Method systems and reagents for DNA sequencing

• US 5,306,618 A
• Filed: 01/16/1992
• Issued: 04/26/1994
• Est. Priority Date: 07/02/1986
• Status: Expired due to Term

• Current Assignee: PerkinElmer Life Sciences, Inc.
• Original Assignee: E. I. du Pont de Nemours and Company (Corteva, Inc.)
• Inventors: Prober, James M., Dam, Rudy J., Trainor, George L., Robertson, Charles W. Jr., Hobbs, Frank W. Jr.
• Primary Examiner(s): YARBROUGH, AMELIA
• Application Number:
  US07/821,569
• Time in Patent Office: 831 Days
• Field of Search: 435/6, 435/291, 435/808, 935/85, 935/87, 422/82.05, 422/82.06, 422/82.07, 422/82.08, 422/82.09, 356/344, 356/317, 356/318, 356/417, 356/721, 356/731, 356/39, 436/171, 436/172
• US Class Current: 435/6.12
• CPC Class Codes: C07D 405/04 directly linked by a ring-member-to-ring-member bond
• CPC Class Codes: C07D 405/12 linked by a chain containing hetero atoms as chain links
• CPC Class Codes: C07D 405/14 containing three or more hetero rings
• CPC Class Codes: C07D 471/04 Ortho-condensed systems
• CPC Class Codes: C07F 9/6512 having the nitrogen atoms in positions 1 and 3
• CPC Class Codes: C07F 9/65586 at least one of the hetero rings does not contain nitrogen as ring hetero atom
• CPC Class Codes: C07F 9/6561 containing systems of two or more relevant hetero rings condensed among themselves or condensed with a common carbocyclic ring or ring system, with or without other non-condensed hetero rings
• CPC Class Codes: C07H 19/06 Pyrimidine radicals
• CPC Class Codes: C07H 19/10 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• CPC Class Codes: C07H 19/20 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: G01N 27/44721 by optical means
• CPC Class Codes: G01N 27/44726 using specific dyes, markers or binding molecules
• CPC Class Codes: Y10S 435/808 Optical sensing apparatus
• CPC Class Codes: Y10S 435/968 High energy substrates, e.g. fluorescent, chemiluminescent, radioactive
• CPC Class Codes: Y10S 436/805 Optical property
• CPC Class Codes: Y10T 436/13 Tracers or tags

Abstract

A DNA sequencing system and method are described to detect the presence of radiant energy emitted from different excited reporter dye-labeled species (DNA fragments) following separation in time and/or space, and the identity of the species which emit radiant energy closely spaced in wavelength. Functions of the emitted energy are obtained which vary over the wavelengths of the closely spaced spectra in different senses and the functions ratioed, whereby the ratio is indicative of the identity of the DNA fragments.

The emitting portion of the reporter-labeled DNA fragment is preferably one of a family of fluorescent dyes based on 9-carboxyethyl-6-hydroxy-3-oxo-3H-xanthene. These xanthene dyes are covalently attached to the DNA fragments through the carboxylic acid functionality, preferably via an amide linkage. The dyes may be protected by including an alkoxy group at the 9-position. A spacer may be inserted between the dye and the amine. The fluorescent dye preferably is attached to the DNA chain terminators and provides many advantages. Thus only DNA sequencing fragments resulting from bona fide termination events will carry a reporter. The DNA sequencing may also be labeled using the xanthene dyes which have general utility as fluorescent labels. Also acyclonucleoside triphosphates are described as being useful as chain terminators in DNA sequencing using a modification of the Sanger method.

Claims

1. A system for detecting the presence of radiant energy emitted from more than two spectrally distinct species following separation in time and/or space and the identity of such species, comprising:

means responsive to the spectra of the species for generating a first signal that varies in amplitude in a first sense as a function of the nature of the species,

means responsive to the spectra of the species for generating a second signal that varies in amplitude in a second sense as a function of the nature of the species,

means responsive only to the first and second signals for obtaining a third signal corresponding to the ratio of the first and second signals, the amplitude of the third signal being indicative of the identity of each of the species.

2. The system as set forth in claim 1 wherein the species are fragments of DNA covalently labeled with reporters capable of emitting radiant energy and which includes means adapted to separate fragments of DNA.

3. The system as set forth in claim 2 wherein the reporters have the structure ##STR22## wherein n=2 or 3, and R₁ and R₂ are H, lower alkyl, halo, lower alkoxy, or cyano.

4. The system as set forth in claim 3 wherein the DNA fragments have reporters covalently attached to their 3'"'"'-terminal residues which have been introduced via chain termination events.

5. The system as set forth in claim 4 which also includes a laser having an output wavelength lying within the excitation region of the different reporters.

6. The system as set forth in claim 2 wherein the DNA fragments have reporters covalently attached to their 3'"'"'-terminal residues which have been introduced via chain termination events.

7. The system as set forth in claim 1 wherein the means for generating first and second signals includes

a means having first and second transmission characteristics, which vary as a function of wavelength, for transmitting the spectra,

the transmission means and the species being relatively positionable to direct such emissions to the transmission means.

first and second detectors positionable to receive respectively the first and second transmitted emissions and generating the first and second signals corresponding to the intensities of each and indicating the presence of each.

8. The system as set forth in claim 7 wherein the device characteristic has a transition from the first to the second transmission characteristic which is centered at about the middle of the reporters'"'"' emission spectra.

9. The system as set forth in claim 8 wherein the transmission means is a dichroic filter.

10. The system as set forth in claim 7 which includes means adapted to separate fragments of DNA or other molecules covalently labeled with reporters.

11. The system as set forth in claim 10 wherein the reporters have a emitting part with the structure ##STR23## wherein n=2 or 3, and R₁ and R₂ are H, lower alkyl, halo, lower alkoxy, and cyano.

12. A method of detecting the presence of radiant energy emitted from different species following a separation in time and/or space and determining the identity of each such species that emit spectra comprising the steps of:

obtaining functions of the emitted energy which vary in different senses according to the nature of the species, and

ratioing such functions, the ratio being indicative of the identity of the species.

13. The method set forth in claim 12 wherein the different senses consist of greater and lesser emission amplitudes.

14. The method as set forth in claim 13 wherein the functions are obtained by passing the emitted radiant energy through a device having a transmission/reflection characteristic which varies as a function of wavelength, and the device is a dichroic filter.

15. The method as set forth in claim 12 wherein the species are fragments of DNA covalently labeled with reporters.

16. The method as set forth in claim 15 wherein the reporters have the structure ##STR24## wherein n=2 or 3, and R₁ and R₂ are H, lower alkyl, halo, lower alkoxy, and cyano.

17. The method as set forth in claim 16 wherein the DNA fragments have reporters attached to their 3'"'"'-terminal residues which have been introduced via chain termination events.