Hybridization of polynucleotides conjugated with chromophores and fluorophores to generate donor-to-donor energy transfer system

• US 6,162,603 A
• Filed: 07/28/1998
• Issued: 12/19/2000
• Est. Priority Date: 11/07/1991
• Status: Expired due to Fees

• Current Assignee: Gamida for Life B.V.
• Original Assignee: Nanogen, Inc.
• Inventors: Heller, Michael J.
• Primary Examiner(s): FREDMAN, JEFFREY NORMAN
• Application Number:
  US09/123,638
• Time in Patent Office: 875 Days
• Field of Search: 435/6, 435/56, 435/800, 536/29.3, 422/882.01, 422/82.02, 422/82.08
• US Class Current: 435/6.12
• CPC Class Codes: B01J 2219/00536 in the shape of disks
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00617 by chemical means
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B82Y 10/00 Nanotechnology for information processing, storage or transmission, e.g. quantum computing or single electron logic
• CPC Class Codes: C12Q 1/6818 involving interaction of two or more labels, e.g. resonant energy transfer
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 2531/113 PCR
• CPC Class Codes: C12Q 2563/107 fluorescence
• CPC Class Codes: C12Q 2565/101 Interaction between at least two labels
• CPC Class Codes: G06N 3/123 DNA computing
• CPC Class Codes: G11B 2007/24624 fluorescent dyes
• CPC Class Codes: G11B 7/244 comprising organic materials only
• CPC Class Codes: G11C 13/0014 comprising cells based on organic memory material
• CPC Class Codes: G11C 13/0019 comprising bio-molecules
• CPC Class Codes: G11C 13/04 using optical elements ; using other beam accessed elements, e.g. electron or ion beam
• CPC Class Codes: H01L 24/95 at chip-level, i.e. with connecting carried out on a plurality of singulated devices, i.e. on diced chips
• CPC Class Codes: H01L 25/50 : Multistep manufacturing processes of assemblies consisting of devices, each device being of a type provided for in group H01L27/00 or H01L29/00 H01L21/50 takes precedence
• CPC Class Codes: H01L 2924/00 : Indexing scheme for arrangements or methods for connecting or disconnecting semiconductor or solid-state bodies as covered by H01L24/00
• CPC Class Codes: H01L 2924/01005 : Boron [B]
• CPC Class Codes: H01L 2924/01006 : Carbon [C]
• CPC Class Codes: H01L 2924/01011 : Sodium [Na]
• CPC Class Codes: H01L 2924/01012 : Magnesium [Mg]
• CPC Class Codes: H01L 2924/01013 : Aluminum [Al]
• CPC Class Codes: H01L 2924/01019 : Potassium [K]
• CPC Class Codes: H01L 2924/0102 : Calcium [Ca]
• CPC Class Codes: H01L 2924/01023 : Vanadium [V]
• CPC Class Codes: H01L 2924/01025 : Manganese [Mn]
• CPC Class Codes: H01L 2924/01032 : Germanium [Ge]
• CPC Class Codes: H01L 2924/01033 : Arsenic [As]
• CPC Class Codes: H01L 2924/01039 : Yttrium [Y]
• CPC Class Codes: H01L 2924/01043 : Technetium [Tc]
• CPC Class Codes: H01L 2924/01044 : Ruthenium [Ru]
• CPC Class Codes: H01L 2924/01054 : Xenon [Xe]
• CPC Class Codes: H01L 2924/0106 : Neodymium [Nd]
• CPC Class Codes: H01L 2924/01074 : Tungsten [W]
• CPC Class Codes: H01L 2924/01075 : Rhenium [Re]
• CPC Class Codes: H01L 2924/01076 : Osmium [Os]
• CPC Class Codes: H01L 2924/01077 : Iridium [Ir]
• CPC Class Codes: H01L 2924/01079 : Gold [Au]
• CPC Class Codes: H01L 2924/01082 : Lead [Pb]
• CPC Class Codes: H01L 2924/12042 : LASER
• CPC Class Codes: H01L 2924/12043 : Photo diode
• CPC Class Codes: H01L 2924/14 : Integrated circuits
• CPC Class Codes: Y10S 435/80 : Elimination or reduction of contamination by undersired ferments, e.g. aseptic cultivation
• CPC Class Codes: Y10S 436/80 : Fluorescent dyes, e.g. rhodamine
• CPC Class Codes: Y10T 436/13 : Tracers or tags

Abstract

The present invention contemplates chromophore-containing polynucleotides having at least two donor chromophores operatively linked to the polynucleotide by linker arms, such that the chromophores are positioned by linkage along the length of the polynucleotide at a donor-donor transfer distance, and at least one fluorescing acceptor chromophore operatively linked to the polynucleotide by a linker arm, such that the fluorescing acceptor chromophore is positioned by linkage at a donor-acceptor transfer distance from at least one of the donor chromophores, to form a photonic structure for collecting photonic energy and transferring the energy to an acceptor chromophore, and methods using the photonic structures.

Claims

1. A method for detection of a target polynucleotide sequence, comprising the steps of:

providing a first polynucleotide sequence having one or more chromophores;

providing a second polynucleotide sequence hybridized to the first polynucleotide sequence, the second polynucleotide sequence having one or more chromophores arranged in a quenching relationship to the acceptor chromophore of the first polynucleotide sequence when the first polynucleotide sequence and second polynucleotide sequence are hybridized;

exposing a target polynucleotide sequence to the hybridized first and second polynucleotide sequences;

denaturing the hybridized first and second polynucleotide sequences;

hybridizing the first polynucleotide sequence to the target polynucleotide sequence;

hybridizing a third polynucleotide sequence having one or more donor chromophores to the target polynucleotide sequence; and

irradiating the mixture to detect hybridization of the first polynucleotide sequence to the target polynucleotide sequence by fluorescence energy transfer from the one or more donor chromophores of the third polynucleotide sequence to the one or more acceptor chromophores of the first polynucleotide sequence.

2. The method of claim 1, wherein the target polynucleotide sequence comprises DNA.

3. The method of claim 1, wherein the target polynucleotide sequence comprises RNA or synthetic polynucleotide.

4. The method of claim 1, wherein the quenching chromophore is selected from the group consisting of 4,4'"'"'-Diisothiocyanatodihydro-stilbene-2,2'"'"'-disulfonic acid, 4-acetamido-4'"'"'-isothiocyanato-stilbene-2,2'"'"'-disulfonic acid, 4,4'"'"'-Diisothiocyanatostilbene-2,2'"'"'-disulfonic acid, Succinimidyl pyrene butyrate, Acridine isothiocyanate, 4-imethylaminophenylazophenyl-4-isothiocyanate (DABITC), Lucifer Yellow vinyl sulfone, Fluorescein isothiocyanate, Reactive Red 4 (Cibacron Brilliant Red 3B-A), Rhodamine X isothiocyanate, Texas Red (Sulforhodamine 101, sulfonyl chloride), Malachite Green isothiocyanate, or IR144.

5. The method of claim 1, wherein the second polynucleotide sequence is shorter than the first polynucleotide sequence.

6. The method of claim 1, wherein the first polynucleotide sequence is bound to a solid support.

7. The method of claim 1, wherein the third polynucleotide sequence is bound to a solid support.

8. The method of claim 7, wherein the donor chromophore is selected from the group consisting of 4,4'"'"'-Diisothiocyanatodihydro-stilbene-2,2'"'"'-disulfonic acid, 4-acetamido-4'"'"'-isothiocyanato-stilbene-2,2'"'"'-disulfonic acid, 4,4'"'"'-Diisothiocyanatostilbene-2,2'"'"'-disulfonic acid, Succinimidyl pyrene butyrate, Acridine isothiocyanate, 4-imethylaminophenylazophenyl-4'"'"'-isothiocyanate (DABITC), Lucifer Yellow vinyl sulfone, Fluorescein isothiocyanate, Reactive Red 4 (Cibacron Brilliant Red 3B-A), Rhodamine X isothiocyanate, Texas Red (Sulforhodamine 101, sulfonyl chloride), Malachite Green isothiocyanate, or IR144.

9. The method of claim 1, wherein the acceptor chromophore is selected from the group consisting of 4,4'"'"'-Diisothiocyanatodihydro-stilbene-2,2'"'"'-disulfonic acid, 4-acetamido-4'"'"'-isothiocyanato-stilbene-2,2'"'"'-disulfonic acid, 4,4'"'"'-Diisothiocyanatostilbene-2,2'"'"'-disulfonic acid, Succinimidyl pyrene butyrate, Acridine isothiocyanate, 4-imethylaminophenylazophenyl-4'"'"'-isothiocyanate (DABITC), Lucifer Yellow vinyl sulfone, Fluorescein isothiocyanate, Reactive Red 4 (Cibacron Brilliant Red 3B-A), Rhodamine X isothiocyanate, Texas Red (Sulforhodamine 101, sulfonyl chloride), Malachite Green isothiocyanate, or IR144.

10. The method of claim 1, wherein each of the donor chromophores, acceptor chromophores, and quenching chromophores is selected from the group consisting of 4,4'"'"'-Diisothiocyanatodihydro-stilbene-2,2'"'"'-disulfonic acid, 4-acetamido-4'"'"'-isothiocyanato-stilbene-2,2'"'"'-disulfonic acid, 4,4'"'"'-Diisothiocyanatostilbene-2,2'"'"'-disulfonic acid, Succinimidyl pyrene butyrate, Acridine isothiocyanate, 4-imethylaminophenylazophenyl-4'"'"'-isothiocyanate (DABITC), Lucifer Yellow vinyl sulfone, Fluorescein isothiocyanate, Reactive Red 4 (Cibacron Brilliant Red 3B-A), Rhodamine X isothiocyanate, Texas Red (Sulforhodamine 101, sulfonyl chloride), Malachite Green isothiocyanate, or IR144.

11. The method of claim 1, wherein the quenching chromophore is selected from Reactive Red 4 and Malachite Green.

12. The method of claim 1, wherein the second polynucleotide sequence is bound to a solid support.

13. The method of claim 1, wherein target nucleic acid is bound to a solid support.

14. The method of claim 1, wherein the polynucleotide sequence comprises a plurality of donor chromophores.

15. A method for detecting the presence of a target nucleic acid sequence, comprising the steps:

providing a first polynucleotide sequence containing an acceptor fluorescent moiety, the first polynucleotide sequence being complementary to a portion of a target nucleic acid sequence;

providing a second polynucleotide sequence hybridized to the first polynucleotide sequence and containing a quencher moiety positioned such that the acceptor moiety is quenched when the first and second polynucleotide sequences are hybridized;

providing a third polynucleotide sequence containing one or more donor fluorescent moieties which is complementary to a portion of the target nucleic acid sequence;

combining the third polynucleotide sequence, the first and second polynucleotide sequences, and the target nucleic acid sequence;

denaturing the hybridized first and second polynucleotide sequences;

hybridizing the first polynucleotide sequence to the target polynucleotide sequence; and

analyzing the hybridization reaction by exciting the sample at a wavelength at or near the excitation for the donor fluorescent moiety and determining emission at or near the wavelength for the acceptor fluorescent moiety.

16. The method of claim 15, wherein the quencher moiety is a fluorescent chromophore.

17. The method of claim 15, wherein the quencher moiety is a non-fluorescent chromophore.