EP1281072A2 - Procede et dispositif pour la separation de biopolymeres marques - Google Patents

Procede et dispositif pour la separation de biopolymeres marques

Info

Publication number
EP1281072A2
EP1281072A2 EP01945120A EP01945120A EP1281072A2 EP 1281072 A2 EP1281072 A2 EP 1281072A2 EP 01945120 A EP01945120 A EP 01945120A EP 01945120 A EP01945120 A EP 01945120A EP 1281072 A2 EP1281072 A2 EP 1281072A2
Authority
EP
European Patent Office
Prior art keywords
microcapillaries
takes place
biopolymers
separation
gel matrix
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP01945120A
Other languages
German (de)
English (en)
Inventor
Rudolf Rigler
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Gnothis Holding SA
Original Assignee
Gnothis Holding SA
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Gnothis Holding SA filed Critical Gnothis Holding SA
Publication of EP1281072A2 publication Critical patent/EP1281072A2/fr
Withdrawn legal-status Critical Current

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869—Methods for sequencing

Definitions

  • the invention relates to a method and a device for the detection of labeled biopolymers, in particular nucleic acid fragments in a gel matrix, a parallel separation taking place in a multiplicity of microcapillaries filled with a gel matrix.
  • labeled DNA molecules are modified chemically in a base-specific manner, partial strand termination is effected, the fragments thus obtained are separated according to size and the sequence is determined on the basis of the label.
  • the object underlying the present invention was to provide a method for the separation of labeled biopolymers and in particular labeled nucleic acid fragments, in which the disadvantages of the prior art are at least partially eliminated, and which in particular enables parallel separation and detection of a large number of traces.
  • This object is achieved by a method for the separation of labeled biopolymers in a gel matrix, the method being characterized in that a parallel separation takes place in a multiplicity of microcapillaries filled with a gel matrix.
  • the method according to the invention enables the separation of labeled biopolymers, for example nucleic acid fragments, in particular DNA or RNA molecules, but also other biopolymers such as peptides, proteins, saccharides.
  • the method is particularly preferably used for the separation of nucleic acid fragment mixtures of different lengths, as they arise in a sequencing reaction.
  • the gel matrix is preferably separated according to the size and / or charge of the biopolymers.
  • non-radioactive labeling groups and particularly preferably labeling groups detectable by optical methods are suitable as labels for the biopolymers.
  • suitable fluorescent labeling groups are rhodamine, Texas red, phycoerythrin, fluorescein or other fluorescent dyes customary in sequencing technology.
  • the labeled biopolymers are separated in parallel in a large number of microcapillaries, it being possible for the microcapillaries to be integrated in a compact body, for example a plate or a block. At least 10 3 microcapillaries and particularly preferably at least 10 5 microcapillaries, for example about 10 6 microcapillaries, are preferably used.
  • the microcapillaries preferably have an essentially identical diameter, which can be in the range from preferably 0.5 ⁇ m to 10 ⁇ m and particularly preferably from 1 ⁇ m to 5 ⁇ m. Furthermore, the microcapillaries preferably have an essentially identical length, which can be in the range from 5 mm or longer, preferably from 5 mm to 200 mm and particularly preferably from 5 mm to 100 mm, and is therefore considerably smaller than in conventional sequencing gels.
  • microcapillaries Suitable arrangements which contain a sufficient number of microcapillaries are, for example, microchannel plates made of glass, such as are used as photomultipliers in night vision detectors. These microchannel plates can be filled with a solution forming the gel matrix by capillary forces. Gel formation can take place within the capillaries after filling.
  • the gel matrix is particularly preferably a denaturing polyacrylamide gel, e.g. Polyacrylamide urea gel.
  • the biopolymers are separated in the microcapillaries of the gel matrix by electrophoretic and / or electroosmotic methods, an electric field being applied, for example, between both ends of the microchannel plate. Due to the short length of the microcapillaries, the separation in the gel matrix can be carried out using a considerably lower voltage than with conventional sequencing gels, e.g. are in the range from 10 to 100 V.
  • the separation method according to the invention takes place in combination with automatic sample application with position addressing of the individual samples.
  • corresponding inkjet or micropipetting devices can be used, with which the approaches to be separated in the respective microcapillaries, e.g. B.
  • a nucleic acid sequencing reaction can be applied to individual openings of the microchannel plate.
  • a sample volume of 10 "12 to 10 " 6 I is applied per microchannel.
  • the method according to the invention preferably further comprises an automatic position-specific detection of the nucleic acid fragments separated in the microchannels.
  • This position-specific detection can include confocal and / or time-resolved detection.
  • the fluorescent markers can be excited via an optical dot matrix, for example a dot matrix of laser dots generated by diffractive optics or a quantum well laser.
  • a confocal detector matrix can be used, which can be an arrangement of fiber-coupled avalanche photodiodes or an avalanche photodiode matrix.
  • an electronic detector matrix for example a CCD camera, can be used, with which a time-resolved detection is made possible.
  • the method according to the invention enables the parallel evaluation of up to more than 1 0 6 , for example 10 7 individual channels.
  • the detection can be carried out according to the method of fluorescence correlation spectroscopy (FCS) described in European Patent 0 679 251.
  • FCS fluorescence correlation spectroscopy
  • This method preferably comprises the measurement of one or a few sample molecules in a measurement volume, the concentration of the molecules to be determined being ⁇ 1 0 '6 mol / l and the measurement volume preferably being ⁇ 1 0 "14 I.
  • the measurement volume preferably is made to the disclosure of European patent 0 679 251. O 01/85990
  • the detection can also be carried out by a time-resolved decay measurement, a so-called time gating, as described, for example, by Rigler et al: Picosecond Single Photon Fluorescence Spectroscopy of Nucleic Acids, in: "Ultrafast Phenomena", D.H. Auston, ed. Springer 1 984.
  • the fluorescence molecules are excited within a measurement volume and then - preferably at a time interval of> 100 ps - the detection interval is opened at the photodetector. In this way, background signals generated by Raman effects can be kept sufficiently low to enable essentially interference-free detection.
  • Another object of the invention is a device for separating labeled nucleic acid fragments by size, comprising (a) a plurality of microcapillaries filled with a gel matrix, (b) means for automatic sample application into the microcapillaries
  • the device can furthermore comprise automatic manipulation devices for positioning microchannel plates in automatic sequencing devices, heating or cooling devices such as Peltier elements in order to maintain a substantially constant temperature, reservoirs and optionally supply lines for sample liquids and reagents as well as electronic evaluation devices.
  • automatic manipulation devices for positioning microchannel plates in automatic sequencing devices, heating or cooling devices such as Peltier elements in order to maintain a substantially constant temperature, reservoirs and optionally supply lines for sample liquids and reagents as well as electronic evaluation devices.
  • the method according to the invention and the device according to the invention can be used for all electrophoretic or electroosmotic methods, for example for the resolution of products of a nucleic acid sequencing reaction, for the analysis of protein fragments or for genome, transcriptome or proteome analysis.
  • the present invention is further to be illustrated by the following figures and examples. Show it:
  • Figure 1 is a schematic representation of a device suitable for performing the method according to the invention.
  • the device contains a microchannel plate (2) with approximately 10 6 microchannels (4) for the separation of nucleic acid fragments.
  • the device also contains an inkjet device (6) for automatic sample application into individual microcapillaries with position addressing and an automatic position-specific detector (8) with which labeled nucleic acids which have passed through the microcapillaries can be detected. The migration of the nucleic acids takes place in an electrical field (from minus to plus).
  • Figure 2 shows a cross section through a microchannel plate.
  • Microchannels (4) are provided with a gel matrix, e.g. filled with a polyacrylamide / 6 M urea gel.

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • Physics & Mathematics (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Analytical Chemistry (AREA)
  • Immunology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Saccharide Compounds (AREA)

Abstract

L'invention concerne un procédé et un dispositif pour la détection de biopolymères marqués, notamment de fragments d'acide nucléique dans une matrice de gel. Selon l'invention, une séparation parallèle a lieu dans une multitude de microcapillaires remplis d'une matrice de gel.
EP01945120A 2000-05-12 2001-05-11 Procede et dispositif pour la separation de biopolymeres marques Withdrawn EP1281072A2 (fr)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
DE10023422A DE10023422A1 (de) 2000-05-12 2000-05-12 Verfahren und Vorrichtung zur Auftrennung von markierten Biopolymeren
DE10023422 2000-05-12
PCT/EP2001/005409 WO2001085990A2 (fr) 2000-05-12 2001-05-11 Procede et dispositif pour la separation de biopolymeres marques

Publications (1)

Publication Number Publication Date
EP1281072A2 true EP1281072A2 (fr) 2003-02-05

Family

ID=7641877

Family Applications (1)

Application Number Title Priority Date Filing Date
EP01945120A Withdrawn EP1281072A2 (fr) 2000-05-12 2001-05-11 Procede et dispositif pour la separation de biopolymeres marques

Country Status (5)

Country Link
US (1) US20030150728A1 (fr)
EP (1) EP1281072A2 (fr)
AU (1) AU2001267429A1 (fr)
DE (1) DE10023422A1 (fr)
WO (1) WO2001085990A2 (fr)

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2000008451A1 (fr) * 1998-08-07 2000-02-17 The Regents Of The University Of California Systeme et procede de localisation optique des positions de microcanaux

Family Cites Families (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5122248A (en) * 1990-05-18 1992-06-16 Northeastern University Pulsed field capillary electrophoresis
US5080771A (en) * 1990-10-26 1992-01-14 Indiana University Foundation Capillary gels formed by spatially progressive polymerization using migrating initiator
DE4301005A1 (de) * 1993-01-18 1994-07-21 Diagen Inst Molekularbio Verfahren und Vorrichtung zur Bewertung der Fitness von Biopolymeren
JP4000605B2 (ja) * 1996-07-24 2007-10-31 株式会社日立製作所 Ｄｎａ試料調整装置及びこれを用いる電気泳動分析装置
EP0854362A3 (fr) * 1997-01-16 2000-12-20 Japan Science and Technology Corporation Appareil d'électrophorèse à capillaires multiples
JP2001517789A (ja) * 1997-09-19 2001-10-09 アクレイラ バイオサイエンシズ，インコーポレイティド 液体移送装置および液体移送方法
DE19830989C1 (de) * 1998-07-10 2000-04-13 Lion Bioscience Ag Verwendung von porösen Membranmaterialien als Beladungsmaterialien bei der Gelelektrophorese

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2000008451A1 (fr) * 1998-08-07 2000-02-17 The Regents Of The University Of California Systeme et procede de localisation optique des positions de microcanaux

Also Published As

Publication number Publication date
WO2001085990A2 (fr) 2001-11-15
US20030150728A1 (en) 2003-08-14
DE10023422A1 (de) 2001-11-15
AU2001267429A1 (en) 2001-11-20
WO2001085990A3 (fr) 2002-05-23

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