Molecular motors

• US 6,210,896 B1
• Filed: 08/13/1999
• Issued: 04/03/2001
• Est. Priority Date: 08/13/1998
• Status: Expired due to Term

• Current Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Original Assignee: U.S. Genomics, Inc (Toxic Reports LLC)
• Inventors: Chan, Eugene Y.
• Primary Examiner(s): Brusca, John S.
• Assistant Examiner(s): SIU, STEPHEN C
• Application Number:
  US09/374,414
• Time in Patent Office: 599 Days
• Field of Search: 436/94, 436/164, 436/177, 436/156, 422/82.01, 422/82.05, 422/82.08, 422/82.12, 422/50, 422/63, 422/65, 435/6
• US Class Current: 435/6.19
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2521/101 DNA polymerase
• CPC Class Codes: C12Q 2521/543 Immobilised enzyme(s)
• CPC Class Codes: C12Q 2565/601 being a microscope, e.g. atomic force microscopy [AFM]
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

The present invention relates to molecular motors and their use in linear analysis of polymers. In particular, molecular motors are used to move polymers with respect to a station such that specific signals arise from the interaction between the polymer and an agent at the station.

Claims

1. A method for analyzing a polymer of linked units, comprising:

exposing a plurality of individual units of a polymer of linked units to an agent selected from the group consisting of an electromagnetic radiation source, a quenching source, and a fluorescence excitation source by causing a molecular motor to move the polymer relative to the agent, and detecting signals resulting from an interaction between the linked units of the polymer and the agent.

2. The method of claim 1, wherein the molecular motor is tethered to a support.

3. The method of claim 2, wherein the agent is attached to the support.

4. The method of claim 1, wherein the agent is attached to the molecular motor.

5. The method of claim 1, wherein the signal is electromagnetic radiation.

6. The method of claim 4, wherein the agent emits electromagnetic radiation.

7. The method of claim 6, wherein a portion of the plurality of individual units of the polymer are labeled with a fluorophore.

8. The method of claim 6, wherein the plurality of individual units of the polymer are sequentially exposed to electromagnetic radiation by bringing the plurality of individual units in proximity to a light emissive compound and exposing the light emissive compound to electromagnetic radiation, and wherein the plurality of individual units of the polymer detectably affect emission of electromagnetic radiation from the light emissive compound.

9. The method of claim 6 wherein the plurality of individual units of the polymer are sequentially exposed to electromagnetic radiation, and wherein the electromagnetic radiation detectably affects emission of electromagnetic radiation from the plurality of individual units of the polymer to produce the detectable signal.

10. The method of claim 8, wherein the individual units detectably affecting emission of electromagnetic radiation from the light emissive compound are labeled with a fluorophore.

11. The method of claim 1, wherein the polymer is a nucleic acid and the molecular motor is a nucleic acid molecular motor.

12. The method of claim 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10, wherein the molecular motor is a nucleic acid molecular motor that is a polymerase.

13. An article of manufacture, comprising:

a support,

a molecular motor tethered to the support, and

an agent selected from the group consisting of an electromagnetic radiation source, a quenching source, and a fluorescence excitation source positioned in interactive proximity with a signal station of the molecular motor.

14. The article of claim 13, wherein a plurality of molecular motors is tethered to the support.

15. The article of claim 14, wherein the plurality of molecular motors is tethered to the support in an organized array.

16. The article of claim 13, wherein the support is selected from the group consisting of a slide, a chip, and a wall material having a channel.

17. The article of claim 16, wherein the support is a wall material having a channel and wherein the molecular motor is positioned at an end of the channel.

18. The article of claim 13, wherein the agent is a fluorophore.

19. The article of claim 13, wherein the molecular motor is selected from the group consisting of polymerase, helicase, kinesin, dynein, actin, and myosin.

20. A nucleic acid molecular motor, wherein the nucleic acid molecular motor includes an agent selected from the group consisting of an electromagnetic radiation source, a quenching source, and a fluorescence excitation source positioned in interactive proximity with a signal station of the nucleic acid molecular motor.

21. A solution comprising the nucleic acid molecular motor of claim 20.

22. The solution of claim 21, wherein the nucleic acid molecular motor is a polymerase.

23. A method for analyzing a polymer of linked units comprising:

(1) causing a labeled polymer of linked units to move relative to a molecular motor;

(2) detecting sequentially polymer dependent impulses from linked unit labels of less than all the linked units, and

(3) storing a signature of said polymer dependent impulses detected to analyze the polymer.

24. The method of claim 23, wherein the method is performed on a plurality of polymers simultaneously.

25. The method of claim 23, wherein the signature of polymer dependent impulses is at least 10 polymer dependent impulses.

26. The method of claim 23, wherein the signature of polymer dependent impulses defines the order of unit labels.

27. The method of claim 23, wherein the signature of polymer dependent impulses defines the distance between unit labels.

28. The method of claim 23, wherein the signature of polymer dependent impulses defines the number of unit labels.

29. The method of claim 23, wherein all of the unit labels are detected.

30. The method of claim 23, wherein only a portion of the unit labels are detected.

31. The method of claim 23, wherein the polymer is partially and randomly labeled with unit labels.

32. The method of claim 30, wherein all of the units of the polymer are labeled with a unit label.

33. The method of claim 23, wherein the labeled polymer of linked units is exposed to an agent selected from the group consisting of electromagnetic radiation, a quenching source and a fluorescence excitation source and wherein the polymer dependent impulses are produced by the interaction between a unit label of the polymer and the agent.

34. The method of claim 23, wherein the molecular motor is a nucleic acid molecular motor.

35. The method of claim 23, wherein the unit label of the polymer is an extrinsic label.

36. The method of claim 34, wherein the nucleic acid molecular motor is a polymerase.

37. The method of claim 23, wherein the method is a method for determining the proximity of two unit labels of the polymer wherein the proximity of the two unit labels is the signature of said polymer dependent impulses, the identity of each unit label being indicative of the identity of at least one unit of the polymer, wherein the labeled polymer is moved relative to a station to expose the two unit labels to the station to produce a characteristic polymer dependent impulse arising from a detectable physical change in the unit label or the station, and further comprising the step of measuring the amount of time elapsed between detecting each characteristic polymer dependent impulse, the amount of time elapsed being indicative of the proximity of the two unit labels.

38. The method of claim 23, wherein the method is a method for determining the order of two sequence unit labels of the polymer, the identity of each unit label being indicative of the identity of at least one unit of the polymer wherein the order of the two unit labels is the signature of said polymer dependent impulses, wherein the labeled polymer is moved linearly with respect to a station, to expose one of the unit labels to the station to produce a polymer dependent impulse which is a signature of polymer dependent impulses, and to expose the other of the unit labels to the station to produce a second detectable impulse which is a signature of said polymer dependent impulses, different from the first polymer dependent impulse, and further comprising the step of determining the order of the polymer dependent impulses as an indication of the order of the two unit labels.

39. The method of claim 23, wherein the method is a method for determining the distance between two unit labels of the polymer, the identity of each unit label being indicative of the identity of at least one unit of the polymer wherein the distance between two unit labels is the signature of said polymer dependent impulses, wherein the labeled polymer is moved linearly relative to a station to produce a characteristic polymer dependent impulse generated as each of the two unit labels passes by the station, and further comprising the step of determining the distance between the polymer dependent impulses as an indication of the distance between the two unit labels.