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

• US 5,565,322 A
• Filed: 05/05/1994
• Issued: 10/15/1996
• Est. Priority Date: 11/07/1991
• Status: Expired due to Term

• Current Assignee: Gamida for Life B.V., Nanogen, Inc.
• Original Assignee: Nanogen, Inc.
• Inventors: Heller, Michael J.
• Primary Examiner(s): Jones, W. Gary
• Assistant Examiner(s): TRAN, PAUL
• Application Number:
  US08/232,233
• Time in Patent Office: 894 Days
• Field of Search: 435/6, 514/4, 436/501, 436/800, 436/56, 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 presence 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.

Claims

1. A duplex nucleic acid structure capable of extended photonic energy transfer, said structure comprising:

a first polynucleotide;

a second polynucleotide hybridized to said first polynucleotide;

a terminal donor chromophore linked by linker arms to one of said first polynucleotide and said second polynucleotide;

at least one intermediate donor chromophore linked by linker arms to one of said first polynucleotide and said second polynucleotide; and

at least one acceptor chromophore linked by linker arms to one of said first polynucleotide and said second polynucleotide;

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 spaced from said terminal donor chromophore by a donor-donor transfer distance; and

wherein said donor and said acceptor chromophores are alternately positioned on said first polynucleotide and said second polynucleotide such that said photonic energy transfer crosses between said first and said second polynucleotides of said duplex.

2. The structure of claim 1, wherein said donor-donor transfer distance is 1.4 to 6.1 nm.

3. The structure of claim 1, 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 (DABITC), Lucifer Yellow vinyl sulfone, fluorescein isothiocyanate, Reactive Red 4 (Cibacron®

Brilliant Red 3B-A) rhodamine X isothiocyanate, sulforhodamine 101, Malachite Green isothiocyanate and IR1446.

4. The structure of claim 1, wherein said donor chromophores are non-fluorescing chromophores.

5. The structure of claim 1, wherein said at least one intermediate donor chromophore comprises 1 to 99 chromophores.

6. The structure of claim 1, further comprising at least one fluorescing acceptor chromophore operatively linked by linker arms to one of said first polynucleotide and said second polynucleotide, wherein said at least one fluorescing accepting chromophore is positioned by said linker arms at a donor-acceptor transfer distance from at least one of said donor chromophores.

7. The structure of claim 6, wherein said donor-acceptor transfer distance is 0.1 to 1.7 nm.

8. The structure of claim 6, wherein said fluorescing acceptor chromophore is selected from the group consisting of pyrene, Lucifer Yellow, acridine, riboflavin, fluorescein, rhodamine, sulforhodamine 101, and IR 144.

9. The structure of claim 1, wherein at least one of said first polynucleotide and said second polynucleotide is linked to a solid support.

10. The structure of claim 9, wherein the solid support is selected from the group consisting of glass, metals, silicon, organic polymers, membranes, and bio-polymers.