

an elongation structure comprising a tapered channel with a longitudinal axis, said tapered channel having a width that is proportional to 1/x² from a first end to a second end, where x is distance along the length of the tapered channel; and

a plurality of side channels oriented at an oblique angle relative to the longitudinal axis,

wherein the elongation structure is adapted to stretch the at least one polymer as the at least one polymer moves along said tapered channel from said first end to said second end.

2. The apparatus according to claim 1 wherein said at least one polymer comprises DNA.

3. The apparatus according to claim 1 wherein said first end has a width between 1 μ

m and 1 cm, and said second end has a width between 1 nm and 1 mm.

4. The apparatus according to claim 1 further comprising a delivery region for delivering said at least one polymer in said fluid sample to said elongation structure.

5. The apparatus according to claim 4 wherein said delivery region comprises a delivery channel, said delivery channel leading into and out of said elongation structure.

6. The apparatus according to claim 1 wherein said plurality of side channels is oriented such that fluid injected from said plurality of side channels moves substantially in the flow direction along said tapered channel.

7. The apparatus according to claim 1 wherein said tapered channel has a tapered-channel cross-sectional area and said plurality of side channels has a total combined side-channel cross-sectional area between 1% and 500% of said tapered-channel cross-sectional area.

8. The apparatus according to claim 7 wherein said total combined side-channel cross-sectional area is about 50% of said tapered-channel cross-sectional area.

9. The apparatus according to claim 1 wherein said plurality of side channels are arranged in a pattern that is repeated.

10. The apparatus according to claim 1, wherein the plurality of side channels are located between the first and second end of the tapered channel.

11. The apparatus according to claim 1, wherein the tapered channel comprises a central channel for containing fluid, and wherein the plurality of side channels branch out from the central channel.

12. The apparatus of claim 1, wherein the elongation structure is formed on a chip.

13. The apparatus of claim 1, wherein at least two side channels are located on different sides of the longitudinal axis.

14. The apparatus of claim 1, wherein the longitudinal axis bisects an angle between at least two side channels.

15. A method for stretching at least one polymer comprising the step of:

moving said at least one polymer along the channel of the apparatus of claim 1;

whereby said at least one polymer is stretched in said channel as said at least one polymer moves along said channel from said first end to said second end.

16. An apparatus for stretching at least one polymer in a fluid sample, comprising:

an elongation structure comprising a tapered channel with a longitudinal axis, said tapered channel decreasing in width at a greater than linear rate from a first end to a second end; and

a plurality of side channels oriented at an oblique angle relative to the longitudinal axis,

wherein the elongation structure is adapted to stretch the at least one polymer as the at least one polymer moves along said tapered channel from said first end to said second end.

17. The apparatus of claim 16, wherein the longitudinal axis bisects an angle between at least two side channels.

18. The apparatus of claim 16, wherein at least two side channels are located on different sides of the longitudinal axis.

19. The apparatus of claim 16, wherein said tapered channel decreases in width as 1/(axⁿ+b), where n is any real number greater than 1, a is a nonzero real number, b is a real number, and x is distance along the length of the tapered channel.

20. The apparatus according to claim 16 wherein said at least one polymer comprises DNA.

21. The apparatus according to claim 16 wherein said first end has a width between 1 μ

m and 1 cm, and said second end has a width between 1 nm and 1 mm.

22. The apparatus according to claim 16 further comprising a delivery region for delivering said at least one polymer in said fluid sample to said elongation structure.

23. The apparatus according to claim 22 wherein said delivery region comprises a delivery channel, said delivery channel leading into and out of said elongation structure.

24. The apparatus according to claim 16 wherein said plurality of side channels is oriented such that fluid injected from said plurality of side channels moves substantially in the flow direction along said tapered channel.

25. The apparatus of claim 16, wherein the elongation structure is formed on a chip.

26. An apparatus for stretching at least one polymer in a fluid sample, comprising:

an elongation structure comprising a tapered channel with a longitudinal axis, said tapered channel decreasing in width as 1/(axⁿ+b) from a first end to a second end, where n is any real number greater than 1, a is a nonzero real number, b is a real number, and x is distance along the length of the tapered channel; and

a plurality of side channels oriented at an oblique angle relative to the longitudinal axis,

wherein the elongation structure is adapted to stretch the at least one polymer as the at least one polymer moves along said tapered channel from said first end to said second end.

27. The apparatus according to claim 26 wherein said at least one polymer comprises DNA.

28. The apparatus according to claim 26 wherein said first end has a width between 1 μ

m and 1 cm, and said second end has a width between 1 nm and 1 mm.

29. The apparatus according to claim 26 further comprising a delivery region for delivering said at least one polymer in said fluid sample to said elongation structure.

30. The apparatus according to claim 29 wherein said delivery region comprises a delivery channel, said delivery channel leading into and out of said elongation structure.

31. The apparatus according to claim 26 wherein said plurality of side channels is oriented such that fluid injected from said plurality of side channels moves substantially in the flow direction along said tapered channel.

32. The apparatus of claim 26, wherein the elongation structure is formed on a chip.

33. The apparatus of claim 26, wherein at least two side channels are located on different sides of the longitudinal axis.