Surface for the immobilisation of nucleic acids

• US 20050009026A1
• Filed: 08/24/2002
• Published: 01/13/2005
• Est. Priority Date: 08/27/2001
• Status: Abandoned Application

• Current Assignee: Bayer Technology Services GmbH (Bayer AG)
• Original Assignee: Bayer Technology Services GmbH (Bayer AG)
• Inventors: Benoit, Vincent, Utinger, Dominic, Vande Vondele, Stephanie, Kauffmann, Ekkehard, De Paul, Susan Margaret, Textor, Marcus, Abel, Andreas Peter, Ehrat, Markus, Hubbell, Jeffrey Alan
• Application Number:
  US10/487,915
• Publication Number:
  US 20050009026A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: B01J 2219/00382 Stamping
• CPC Class Codes: B01J 2219/00385 Printing
• CPC Class Codes: B01J 2219/00387 Applications using probes
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/0054 Means for coding or tagging the apparatus or the reagents
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/0063 Other, e.g. van der Waals forces, hydrogen bonding
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 60/14 for creating libraries
• CPC Class Codes: C40B 70/00 Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or bar codes

Abstract

The invention relates to a surface for the immobilization of one or several first nucleic acids as recognition elements (“immobilization surface”), for the production of a recognition surface for the detection of one or several second nucleic acids in one or more samples which are brought into contact with the recognition surface, the first nucleic acids being applied to a layer of the graft copolymer poly(L-lysine)-g-poly(ethyleneglycol) (PLL-g-PEG) as surface for immobilization, characterized in that the grafting ratio g, in other words the ratio between the number of lysine units and the number of polyethylene glycol side chains (“PEG” side chains) has an average value between 7 and 13. The invention also relates to a method for the qualitative and/or quantitative detection of one or more second nucleic acids in one or more samples, characterized in that said samples and optionally further reagents are brought into contact with an immobilization surface according to the invention, upon which one or several first nucleic acids are immobilized as recognition elements for specific binding/hybridization with said second nucleic acids and changes in optical or electronic signals resulting from the binding/hybridization of said second nucleic acid, or further, resulting from applied tracer substances applied for analyte detection, are measured.

Claims

1. A surface for the immobilization of one or several first nucleic acids as recognition elements (“

immobilization surface”

), for the production of a recognition surface for the detection of one or several second nucleic acids in one or more samples which are brought into contact with the recognition surface, the first nucleic acids being applied to a layer of PLL-g-PEG (graft copolymer poly(L-lysine)-g-poly(ethyleneglycol)) as a surface for immobilization, characterized in that the grafting ratio g, in other words the ratio between the number of lysine units and the number of polyethylene glycol side chains (“

PEG”

side chains) has an average value between 7 and 13.

2. A surface for the immobilization of one or several first nucleic acids according to claim 1, wherein the grafting ratio g has a medium value between 8 and 12.

3. A surface for the immobilization of one or several first nucleic acids according to claim 1, wherein the molecular weight of the polyetheyleneglycol side chains (“

PEG”

side chains) is between 500 Da and 7000 Da.

4. A surface for the immobilization of one or several first nucleic acids according to claim 1, wherein the molecular weight of the polyetheyleneglycol side chains (“

PEG”

side chains) is between 1500 Da and 5000 Da.

5. A surface for the immobilization of one or several first nucleic acids according to claim 1, wherein said surface is deposited on a solid carrier.

6. A surface for the immobilization of one or several first nucleic acids according to claim 5, wherein said solid carrier is an essentially optically transparent carrier.

7. A surface for the immobilization of one or several first nucleic acids according to claim 6, wherein the essentially optically transparent carrier comprises a material from the group comprising moldable, sprayable or millable plastics, metals, metal oxides, silicates, such as glass, quartz or ceramics.

8. A surface for the immobilization of one or several first nucleic acids according to claim 1, wherein said surface is essentially optically transparent.

9. A surface for the immobilization of one or several first nucleic acids according to claim 1, wherein said surface (as a PLL-g-PEG layer) has a thickness of less than 200 nm, preferably of less than 20 nm.

10. An immobilization surface according to claim 6, wherein said surface for immobilization is deposited on a solid carrier, in the surface of which are structured recesses for generation of sample compartments.

11. An immobilization surface according to claim 10, wherein said recesses in the surface of the carrier have a depth of 20 μ

m to 500 μ

m, especially preferably 50 μ

m to 300 μ

m.

12. An immobilization surface according to claim 6, wherein the essentially optically transparent carrier comprises a continuous optical waveguide or an optical waveguide divided into individual waveguiding areas.

13. An immobilization surface according to claim 12, wherein the optical waveguide is an optical film waveguide with a first essentially optically transparent layer (a) facing the immobilization surface on a second essentially optically transparent layer (b) with a refractive index lower than that of layer (a).

14. An immobilization surface according to claim 13, wherein said optical film waveguide is essentially planar.

15. An immobilization surface according to claim 13, wherein, for the in-coupling of excitation light into the optically transparent layer (a), this layer is in optical contact with one or more optical in-coupling elements from the group comprising prism couplers, evanescent couplers with combined optical waveguides with overlapping evanescent fields, butt-end couplers with focusing lenses, preferably cylinder lenses, arranged in front of one face of the waveguiding layer, and grating couplers.

16. An immobilization surface according to claim 15, wherein the excitation light is in-coupled into the optically transparent layer (a) using one or more grating structures (c) which are featured in the optically transparent layer (a).

17. An immobilization surface according to claim 15, wherein light guided in the optically transparent layer (a) is out-coupled using one or more grating structures (c′

) which are featured in the optically transparent layer (a) and have the same or different period and grating depth as grating structures (c).

18. An immobilization surface according to claim 1, wherein the nucleic acids immobilized thereon as recognition elements are arranged in discrete (laterally separated) measurement areas.

19. An immobilization surface according to claim 18, wherein up to 1,000,000 measurement areas are provided in a 2-dimensional arrangement and a single measurement area covers an area of 10⁻

4 mm²-10 mm².

20. An immobilization surface according to claim 18, wherein the measurement areas are arranged in a density of more than 10, preferably more than 100, especially preferably more than 1000 measurement areas per square centimeter.

21. An immobilization surface according to claim 18, wherein discrete (laterally separated) measurement areas are generated on said immobilization surface by the laterally selective application of nucleic acids as recognition elements, preferably using one or more methods from the group of methods comprising ink-jet spotting, mechanical spotting by means of pin, pen or capillary, micro-contact printing, fluidic contact of the measurement areas with the biological or biochemical or synthetic recognition elements through their application in parallel or intersecting microchannels, upon exposure to pressure differences or to electric or electromagnetic potentials, and photochemical or photolithographic immobilization methods.

22. A method for the simultaneous or sequential, qualitative and/or quantitative detection of one or more second nucleic acids in one or more samples, wherein said samples and if necessary further reagents are brought into contact with an immobilization surface according to claim 1, on which surface one or several first nucleic acids are immobilized as recognition elements for the specific binding/hybridization with said second nucleic acids, and changes in optical or electronic signals resulting from the binding/hybridization with these second nucleic acids or of further tracer substances used for analyte detection are measured.

23. A method according to claim 22, wherein the one or more samples are pre-incubated with a mixture of the various tracer reagents for determining the second nucleic acids to be detected in said samples, and these mixtures are then brought into contact with the first nucleic acids immobilized on said immobilization surface in a single addition step.

24. A method according to claim 22, wherein the detection of the one or more second nucleic acids is based on the determination of the change in one or more luminescences.

25. A method according to claim 22, wherein the excitation light from one or more light sources for the excitation of one or more luminescences is delivered in an epi-illumination configuration.

26. A method according to claim 22, wherein the excitation light from one or more light sources for the excitation of one or more luminescences is delivered in a transillumination configuration.

27. A method according to one of claims 22-24claim 22, wherein the immobilization surface is arranged on an optical waveguide which is preferably essentially planar, wherein one or more samples with second nucleic acids to be detected therein and, if necessary further tracer reagents, are brought sequentially or in a single addition step after mixture with said tracer reagents, into contact with said first nucleic acids immobilized as recognition elements on said immobilization surface, and wherein the excitation light from one or more light sources is in-coupled into the optical waveguide using one or more optical coupling elements from the group comprising prism couplers, evanescent couplers with combined optical waveguides with overlapping evanescent fields, butt-end couplers with focusing lenses, preferably cylinder lenses, arranged in front of one face of the waveguiding layer, and grating couplers.

28. A method according to claim 27, wherein the detection of one or more second nucleic acids is performed on a grating structure (c) or (c′

) formed in the layer (a) of an optical film waveguide, based on changes in the resonance conditions for the in-coupling of excitation light into layer (a) of a carrier formed as film waveguide or for out-coupling of light guided in layer (a), these changes resulting from binding/hybridization of said second nucleic acids or further tracer reagents to the first nucleic acids immobilized as recognition elements in the region of said grating structure on said immobilization surface.

29. A method according to claim 27, wherein said optical waveguide is designed as an optical film waveguide with a first optically transparent layer (a) on a second optically transparent layer (b) with lower refractive index than layer (a), wherein excitation light is further in-coupled into the optically transparent layer (a) with the aid of one or more grating structures, which are featured in the optically transparent layer (a), and delivered as a guided wave to measurement areas (d) located, and wherein the luminescence of molecules capable of luminescence, generated in the evanescent field of said guided wave, is further determined using one or more detectors, and the concentration of one or more nucleic acids to be detected is determined from the intensity of these luminescence signals.

30. A method according to claim 29, wherein (1) the isotropically emitted luminescence or (2) luminescence in-coupled into the optically transparent layer (a) and out-coupled via grating structure (c) or (c′

) or luminescences of both (1) and (2) are measured simultaneously.

31. A method according to claim 29, wherein, for the generation of luminescence, a luminescence dye or luminescent nanoparticle is used as a luminescence label, which can be excited and emits at a wavelength between 300 nm and 1100 nm.

32. A method according to claim 31, wherein the luminescence label is bound to the second nucleic acids themselves to be detected as analytes or, in a competitive assay, to nucleic acids with the same sequence as said second nucleic acids to be detected and added to the sample as competitors at a known concentration, or, in a multistep assay, to one of the binding partners of the first nucleic acids immobilized as recognition elements, or to said immobilized first nucleic acids.

33. A method according to claim 31, wherein a second luminescence label or further luminescence labels are used with excitation wavelengths either the same as or different from that of the first luminescence label and the same or different emission wavelength.

34. A method according to claim 33, wherein the second or further luminescence labels can be excited at the same wavelength as the first luminescence label, but emit at different wavelengths.

35. A method according to claim 33, wherein the excitation spectra and emission spectra of the luminescence dyes used overlap only little or not at all.

36. A method according to claim 33, wherein charge or optical energy transfer from a first luminescence label serving as donor to a second luminescence label serving as acceptor is used for the purpose of detecting the second nucleic acids as analytes.

37. A method according to claim 29, wherein changes in the effective refractive index on the measurement areas are determined in addition to the determination of one or more luminescences.

38. A method according to claim 29, wherein the one or more luminescences and/or determinations of light signals at the excitation wavelength are carried out using a polarization-selective procedure.

39. A method according to claim 29, wherein the one or more luminescences are measured at a polarization different from that of the excitation light.

40. A method according to claim 22, wherein the samples to be analyzed are aqueous solutions, especially buffer solutions, or naturally occurring body fluids such as blood, serum, plasma, urine or tissue fluids.

41. A method according to claim 22, wherein the sample to be analyzed is an optically turbid fluid, surface water, a soil or plant extract, a biological or synthetic process broth.

42. A method according to claim 22, wherein the samples to be analyzed are prepared from biological tissue parts or cells.

43. Use of an immobilization surface according to claim 1 for quantitative or qualitative analyses in screening methods in pharmaceutical research, clinical and pre-clinical development, for real-time binding studies and the determination of kinetic parameters in affinity screening and in research, for qualitative and quantitative analyte determinations, especially for DNA and RNA analytics and for the determination of genomic or proteomic differences in the genome, such as single nucleotide polymorphisms, for the measurement of protein-DNA interactions, for the determination of control mechanisms for mRNA expression and for protein (bio)synthesis, for the generation of toxicity studies and the determination of expression profiles, especially for the determination of biological and chemical marker compounds, such as mRNA, pathogens or bacteria in pharmaceutical product research and development, human and veterinary diagnostics, agrochemical product research and development, for symptomatic and pre-symptomatic plant diagnostics, for patient stratification in pharmaceutical product development and for therapeutic drug selection, for the determination of pathogens, nocuous agents and germs, especially of salmonella, prions, viruses and bacteria, especially in food and environmental analytics.

44. An immobilization surface according to claim 8, wherein said surface for immobilization is deposited on a solid carrier, in the surface of which are structured recesses for generation of sample compartments.

45. An immobilization surface according to claim 9, wherein said surface for immobilization is deposited on a solid carrier, in the surface of which are structured recesses for generation of sample compartments.

46. An immobilization surface according to claim 8, wherein the essentially optically transparent carrier comprises a continuous optical waveguide or an optical waveguide divided into individual waveguiding areas.

47. An immobilization surface according to claim 46, wherein the optical waveguide is an optical film waveguide with a first essentially optically transparent layer (a) facing the immobilization surface on a second essentially optically transparent layer (b) with a refractive index lower than that of layer (a).

48. An immobilization surface according to claim 9, wherein the essentially optically transparent carrier comprises a continuous optical waveguide or an optical waveguide divided into individual waveguiding areas.

49. An immobilization surface according to claim 48, wherein the optical waveguide is an optical film waveguide with a first essentially optically transparent layer (a) facing the immobilization surface on a second essentially optically transparent layer (b) with a refractive index lower than that of layer (a).

50. A method for the simultaneous or sequential, qualitative and/or quantitative detection of one or more second nucleic acids in one or more samples, wherein said samples and if necessary further reagents are brought into contact with an immobilization surface according to claim 6, on which surface one or several first nucleic acids are immobilized as recognition elements for the specific binding/hybridization with said second nucleic acids, and changes in optical or electronic signals resulting from the binding/hybridization with these second nucleic acids or of further tracer substances used for analyte detection are measured.

51. A method according to claim 50, wherein the immobilization surface is arranged on an optical waveguide which is preferably essentially planar, wherein one or more samples with second nucleic acids to be detected therein and, if necessary further tracer reagents, are brought sequentially or in a single addition step after mixture with said tracer reagents, into contact with said first nucleic acids immobilized as recognition elements on said immobilization surface, and wherein the excitation light from one or more light sources is in-coupled into the optical waveguide using one or more optical coupling elements from the group comprising prism couplers, evanescent couplers with combined optical waveguides with overlapping evanescent fields, butt-end couplers with focusing lenses, preferably cylinder lenses, arranged in front of one face of the waveguiding layer, and grating couplers.

52. A method for the simultaneous or sequential, qualitative and/or quantitative detection of one or more second nucleic acids in one or more samples, wherein said samples and if necessary further reagents are brought into contact with an immobilization surface according to claim 8, on which surface one or several first nucleic acids are immobilized as recognition elements for the specific binding/hybridization with said second nucleic acids, and changes in optical or electronic signals resulting from the binding/hybridization with these second nucleic acids or of further tracer substances used for analyte detection are measured.

53. A method according to claim 52, wherein the immobilization surface is arranged on an optical waveguide which is preferably essentially planar, wherein one or more samples with second nucleic acids to be detected therein and, if necessary further tracer reagents, are brought sequentially or in a single addition step after mixture with said tracer reagents, into contact with said first nucleic acids immobilized as recognition elements on said immobilization surface, and wherein the excitation light from one or more light sources is in-coupled into the optical waveguide using one or more optical coupling elements from the group comprising prism couplers, evanescent couplers with combined optical waveguides with overlapping evanescent fields, butt-end couplers with focusing lenses, preferably cylinder lenses, arranged in front of one face of the waveguiding layer, and grating couplers.

54. A method for the simultaneous or sequential, qualitative and/or quantitative detection of one or more second nucleic acids in one or more samples, wherein said samples and if necessary further reagents are brought into contact with an immobilization surface according to claim 9, on which surface one or several first nucleic acids are immobilized as recognition elements for the specific binding/hybridization with said second nucleic acids, and changes in optical or electronic signals resulting from the binding/hybridization with these second nucleic acids or of further tracer substances used for analyte detection are measured.

55. A method according to claim 54, wherein the immobilization surface is arranged on an optical waveguide which is preferably essentially planar, wherein one or more samples with second nucleic acids to be detected therein and, if necessary further tracer reagents, are brought sequentially or in a single addition step after mixture with said tracer reagents, into contact with said first nucleic acids immobilized as recognition elements on said immobilization surface, and wherein the excitation light from one or more light sources is in-coupled into the optical waveguide using one or more optical coupling elements from the group comprising prism couplers, evanescent couplers with combined optical waveguides with overlapping evanescent fields, butt-end couplers with focusing lenses, preferably cylinder lenses, arranged in front of one face of the waveguiding layer, and grating couplers.

56. Use of a method according to claim 22 for quantitative or qualitative analyses in screening methods in pharmaceutical research, clinical and pre-clinical development, for real-time binding studies and the determination of kinetic parameters in affinity screening and in research, for qualitative and quantitative analyte determinations, especially for DNA and RNA analytics and for the determination of genomic or proteomic differences in the genome, such as single nucleotide polymorphisms, for the measurement of protein-DNA interactions, for the determination of control mechanisms for mRNA expression and for protein (bio)synthesis, for the generation of toxicity studies and the determination of expression profiles, especially for the determination of biological and chemical marker compounds, such as mRNA, pathogens or bacteria in pharmaceutical product research and development, human and veterinary diagnostics, agrochemical product research and development, for symptomatic and pre-symptomatic plant diagnostics, for patient stratification in pharmaceutical product development and for therapeutic drug selection, for the determination of pathogens, nocuous agents and germs, especially of salmonella, prions, viruses and bacteria, especially in food and environmental analytics.