Sequencing on perforated membranes

• US 20050130159A1
• Filed: 12/18/2002
• Published: 06/16/2005
• Est. Priority Date: 12/19/2001
• Status: Abandoned Application

• Current Assignee: Gnothis Holding SA
• Original Assignee: Gnothis Holding SA
• Inventors: Rigler, Rudolf, Vogel, Horst
• Application Number:
  US10/503,562
• Publication Number:
  US 20050130159A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/34 involving hydrolase
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2521/319 Exonuclease
• CPC Class Codes: C12Q 2563/107 fluorescence
• CPC Class Codes: C12Q 2565/137 Chromatographic separation
• CPC Class Codes: C12Q 2565/625 being a nucleic acid test strip device, e.g. dipsticks, strips, tapes, CD plates

Abstract

The invention concerns a method and device for sequencing nucleic acid molecules on a perforated membrane. The invention can be used in particular for multiplex sequencing.

Claims

1-26. -26. (canceled)

27. A method for sequencing nucleic acids comprising the steps:

(a) providing a nucleic acid molecule to be sequenced which contains a plurality of flourescence-labelling groups,

(b) proving a membrane structure through which at least one channel extends having a suitable diameter for the passage of single nucleic acid molecules, wherein an enzyme which catalyses the cleavage of single nucleotide building blocks from a nucleic acid molecule is immobilized on the membrane structure,

(c) passing the nucleic acid molecule to be sequenced into and/or through the channel under conditions that allow successive cleavage of single nucleotide building blocks from the nucleic acid molecule and

(d) determining the base sequence of the nucleic acid molecule by fluorescence measurement.

28. The method as claimed in claim 27, wherein the nucleic acid molecule to be sequenced is present in a single-stranded form.

29. The method as claimed in claim 27, wherein the nucleic acid molecule to be sequenced is present in a double-stranded form wherein labelled nucleotide building blocks can only be cleaved from a single strand.

30. The method as claimed in claim 27, wherein the nucleic molecules are labelled in such a manner that at least 50% of all nucleotide building blocks of one base type carry a fluorescence-labelling group.

31. The method as claimed in claim 30, wherein essentially all nucleotide building blocks of one base type carry a fluorescence-labelling group.

32. The method as claimed in claim 27, wherein the membrane structure comprises one or more of metals, semimetals, metal oxides, glass, quartz, plastics and composite materials.

33. The method as claimed in claim 27, wherein the channel has a diameter of 10-100 nm.

34. The method as claimed in claim 27, wherein the membrane structure comprises a first layer having a first channel which has a diameter that is adequate for the passage of several nucleic acid molecules, and a second layer having a second channel which has a suitable diameter for the passage of single nucleic acid molecules.

35. The method as claimed in claim 27, wherein the enzyme comprises an exonuclease.

36. The method as claimed in claim 34, wherein the enzyme is selected from the group consisting of T7 DNA polymerase, E. coli exonuclease I and E. coli exonuclease III.

37. The method as claimed in claim 27, wherein step (c) comprises a hydrodynamic or/and an electroosmotic flow through the channel.

38. The method as claimed in claim 27, wherein step (c) comprises applying an electric field across the membrane.

39. The method as claimed in claim 27, wherein the enzyme is immobilized on the membrane structure in the area of the outlet port of the channel.

40. The method as claimed in claim 27, wherein the base sequence is determined on the basis of the time-dependent change in the fluorescence of the nucleic acid molecule or/and of the cleaved nucleotide building blocks caused by the cleavage of nucleotide building blocks.

41. The method as claimed in claim 27, wherein a plurality of nucleic acid molecules to be sequenced are passed into respective separate channels of the membrane structure and the base sequence of this plurality of nucleic acid molecules is determined simultaneously.

42. The method as claimed in claim 41, wherein the simultaneous determination of the base sequence of a plurality of nucleic acid molecules comprises a multipoint fluorescence excitation by a laser.

43. The method as claimed in claim 41, wherein the simultaneous determination of the base sequence of a plurality of nucleic acid molecules comprises a detection of the fluorescence emission of a plurality of nucleic acid strands by a detection matrix.

44. The method as claimed in claim 43, wherein a CCD camera or an avalanche photodiode matrix is used.

45. The method as claimed in claim 41, wherein fluorescence excitation and detection is carried out in parallel on all examined nucleic acid strands.

46. The method as claimed in claim 41, wherein fluorescence excitation and detection are carried out in several steps in each case on a portion of the examined nucleic acid strands using a submatrix of laser points and detectors.

47. The method as claimed in claim 27, wherein the fluorescence-labelling groups are at least partially quenched when they are incorporated into the nucleic acid strands and the fluorescence intensity is increased after cleavage.

48. A carrier for sequencing nucleic acids, comprising:

a membrane structure through which a channel extends which has a diameter suitable for the passage of single nucleic acid molecules, an enzyme which catalyses cleavage of single nucleotide building blocks from a nucleic acid molecule being immobilized on the membrane structure.

49. The carrier as claimed in claim 48, wherein the channel has a diameter of 10-100 nm.

50. The carrier as claimed in claim 48, wherein the membrane structure has a plurality of channels for the concurrent sequencing of a plurality of nucleic acids.

51. A device for sequencing nucleic acids comprising:

(a) a carrier as claimed in claim 48,

(b) means for passing the nucleic acid molecules to be sequenced through the channels of the carrier and

(c) means for simultaneously determining the base sequence of a plurality of nucleic acid molecules on the basis of the time-dependent change in the fluorescence of the nucleic acid molecules or/and of the cleaved nucleotide building blocks caused by the cleavage of nucleotide building blocks.