Systems and methods for detecting and analyzing polymers

• US 7,351,538 B2
• Filed: 08/23/2005
• Issued: 04/01/2008
• Est. Priority Date: 08/23/2004
• Status: Expired due to Fees

• Current Assignee: U.S. Genomics, Inc (Toxic Reports LLC)
• Original Assignee: U.S. Genomics, Inc (Toxic Reports LLC)
• Inventors: Harris, John, Meyers, Ray, Fuchs, Martin
• Primary Examiner(s): WHISENANT, ETHAN C
• Application Number:
  US11/210,155
• Publication Number:
  US 20060078915A1
• Time in Patent Office: 952 Days
• Field of Search: 435/6, 536/23.1, 536/24.3, 356/318, 356/417
• US Class Current: 435/6.19
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 2565/102 Multiple non-interacting labels
• CPC Class Codes: G01N 2021/6419 Excitation at two or more wavelengths
• CPC Class Codes: G01N 2021/6421 Measuring at two or more wavelengths
• CPC Class Codes: G01N 2021/6441 with two or more labels
• CPC Class Codes: G01N 21/6428 Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" in vivo A61B5/00; immunoassay G01N33/53
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

A detection system and methods for improving the ability of the detection system to recognize labels that are disposed on a polymer. Embodiments of the invention include schemes for selecting emitters and labels used within the system in a manner that allows an increase in the number of distinct labels that can be used together in a system. In other embodiments, the detection system and methods are directed to identifying portions of a detection signal that may be associated with extra labels residing within a detection zone. In other embodiments, the detection system and methods relate to using wide field imaging detectors while reducing out of focus noise contributions to detection signals of the system. Still, other embodiments relate to the use of linear array detectors to detect labels.

Claims

1. A detection system for analyzing a polymer having three or more distinct fluorophores, each fluorophore having an excitation wavelength and a corresponding emission bandwidth, the detection system comprising:

at least three different emitters that together create an excitation signal configured to excite each of the at least three fluorophores such that each fluorophore emits a distinct emission signal within its respective emission bandwidth and each distinct emission signal has an emission maximum separated by at least 60 nm from any other of the emission maximums;

a polymer excitation zone that accepts the polymer, the polymer excitation zone being illuminated by the excitation signal of the at least three different emitters;

a detector constructed and arranged to distinctly detect the emission signal from each of the at least three fluorophores; and

a polychroic mirror adapted to prevent excitation signals emitted from the at least three different emitters from reaching the detector.

6. The detection system of claim 1, wherein the at least three fluorophores are selected from the group consisting of:

Bodipy FL fluorophore, Tamra fluorophore, Alexa 647 fluorophore, Alexa 750 fluorophore, and IR 38 fluorophore.

9. The detection system of claim 1, wherein the detector comprises a plurality of detectors.

10. The detection system of claim 9, wherein the plurality of detectors comprises a plurality of avalanche photon detectors.

11. The detection system of claim 9, further comprising:

a plurality of dichroic mirrors constructed and arranged to direct each of the distinct emission signals into one of the plurality of detectors.

12. The detection system of claim 1, further comprising:

a bandpass filter for removing noise from each of the emission signals.

13. The detection system of claim 1, wherein the at least three different emitters comprise four different emitters and the at least three different fluorophores comprise four different fluorophores.

14. A detection system of claim 1, wherein the emitters comprise lasers.

15. A detection system of claim 1, wherein the excitation signals comprise coherent light.

2. A detection system for analyzing a polymer having three or more distinct fluorophores, each fluorophore having an excitation wavelength and a corresponding emission bandwidth, the detection system comprising:

at least three different emitters that together create an excitation signal configured to excite each of the at least three fluorophores such that each fluorophore emits a distinct emission signal within its respective emission bandwidth that does not overlap any other of the distinct emission signals at normalized intensities above 70%;

a polymer excitation zone that accepts the polymer, the polymer excitation zone being illuminated by the excitation signal of the at least three different emitters;

a detector constructed and arranged to detect the distinct emission signal from each of the at least three fluorophores; and

a polychroic mirror adapted to prevent excitation signals emitted from the at least three different emitters from reaching the detector.

3. The detection system of claim 2, wherein each of the emitters is constructed and arranged to emit a portion of the excitation signal within an excitation wavelength of one of the at least three distinct fluorophores such that each fluorophore emits a distinct emission signal within its respective emission bandwidth that does not overlap any other of the distinct emission signal at normalized intensities above 50%.

4. The detection system of claim 3, wherein each of the emitters is constructed and arranged to emit a portion of the excitation signal within an excitation wavelength of one of the at least three distinct fluorophores such that each fluorophore emits a distinct emission signal within its respective emission bandwidth that does not overlap any other of the distinct emission signal at normalized intensities above 30%.

5. A detection system for analyzing a polymer having three or more distinct fluorophores, each fluorophore having an excitation wavelength and a corresponding emission bandwidth, the detection system comprising:

at least three different emitters that together create an excitation signal having wavelengths configured to excite each of a corresponding one of the at least three fluorophores such that each fluorophore emits a distinct emission signal within its respective emission bandwidth, each of the at least three emitters and corresponding at least three fluorophores selected from a group consisting of;

an emitter emitting an excitation wavelength of 488 nm and a corresponding fluorophore having an emission maximum substantially located at 512 nm, an emitter emitting an excitation a wavelength of 532 nm and a corresponding fluorophore having an emission maximum substantially located at 575 nm, an emitter emitting an excitation wavelength of 633 nm and a corresponding fluorophore having an emission maximum substantially located at 665 nm, and an emitter emitting an excitation wavelength of 750 nm and a corresponding fluorophore having an emission maximum substantially located at 775 nm or 806 nm;

a polymer excitation zone that accepts the polymer, the polymer excitation zone being illuminated by the excitation wavelengths of the at least three different emitters;

a detector constructed and arranged to detect the distinct emission signal from each of the at least three fluorophores; and

a polychroic mirror adapted to prevent excitation signals emitted from the at least three different emitters from reaching the detector.

7. A method of detecting emissions of three or more distinct fluorophores bound to a polymer, the method comprising:

selecting three or more fluorophores, each of the fluorophores characterized by an excitation wavelength and a corresponding emission bandwidth, the emission bandwidth of each of the fluorophores not overlapping the emission bandwidth of any other of the fluorophores at normalized intensities above 70%;

attaching the three or more fluorophores to the polymer in a sequence specific manner;

illuminating each of the fluorophores with an excitation signal of multiple emitters, the excitation signal comprising excitation wavelengths of the corresponding fluorophores that cause each of the fluorophores to emit an emission signal within the emission bandwidth of the fluorophore;

removing the excitation signal from each of the emission signals with a polychroic filter; and

detecting and analyzing the emission signal of each of the fluorophores.

16. The method of claim 7 wherein, selecting three or more fluorophores comprises selecting three or more fluorophores, each of the fluorophores characterized by an excitation bandwidth and a corresponding emission bandwidth, the emission bandwidth of each of the fluorophores not overlapping the emission bandwidth of any other of the fluorophores at normalized intensities above 50%.

17. The method of claim 16, wherein selecting three or more fluorophores comprises selecting three or more fluorophores, each of the fluorophores characterized by an excitation bandwidth and a corresponding emission bandwidth, the emission bandwidth of each of the fluorophores not overlapping the emission bandwidth of any other of the fluorophores at normalized intensities above 30%.

18. The method of claim 7, wherein selecting three or more fluorophores comprises selecting three or more different fluorophores from a group consisting of:

Bodipy FL fluorophore, Tamra fluorophore, Alexa 647 fluorophore, Alexa 750 fluorophore, and IR 38 fluorophore.

19. The method of claim 7, wherein selecting at least three distinct fluorophores and at least three emitters comprises selecting four fluorophores and four emitters.

20. The method of claim 7, wherein the polymer is a nucleic acid.

21. The method of claim 7, wherein detecting the emission signal from each of the fluorophores comprises:

separating each of the emission signals from one another with dichroic filters.

22. The method of claim 7, wherein detecting the emission signal from each of the fluorophores comprises:

passing the emission signal of some of the fluorophores through a bandpass filter.

23. The method of claim 7, wherein illuminating each of the fluorophores with the excitation signal comprises eliminating each of the fluorophores multiple lasers.

8. A method for analyzing a polymer, the method comprising:

selecting at least three distinct fluorophores and an excitation signal emitted from at least three emitters, each of the at least three fluorophores having an excitation wavelength and a corresponding emission bandwidth, the excitation signal having excitation wavelengths that correspond to each of the at least three fluorophores such that each fluorophore emits a distinct emission signal having an emission maximum within its respective emission bandwidth, each of the at least three excitation wavelengths and corresponding at least three fluorophores selected from a group consisting of;

an excitation wavelength of 488 nm and a corresponding fluorophore having an emission maximum substantially located at 512 nm, an excitation wavelength of 532 nm and a corresponding fluorophore having an emission maximum substantially located at 575 nm, an excitation wavelength of 633 nm and a corresponding fluorophore having an emission maximum substantially located at 665 nm, and an excitation wavelength of 750 nm and a corresponding fluorophore having an emission maximum substantially located at 775 nm or 806 nm;

binding the at least three fluorophores to a polymer in a sequence specific manner;

illuminating each of the fluorophores with the corresponding emitter at a common time;

removing the excitation signal from each of the emission signals with a polychroic filter; and

detecting and analyzing the emission signal of each of the fluorophores for analysis.