EP1268769A2 - Procede d'extraction d'acides nucleiques - Google Patents
Procede d'extraction d'acides nucleiquesInfo
- Publication number
- EP1268769A2 EP1268769A2 EP01936163A EP01936163A EP1268769A2 EP 1268769 A2 EP1268769 A2 EP 1268769A2 EP 01936163 A EP01936163 A EP 01936163A EP 01936163 A EP01936163 A EP 01936163A EP 1268769 A2 EP1268769 A2 EP 1268769A2
- Authority
- EP
- European Patent Office
- Prior art keywords
- oligonucleotide
- nucleic acid
- linker
- anchor
- linker oligonucleotide
- 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- Withdrawn
Links
Classifications
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
- C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
- C12N15/1003—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor
- C12N15/1006—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor by means of a solid support carrier, e.g. particles, polymers
- C12N15/1013—Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor by means of a solid support carrier, e.g. particles, polymers by using magnetic beads
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
- C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
- C12N15/1096—Processes for the isolation, preparation or purification of DNA or RNA cDNA Synthesis; Subtracted cDNA library construction, e.g. RT, RT-PCR
Definitions
- the present invention relates to a nucleic acid complex with an anchor oligonucleotide, any nucleic acid or any oligonucleotide and a linker oligonucleotide, a nucleic acid or oligonucleotide hybridization product and a method for producing and separating nucleic acids or oligonucleotides after their synthesis using the nucleic acid complex according to the invention.
- the invention further relates to a device which makes it possible to extract, purify, rewrite, rewrite and re-purify RNA from homogenized tissue or cells in a combined and automatable one-tube reaction.
- the analysis of gene expression requires the extraction, purification and labeling of the mRNA.
- the labeling of the mRNA is often carried out via the step of cDNA synthesis, since labeled nucleotides can be inserted here.
- the process of mRNA isolation includes the selective extraction of the RNA from the mixture of the materials present in a cell or in tissue (lipids, proteins, saccharides, DNA, RNA, low-molecular substances) and the subsequent enrichment of the mRNA from the mixture of tRNA, rRNA, snRNA and mRNA with the help of oligo (dT) nucleic acids, which are bound to a column (affinity chromatography) or to (magnetic) spherical particles (batch process).
- oligo (dT) nucleic acids which are bound to a column (affinity chromatography) or to (magnetic) spherical particles (batch process).
- the mRNA is then eluted from the oligo (dT) and subjected to further enzymatic reactions separately therefrom, or is still enzymatically converted to oligo (dT) (and a solid phase).
- the RT reaction for the production of the cDNAs is an enzymatic reaction which can also be carried out in the presence of the oligo (dT) and a solid phase coupled to it.
- the synthesized cDNA cannot easily be separated from the solid phase, since the oligo (dT) s serve as primers and the cDNA is thus ultimately covalently bound to the solid phase. Another It is therefore not possible to use the cDNA, which requires this to be separated from the solid phase.
- WO-A-98/31838 relates to a method for identifying gene expression patterns in mRNA populations.
- the method is useful for determining differential gene expressions in different cells or tissues, including cells or tissues of target organisms. Methods are disclosed for determining the frequency of gene expression in mRNA populations, whereby a method for comparing the frequency of gene expression of different cells or tissues becomes available. Also described is a method for isolating genes that were identified using so-called tag sequences according to the method described there. The sequences can be used to diagnose certain diseases.
- WO-A-95/13368 relates to the isolation of a nucleic acid from a sample.
- the sample is boiled and then cooled.
- the nucleic acids are condensed on a solid support.
- the method is used to prepare nucleic acids for subsequent amplification.
- the method can be used in the isolation of nucleic acids from aged, fixed or otherwise treated samples.
- WO-A-97/10363 relates to the Serial Analysis of Gene Expression (SAGE), a method for the rapid, quantitative and qualitative analysis of transcripts. Short, defined sequences that correspond to expressed genes are isolated and analyzed. The sequencing of over 1000 defined tags in a short time results in a gene expression pattern that is characteristic of the function of a cell or a tissue. The SAGE method is useful as a tool for identifying and isolating new tag sequences that correspond to new transcripts and genes.
- SAGE Serial Analysis of Gene Expression
- the technical problem on which the invention is based is to provide a simple and reliable method and means for carrying out the method in order to avoid the disadvantages described above.
- the object is achieved by a nucleic acid complex with an anchor oligonucleotide, any nucleic acid or any oligonucleotide as well as a linker oligonucleotide, the linker oligonucleotide being partially hybridized with the anchor oligonucleotide and partially with the arbitrary nucleic acid or any oligonucleotide and the anchor oligonucleotide with its 3 ⁇ -T is immobilized on a carrier.
- the anchor oligonucleotide is immobilized on a support.
- the linker oligonucleotide has a sequence which allows hybridization both with the anchor oligonucleotide and with a further nucleic acid or a further oligonucleotide.
- the sequence of the linker oligonucleotide must therefore be chosen so that it matches the sequence of the further nucleic acid / the further oligonucleotide. If, for example, cDNA is to be obtained from mRNA (poly (A + ) RNA), the linker oligonucleotide has a poly (dT) part.
- a carrier preferably a bead
- a linker oligonucleotide is bound via an anchor oligonucleotide in such a way that a poly (dT) part is present.
- MRNA is now attached to this poly (dT) part, and the linker oligonucleotide is lengthened by a polymerase reaction by means of a conventional RT reaction - if appropriate with the incorporation of labeled nucleotides.
- the mRNA can then be destroyed, for example by RNaseH or NaOH, and the linker oligonucleotide extended by the cDNA can be cleaved off by increasing the temperature, if necessary by changing the buffer.
- the method can also be used to synthesize any nucleic acid (with an at least partially known sequence). This is it required that the linker oligonucleotide again has a sequence that partially overlaps with the target molecule. Then a nucleic acid complementary to the target nucleic acid can be synthesized on the linker oligonucleotide, possibly with the incorporation of labeled nucleotides. The nucleic acid can then be split off as a double strand (with a single strand end) and processed further.
- Such a method is useful, for example, for the direct, non-PCR-amplified production of cDNA libraries with selectively enriched cDNA molecules in accordance with the selected sequence of the linker oligonucleotide, by ligating the isolated and double-stranded cDNAs directly into a suitably prepared cloning vector ,
- z. B a temperature of 35 ° C to 85 ° C, preferably 45 ° C to 65 ° C, for annealing of anchor oligonucleotide and linker oligonucleotide.
- the hybridizing region of anchor and linker oligonucleotide in the nucleic acid complex according to the invention preferably has a ratio of the nucleotides GC: AT of 20:80 to 80:20.
- annealing between anchor oligonucleotide and linker oligonucleotide is preferably carried out at a higher temperature than between linker oligonucleotide and any nucleic acid or oligonucleotide.
- the nucleic acid complex according to the invention has the anchor oligonucleotide covalently bound or immobilized on the support via an affinity group.
- the present invention also relates to a nucleic acid or oligonucleotide hybridization product comprising an anchor oligonucleotide and a linker oligonucleotide, the linker oligonucleotide being partially hybridized with the anchor oligonucleotide and the anchor oligonucleotide with the 3'- Term can be immobilized on a carrier.
- the anchor oligonucleotide and the linker oligonucleotide which can be immobilized on the support with the 3'-terminus, can be sold in the form of a kit, optionally together with other components for carrying out the method according to the invention.
- the invention also relates to a method for producing and separating nucleic acids or oligonucleotides after their synthesis using an embodiment of the nucleic acid complex according to the invention. The following steps are carried out:
- the target nucleic acid is preferably mRNA.
- the target nucleic acid can be degraded by RnaseH or NaOH, in particular before the extended linker oligonucleotide is split off.
- the invention allows a temporary non-covalent binding of the cDNA to the solid phase, which can be split off by a simple heat step. This means that all reactions required for the isolation, purification, marking and renewed cleaning of the finished probe can be carried out on the solid phase (FIG. 2).
- the implementation on the solid phase in turn enables simple automation of the complete process (FIG. 3).
- the invention is illustrated by the following examples. The method according to the invention was used to produce fluorescence-labeled cDNA starting from total RNA. Dynabeads M-280 streptavidin (DYNAL) was used as the solid phase.
- the conventional labeling was carried out as follows: incorporation of fluorescence-labeled Cy3 nucleotides in solution during a reverse transcriptase reaction (Superscript II (GIBCO) starting from purified mRNA which was isolated from the same total RNA as was used for the other probe, Subsequent cleavage of the mRNA by RnaseH treatment and purification of the labeled cDNA over silica membranes (Qiaquick, QIAGEN) On the basis of the Cy3 / Cy5 signal ratio of the individual cDNAs immobilized on the array, it was possible to make a statement about the quality of the labeling method according to the invention compared to the conventional one Marking procedures are carried out as follows:
- biotin anchor and linker were adjusted to a concentration of 350 ng / ⁇ l in RNase-free, double-distilled water.
- a concentration of 350 ng / ⁇ l in RNase-free, double-distilled water In a 0.2 ml Eppendorf reaction vessel, 9.1 ⁇ l biotin anchor (400 pmol; 8000 pg / pmol), 15.6 ⁇ l linker (400 pmol; 13647 pg / pmol) and 25 ⁇ l of a solution of 10 mM Tris-HCl, pH 7.5; 1 mM EDTA and 2 M NaCI combined and incubated for 2 min at 95 ° C, 10 min at 65 ° C, 10 min at 37 ° C and 20 min at RT.
- 0.2 mM EDTA and 50 ⁇ l of the anchor-linker hybrids obtained under a) were added and incubated for 15 min at RT with occasional shaking.
- Using the magnetic stand provided for this purpose (DYNAL), twice with a solution of 10 mM Tris-HCl, pH 7.5; 1 mM EDTA and 2 M NaCl and then resuspended in 200 ⁇ l of a solution of 20 mM Tris-HCl, pH 7.5, 1 M LiCI, 2 mM EDTA.
- RNA 100 ⁇ g of total RNA were heated to 65 ° C. in 100 ⁇ l of H 2 O for 2 min and then added to the derivatized beads obtained from c) and freed from the solution.
- the reaction vessel was at RT for 5 min shaken, placed in the magnetic stand for 5 min and then the beads washed twice with 200 ⁇ l of a solution of 10 mM Tris-HCl, pH 7.5, 0.15 M LiCl, 1 mM EDTA.
- the isolated mRNA was washed once with a solution of 3 mM Tris-HCl (pH7.5), 0.2 mM EDTA and 2 with 1 x RT buffer (GIBCO). 21 ⁇ l H 2 O, 8 ⁇ l 5 ⁇ First Strand Buffer (GIBCO), low C dNTPs (10 mM dATP, 10 mM dGTP, 10 mM dTTP; 4 mM dCTP) (GIBCO), 2 ⁇ l FluoroLink TM were placed in an Eppendorf reaction vessel Cy3 / 5-dCTP (Amersham Pharmacia), 4 ⁇ l 0.1 M DTT and 1 ⁇ l Rnasin (20-40 u) (PROMEGA) combined and shaken briefly.
- the isolated mRNA was resuspended with this solution, incubated for 5 min at 42 ° C., provided with 1 ⁇ l (200 U) Superscript II (SSII, GIBCO), incubated for 30 min with constant shaking at 37 ° C., again with 1 ⁇ l SSII and shaken again at 37 ° C for 30 min.
- 0.5 ul RNAseH (GIBCO) was added and incubated at 37 ° C for 20 min.
- both the Cy3 and the Cy5-labeled probe are to be produced in the manner according to the invention, then both labeling reactions could now be given together and processed further together.
- the two labeling approaches were worked up separately from one another.
- the probe produced by the method according to the invention was washed twice with 400 ⁇ l 10 mM Tris-HCl pH 7.5, resuspended in 10 ⁇ l 10 mM Tris-HCl pH 7.5, incubated for 2 min at 65 ° C. and immediately placed in the magenta stand.
- the supernatant was transferred to a new Eppendorf reaction vessel.
- the beads were resuspended in 10 ⁇ l of 10 mM Tris-HCl pH 7.5, incubated for 2 min at 65 ° C. and the The supernatant was again transferred to the new Eppendorf reaction vessel.
- the combined supernatants were combined with the Cy3 probe labeled in a conventional manner, evaporated to 20 ⁇ l, provided with 5 ⁇ l of a hybridization solution and applied to a pre-hybridized cDNA array.
- the cDNA array was hybridized overnight and then washed with suitable solutions, dried and read out with a laser scanning device.
- the images (Cy3 and Cy5) obtained at different wavelengths are shown in FIG. 5.
- the evaluation of the relative signal intensities showed that, starting from the same amount of total RNA, the probe labeled by the method according to the invention gave an average 2.2 times stronger signals than the conventionally labeled probe, FIG. 6.
- the evaluation further showed that after Comparison of the absolute signal intensities with a constant normalization factor, which was calculated from the median of the signal quotients of all signal quotients, none of the array elements hybridized on the cDNA array gave a signal quotient of> ⁇ 2, FIG. 7.
- the variance is not greater than at the comparison of two probes that were labeled differently from the same RNA using the conventional method using different fluorophores and hybridized on the same array.
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- Health & Medical Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Genetics & Genomics (AREA)
- Chemical & Material Sciences (AREA)
- Engineering & Computer Science (AREA)
- Biomedical Technology (AREA)
- Organic Chemistry (AREA)
- Zoology (AREA)
- Wood Science & Technology (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Biotechnology (AREA)
- General Engineering & Computer Science (AREA)
- Molecular Biology (AREA)
- Plant Pathology (AREA)
- Biophysics (AREA)
- Microbiology (AREA)
- Physics & Mathematics (AREA)
- Crystallography & Structural Chemistry (AREA)
- Biochemistry (AREA)
- General Health & Medical Sciences (AREA)
- Bioinformatics & Computational Biology (AREA)
- Analytical Chemistry (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
- Peptides Or Proteins (AREA)
- Saccharide Compounds (AREA)
Abstract
L'invention concerne un complexe d'acides nucléiques comprenant un nucléotide d'ancrage, un acide nucléique quelconque ou un oligonucléotide quelconque et un acide nucléique de liaison. La séquence de liaison est partiellement hybridée avec le nucléotide d'ancrage et partiellement avec l'acide nucléique quelconque ou avec l'oligonucléotide quelconque, et le nucléotide d'ancrage est immobilisé par son extrémité 3' sur un support.
Priority Applications (1)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
EP01936163A EP1268769A2 (fr) | 2000-03-31 | 2001-03-30 | Procede d'extraction d'acides nucleiques |
Applications Claiming Priority (6)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
DE10016138 | 2000-03-31 | ||
DE10016138 | 2000-03-31 | ||
EP00109297 | 2000-04-29 | ||
EP00109297 | 2000-04-29 | ||
PCT/EP2001/003669 WO2001072998A2 (fr) | 2000-03-31 | 2001-03-30 | Procede d'extraction d'acides nucleiques |
EP01936163A EP1268769A2 (fr) | 2000-03-31 | 2001-03-30 | Procede d'extraction d'acides nucleiques |
Publications (1)
Publication Number | Publication Date |
---|---|
EP1268769A2 true EP1268769A2 (fr) | 2003-01-02 |
Family
ID=26005130
Family Applications (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
EP01936163A Withdrawn EP1268769A2 (fr) | 2000-03-31 | 2001-03-30 | Procede d'extraction d'acides nucleiques |
Country Status (5)
Country | Link |
---|---|
US (2) | US20040142324A1 (fr) |
EP (1) | EP1268769A2 (fr) |
JP (1) | JP2003530094A (fr) |
AU (1) | AU2001262152A1 (fr) |
WO (1) | WO2001072998A2 (fr) |
Families Citing this family (8)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
JP2006158276A (ja) * | 2004-12-06 | 2006-06-22 | Institute Of Physical & Chemical Research | Dnaコンジュゲート、dnaコンジュゲートの作製方法、及びdna検出方法 |
US20070072223A1 (en) * | 2005-09-16 | 2007-03-29 | Primera Biosystems, Inc. | Compositions and methods for purifying nucleic acids |
US8383338B2 (en) * | 2006-04-24 | 2013-02-26 | Roche Nimblegen, Inc. | Methods and systems for uniform enrichment of genomic regions |
US9340416B2 (en) * | 2008-08-13 | 2016-05-17 | California Institute Of Technology | Polynucleotides and related nanoassemblies, structures, arrangements, methods and systems |
KR101230913B1 (ko) * | 2009-11-06 | 2013-02-07 | 중앙대학교 산학협력단 | 나노입자-기반된 유전자 운반체 |
EP3313334A1 (fr) | 2015-06-29 | 2018-05-02 | The Procter and Gamble Company | Pessaire associé à un applicateur |
KR101949371B1 (ko) * | 2015-10-07 | 2019-02-18 | 주식회사 엘지화학 | 내후성 열가소성 수지, 이를 포함하는 열가소성 수지 조성물 및 이 조성물을 제조하는 방법 |
GB201607817D0 (en) * | 2016-05-04 | 2016-06-15 | Univ Leiden | Methods |
Family Cites Families (6)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
US6022714A (en) * | 1985-05-02 | 2000-02-08 | Genetics Institute | Methods for attachment of a polynucleotide to a preselected material |
GB9323305D0 (en) * | 1993-11-11 | 1994-01-05 | Medinnova Sf | Isoaltion of nucleic acid |
US5866330A (en) * | 1995-09-12 | 1999-02-02 | The Johns Hopkins University School Of Medicine | Method for serial analysis of gene expression |
US5837466A (en) * | 1996-12-16 | 1998-11-17 | Vysis, Inc. | Devices and methods for detecting nucleic acid analytes in samples |
US5968784A (en) * | 1997-01-15 | 1999-10-19 | Chugai Pharmaceutical Co., Ltd. | Method for analyzing quantitative expression of genes |
CA2377468C (fr) * | 1999-07-27 | 2010-04-20 | Phylos, Inc. | Methodes de ligature d'un accepteur de peptide |
-
2001
- 2001-03-30 AU AU2001262152A patent/AU2001262152A1/en not_active Abandoned
- 2001-03-30 WO PCT/EP2001/003669 patent/WO2001072998A2/fr active Application Filing
- 2001-03-30 US US10/239,195 patent/US20040142324A1/en not_active Abandoned
- 2001-03-30 JP JP2001570715A patent/JP2003530094A/ja active Pending
- 2001-03-30 EP EP01936163A patent/EP1268769A2/fr not_active Withdrawn
-
2006
- 2006-11-16 US US11/600,326 patent/US20080009614A1/en not_active Abandoned
Non-Patent Citations (1)
Title |
---|
See references of WO0172998A2 * |
Also Published As
Publication number | Publication date |
---|---|
WO2001072998A3 (fr) | 2002-01-24 |
AU2001262152A1 (en) | 2001-10-08 |
WO2001072998A2 (fr) | 2001-10-04 |
JP2003530094A (ja) | 2003-10-14 |
US20080009614A1 (en) | 2008-01-10 |
US20040142324A1 (en) | 2004-07-22 |
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