Self-organizing molecular photonic structures based on chromophore- and fluorophore-containing polynucleotides and methods of their use

• US 5,532,129 A
• Filed: 05/27/1994
• Issued: 07/02/1996
• Est. Priority Date: 11/07/1991
• Status: Expired due to Term

• Current Assignee: Nanogen, Inc.
• Original Assignee: Enterprise Partners II LP (Enterprise Partners Venture Capital)
• Inventors: Heller, Michael J.
• Primary Examiner(s): Jones, W. Gary
• Assistant Examiner(s): TRAN, PAUL
• Application Number:
  US08/250,951
• Time in Patent Office: 767 Days
• Field of Search: 435/6, 436/56, 436/501, 436/800, 514/4, 536/24.3, 536/24.2, 536/25.32, 935/77, 935/78
• 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 polynucleotide having a terminal donor chromophore, at least one intermediate donor-acceptor chromophore, and at least one acceptor chromophore all said chromophores are linked to said polynucleotide by linker arms, wherein the distance between said terminal donor chromophore and one said acceptor chromophore is greater than 5 nm and there is at least one said intermediate donor chromophore within said distance.

2. The polynucleotide of claim 1, wherein at least one said acceptor chromophore is able to re-emit light.

3. The polynucleotide of claim 2, wherein light transferred from at least one said donor chromophore produces an increase in acceptor re-emission.

4. The polynucleotide of claim 2 wherein said donor chromophores are 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-dimethylaminophenylazophenyl-4'"'"'-isothiocyanate, Lucifer Yellow vinyl sulfone, fluorescein isothiocyanate, Cibacron Brilliant Red 3B-A, Rhodamine X isothiocyanate, Sulforhodamine 101 acid chloride, Malachite Green isothiocyanate and IR1446.

5. The polynucleotide of claim 2 wherein said terminal donor chromophore and said at least one intermediate donor chromophore are non-fluorescing chromophores.

6. The polynucleotide of claim 2 wherein said terminal donor chromophone and said at least one intermediate donor chxomophore comprise 2 to 100 chromophores.

7. The polynucleotide of claim 2 wherein the acceptor chromophore is a fluorescing acceptor chromophore.

8. The polynucleotide of claim 7 wherein said fluorescing chromophore is selected from the group consisting of pyrene, Lucifer Yellow vinyl sulfone, acridine isothiocyanate, riboflavin, fluorescein isothiocyanate, Rhodamine X isothiocyanate, Sulforhodamine 101 acid chloride and IR 144.

9. A diagnostic assay system for photonic detection of a preselected nucleotide sequence comprising, in an amount sufficient for at least one assay, a polynucleotide having a terminal donor chromophore, at least one intermediate donor-acceptor chromophore, all said chromophores are and at least one acceptor chromophore linked to said polynucleotide by linker arms, wherein the distance between said terminal donor chromophore and one said acceptor chromophore is greater than 5 nm and there is at least one said intermediate donor chromophore within said distance.

10. The diagnostic system of claim 9 wherein at least one of said terminal donor chromophore, said at least. One intermediate donor chromophore, .and said at least one acceptor chromophore is a fluorescing chromophore operatively linked to said polynucleotide by a linker and, wherein said fluorescing chromophore is positioned by said linkage at a donor-acceptor transfer distance from at least one of said non-fluorescing chromophores.

11. The diagnostic system of claim 9 that further contains a second polynucleotide containing at least one fluorescing acceptor chromophore linked to said second polynucleotide by a linker arm.

12. A method for detecting the presence of a preselected nucleic acid target sequence in a nucleic acid-containing sample comprising the steps of:

(a) admixing;

(i) a polynucleotide having a terminal donor chromophore, at least one intermediate donor-acceptor chromophore, and at least one acceptor chromophore, said chromophores are linked to said polynucleotide by linker arms, all wherein the distance between said terminal donor chromophore and one said acceptor chromophore is greater than 5 nm and there is at least one said intermediate donor chromophore within said distance, and

(ii) said nucleic acid-containing sample to form a hybridization reaction admixture, said polynucleotide having a preselected nucleic acid sequence adapted to hybridize to said target sequence;

(b ) subjecting said hybridization reaction admixture to hybridization conditions for a time period sufficient for said polynucleotide to hybridize to said preselected nucleic acid base sequence and form a donor chromophore containing- and acceptor chromophore containing-hybridized nucleic acid duplex;

(c) exciting said donor chromophores in said nucleic acid duplex formed in step (b) by exposing said donor chromophores to sufficient photonic energy to induce emission of photonic energy from said acceptor chromophore; and

(d) detecting the presence of photonic energy re-emitted from said acceptor chromophore using a photon sensing means, thereby detecting the presence of said preselected nucleic acid target sequence in said sample.

13. The method of claim 12 wherein said terminal donor chromophore and said at least one intermediate donor chromophore are excited by photonic energy at a wavelength corresponding to the excitation maximum of the donor, and wherein the photonic energy re-emitted from said acceptor is detected at its emission wavelength.

14. The method of claim 12, wherein at least one of the polynucleotide and the nucleic acid target sequence is attached to a solid support or matrix.

15. The method of claim 14, wherein the solid support or matrix is selected from the group consisting of glass, metals, silicon, organic polymers, membranes, and bio-polymers.

16. The method of claim 14, wherein the photon sensing means is closely associated with said solid support or matrix.

17. A method for detecting the presence of a preselected nucleic acid target sequence in a nucleic acid-containing sample comprising the steps of:

(a) admixing;

(i) a first polynucleotide having a terminal donor chromophore and at least one intermediate donor acceptor chromophore, said donor and donor-acceptor chromophores are linked to said first polynucleotide by linker arms; and

(ii) a second polynucleotide having at least one acceptor chromophore linked to said second polynucleotide by a linker arm, and

(iii) said nucleic acid-containing sample to form a hybridization reaction admixture, said first and second polynucleotides having preselected nucleic acid sequences adapted to hybridize to said target sequence and thereby position said terminal donor chromophore on said first polynucleotide and one said acceptor chromophore on said second polynucleotide at a distance which is greater than 5 nm, and wherein there is at least one said intermediate donor chromophore within said distance;

(b) subjecting said hybridization reaction admixture to hybridization conditions for a time period sufficient for said polynucleotide to hybridize to said preselected nucleic acid base sequence and form a donor chromophore containing- and acceptor chromophore containing-hybridized nucleic acid duplex;

(c) exciting said donor chromophores in said nucleic acid duplex formed in step (b) by exposing said donor chromophores to sufficient photonic energy to induce emission of photonic energy from said acceptor chromophore; and

(d) detecting the presence of photonic energy re-emitted from said acceptor chromophore using a photon sensing means, thereby detecting the presence of said preselected nucleic acid target sequence in said sample.

18. The method of claim 17, wherein said donor chromophores are excited by photonic energy at a wavelength corresponding to the excitation maximum of the donor, and wherein the photonic energy re-emitted from said acceptor is detected at its emission wavelength.

19. The method of claim 17, wherein at least one of the first polynucleotide, the second polynucleotide, and the nucleic acid target sequence is attached to a solid support or matrix.

20. The method of claim 19, wherein the solid support or matrix is selected from the group consisting of glass, metals, silicon, organic polymers, membranes, and bio-polymers.

21. The method of claim 19, wherein the photon sensing means is closely associated with said solid support or matrix.