WO2009040444A1 - Rna isolation method - Google Patents
Rna isolation method Download PDFInfo
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- WO2009040444A1 WO2009040444A1 PCT/EP2008/063039 EP2008063039W WO2009040444A1 WO 2009040444 A1 WO2009040444 A1 WO 2009040444A1 EP 2008063039 W EP2008063039 W EP 2008063039W WO 2009040444 A1 WO2009040444 A1 WO 2009040444A1
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- solid phase
- rna
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- salt
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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
-
- 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
Definitions
- the present invention relates to a method for isolating RNA from a biological sample, kits therefore, to purification of the isolated RNA, to the use of automated magnetic separation apparatus in the method and provision to the apparatus of data comprising instructions for operating steps of the method.
- This invention is of great importance in the fields of molecular biology, biochemistry, gene technology, medicine, veterinary medicine and all related fields.
- DNA and RNA have core functions in the control of biological processes.
- genetic information is stored as DNA, which is a stable, double-stranded polynucleotide. Expression of the genetic information stored in DNA is accomplished by transcription of RNA from a DNA template, followed by translation of the RNA-encoded information into protein.
- RNA purification methods have often comprised isolating DNA and RNA together from biological sources. Typically these methods have utilized phenol or a mixture of phenol and chloroform in a manor that denatures and precipitates proteins while leaving nucleic acids in solution. These methods are hazardous, laborious and of limited utility for isolation of RNA from biological sources containing high amounts of ribonuclease (RNAse), an extremely stable enzyme that degrades RNA.
- RNAse ribonuclease
- Cells are first lysed then the cellular proteins are salted out by dehydration and precipitation with a saturated salt solution.
- the DNA is subsequently precipitated out from the supernatant using alcohols.
- RNA typically incorporate techniques to disrupt or lyse cells and protect RNA from degradation by endogenous RNases. Lysis liberates RNA along with DNA and protein from which the RNA must then be separated.
- Another method for isolating nucleic acids is disclosed in U.S. Pat. No. 6,355,792.
- the method comprises acidifying a liquid sample with a buffer having a pH less than 6.5 and contacting the acidic solution with an inorganic oxide material having hydroxyl groups, separating the solid material with bound nucleic acids on it from the liquid, and eluting with alkaline solution having a pH between 7.5 and 11.
- WO00/66783 discloses a method of extracting nucleic acids from a sample in the absence of a lysis step by contacting a sample containing a nucleic acid at a pH of less than 7, with a water-soluble, weakly basic polymer to form a water-insoluble precipitate of the weakly basic polymer and the nucleic acids, separating the precipitate from the sample, and contacting the precipitate with a base to raise the solution pH to greater than 7, thereby releasing the nucleic acids from the weakly basic polymer.
- U.S. Pat. No. 5,973,137 to Heath discloses a method for isolating substantially undegraded RNA from a biological sample by carefully treating (not mixing more than 3 times) the sample with a cell lysis reagent consisting of an anionic detergent, a chelating agent and a buffer solution having a pH less than 6.
- the role of the anionic detergent is said to lyse cells and/or solubilize proteins and lipids as well as to denature proteins.
- red blood cells are first lysed with a reagent containing NH 4 Cl, NaHCO 3 and EDTA, the white blood cells are separated and separately lysed in the presence of a protein-DNA precipitation reagent.
- the latter is typically a high concentration of a sodium or potassium salt such as acetate or chloride.
- the supernatant containing RNA is precipitated by addition of a lower alcohol.
- U.S. Pat. No. 5,973,138 discloses a method for the reversible binding of DNA and RNA to a suspension of paramagnetic particles in acidic solution.
- the paramagnetic particles disclosed therein are bare iron oxide, iron sulfide or iron chloride.
- the acidic solution is said to enhance the electropositive nature of the iron portion of the particles and thereby promote binding to the electronegative phosphate groups of the nucleic acids.
- U.S. Pat. No. 6,433,160 discloses a similar method wherein the acidic solution contains glycine HCl.
- U.S. Pat. No. 6,737,235 to Cros et al. discloses a method for isolating nucleic acids using particles comprising or coated with a hydrophilic, cross-linked polyacrylamide polymer containing cationic groups. Cationic groups are formed by protonation at low pH of amine groups on the polymer. Nucleic acids are bound in a low ionic strength buffer at low pH and released in a higher ionic strength buffer.
- GB 2419594 Al discloses the stabilization of nucleic acids with amino surfactants and optionally with nonionic surfactants
- Cationic detergents are preferred stabilizing agents in U.S. Pat. Nos. 6,602,718; 6,617,170; and 6,821,789; and US Patent Application Publ. 2005/0153292 disclose.
- the cationic detergent is said to preserve RNA and/or DNA by inhibiting or blocking gene induction or nucleic acid degradation.
- the gene induction blocking agent can comprise a stabilizing agent and an acidic substance. The latter agents lyse cells and cause precipitation of nucleic acids as a complex with the detergent.
- compositions and methods for stabilizing nucleic acids comprising alcohols and/or ketones in admixture with dimethyl sulfoxide have been disclosed (U.S. Pat. No. 6,916,608B2).
- the stabilization of the RNA content of cells can be effected by adding a solution of a salt such as ammonium sulfate at a pH between 4 and 8 (U.S. Pat. Nos. 6,204,375 and 6,528,641).
- the salt solution is said to permeate cells and causes precipitation of RNA along with cellular protein and renders the RNA inaccessible to nucleases which might otherwise degrade it.
- the present invention provides a method for isolating RNA from a biological sample, which comprises:
- step (ii) which favours precipitation of DNA and protein enables a relatively simple means for isolating RNA from contaminants typically found in biological samples.
- step (iv) which favours precipitation of RNA enables a relatively simple means for isolating RNA from contaminants typically found in biological samples.
- the present invention is applicable to a variety of starting materials which may contain a mixture of biological substances such as proteins, carbohydrates, lipids and nucleic acids.
- biological samples include complex mixtures of these components and may comprise prokaryotic or eukaryotic cells including cultured cells, cellular inclusions such as mitochondria, viruses, protozoa, fungi, other microbes, and fresh or preserved tissue samples.
- Biological samples also include biological fluids, for example blood and cerebrospinal fluid.
- step (i) of the method according to the invention the biological sample is treated with a lysis solution to form a lysate.
- the primary aim of this step is to release the RNA from its biological environment, where it may be bound to other components, so as to form a lysate comprising an RNA-containing liquid phase.
- RNA-containing liquid phase For example, in cells, it would be necessary to disrupt the cell membrane and any lipid, protein, carbohydrate and DNA associated with the RNA. In certain viruses, it would be necessary to disrupt the viral coat protein.
- the RNA is desirably released into the liquid phase, preferably in solution. Precipitation of RNA at this point in the method is preferably completely avoided.
- a detergent is used to treat the sample at a pH of at least 6, preferably at least 6.5, more preferably at least pH 7.0 and preferably no more than pH 9.5, more preferably no more than pH 8.5.
- the detergent used in the lysis solution may be ionic or non-ionic and is preferably an anionic detergent.
- a particularly preferred detergent is a dodecyl sulphate, such as sodium dodecyl sulphate (SDS).
- SDS sodium dodecyl sulphate
- the lysis solution may be buffered and may include components such as metal ion chelators such as ethylenedi amine tetraacetic acid (EDTA) or ethylene glycol tetraacetic acid (EGTA). However, no components should be included which are likely to precipitate RNA. High lower alcohol contents such as 70% ethanol or 50% isopropanol would precipitate most or all of the RNA.
- the lysis solution is substantially free of alcohols. It is further preferred that the lysis solution is substantially free of chaotropic salts.
- step (ii) the lysate is contacted with a first solid phase bearing a positive charge in the presence of a salt so as to precipitate DNA and protein.
- Conditions may be selected so as to precipitate DNA and protein selectively without substantial precipitation of RNA. This enables subsequent removal of the solid phase without substantial removal of the RNA target material.
- a positively charged solid phase is used and such solid phases include positively charged or electropositive surfaces such as positively functionalised silica, positively functionalised silanol, positively functionalised metal oxides, positively functionalised vinyl polymers, such as polyvinyl alcohol, and other positively charged polymeric surfaces.
- An aminated surface is particularly preferred because it binds well to DNA without substantial RNA removal.
- the first solid phase comprises polyvinyl alcohol functionalised with amine groups.
- the first solid phase comprises iron oxide functionalised with amine groups.
- the positively functionalised solid phase may comprise chitosan, a naturally occurring polysaccharide comprising amine groups, or other naturally occurring polymers which bear positively-charged groups.
- the solid phase is positively charged at the pH at which the lysate is contacted.
- the lysate and first solid phase are contacted in the presence of a salt so as to precipitate DNA and protein from the RNA-containing liquid phase.
- a salt so as to precipitate DNA and protein from the RNA-containing liquid phase.
- organic and inorganic salts may be used in this step, preferably monovalent salts.
- Sodium salts, potassium salts and ammonium salts have been found to be particularly useful, especially ammonium salts such as ammonium acetate.
- the concentration of salt must be sufficient to precipitate the DNA and protein and a concentration of at least 1 molar is preferred. It may be necessary to contact the lysate with the first solid phase for a period from 10 seconds to 20 minutes to achieve precipitation. Typically proteins and genomic or high molecular weight DNA will precipitate in this step onto the solid surface of the first solid phase.
- the inventors understand that the DNA and protein bind to the solid phase in the form of a protein-DNA complex, such as for example chromatin.
- the form which the first solid phase takes will depend upon the apparatus to be used to perform the method of the invention.
- the solid phase may take the form of a filter, column, non-magnetic particles, or magnetic particles such as a ferrimagnetic or paramagnetic particles.
- Magnetic particles may be used in a magnetic separation apparatus, which may be an automated magnetic separation apparatus, as discussed in further detail below.
- the RNA-containing liquid phase is separated from the solid phase.
- separation may be effected by any conventional means.
- separation may be effected by centrifugation or pressure/vacuum or gravity in the case of columns; pressure/vacuum in the case of filters; centrifugation or gravity in the case of non-magnetic particles; and magnetic separation in the case of magnetic particles.
- step (iv) the RNA-containing liquid phase is contacted with a non-ionic solid phase in the presence of a lower alcohol to precipitate RNA onto the non-ionic solid phase to form an RNA-containing solid phase. It is preferred that conditions are selected so as to precipitate RNA selectively without substantial precipitation of any residual DNA in the RNA-containing liquid phase. This enables subsequent isolation of the RNA-containing solid phase with contaminants remaining in the liquid phase.
- a non-ionic solid phase is used in this step because a positively charged surface binds little RNA or DNA under these conditions and a negatively-charged surface binds both RNA and DNA.
- the nucleic acid that binds thereto in the presence of a lower alcohol comprising ethanol or propanol consists of RNA; RNA binds preferably to DNA.
- the non-ionic solid phase preferably comprises a non-ionic surface, which is preferably a surface with polar or non-polar non-ionic functional groups. Particularly preferred surfaces are those which comprise functional groups of the hydroxyl or ether type. A preferred surface comprising ether groups is an epoxy surface.
- the step of contacting the RNA-containing liquid phase with a non-ionic solid phase takes place in the presence of a lower alcohol comprising ethanol or propanol.
- concentration of the lower alcohol is preferably sufficient to precipitate the RNA onto the non-ionic solid phase without substantial precipitation of DNA.
- a preferred amount of ethanol used in this step is in the range of from 1 to 2.5 vol/vol RNA- containing liquid phase. If propanol is used in this step, this is preferably isopropanol, although n-propanol could be used.
- a preferred amount of isopropanol is in the range of 0.5 to 1 vol/vol RNA-containing liquid phase.
- the non- ionic solid phase may be in the form of a filter, column, non-magnetic particle or magnetic particle such as a ferrimagnetic or paramagnetic particle. Again, the choice of solid phase will depend upon the apparatus used to perform the method.
- step (v) the RNA-containing solid phase is separated from the liquid phase.
- step (v) is also conventional and will depend upon the form of the non-ionic solid phase. For example, separation may be effected by centrifugation or pressure/vacuum or gravity in the case of columns; pressure/vacuum in the case of filters; centrifugation or gravity in the case of non-magnetic particles; and magnetic separation in the case of magnetic particles.
- the step may comprise one or more steps of washing the RNA-containing solid phase and a step of eluting RNA from the RNA-containing solid phase.
- a first washing solution comprising 70% ethanol or 50% isopropanol is applied to the RNA-containing solid phase from step (v) in a first washing step.
- a second washing buffer is applied, which comprises a mixture of a chaotropic salt and a lower alcohol such as ethanol or isopropanol, typically at a concentration of 20 to 40%.
- the RNA may be eluted from the solid phase into an elution solution containing low salt concentrations.
- 0.1 to 10 mM Tris-HCl may be used at a slightly alkaline pH e.g. pH 8.0 or, alternatively, water.
- the first solid phase and the second, non-ionic solid phase both comprise magnetic particles and at least steps (ii) to (vi) are performed on an automated magnetic separation apparatus.
- the automated magnetic separation apparatus may include a computer which processes data comprising instructions for operating steps of the method, such as at least steps (ii) to (vi).
- One type of magnetic separation apparatus is disclosed, for example, in GB 0717452.7, filed on 7 1 September 2007 by the present applicants. This and similar apparatus typically includes an automated pipette head assembly movable within the apparatus so that it may be aligned with test tubes or vials for reagent liquid handling.
- a step of magnetic separation may be performed using a magnetic rod which is also movable within the apparatus for alignment with test tubes or vials.
- Alignment steps and steps of liquid aspiration and liquid dispensing may all be controlled by a computer such as a micro computer which is linked to or forms part of the automated magnetic separation apparatus.
- Data comprising instructions for operating steps of the present method may be processed by the computer.
- the data may be provided to the computer from a removable data carrier such as a compact disc or through a communications network from a remote computer.
- the remote computer may be a server which may be linked to the computer through the internet thereby allowing data comprising the instructions to be downloaded for use by the apparatus.
- the present invention provides a remote computer or a removable data carrier, configured to provide data comprising instructions for operating steps of the method as described herein.
- the present invention provides a kit for use in the method as described herein.
- the kit comprises the following components:
- a lysis solution comprising a detergent at a pH of greater than 6 for forming from a biological sample a lysate comprising an RNA-containing liquid phase;
- a lower alcohol comprising ethanol or propanol for precipitating RNA onto the non-ionic solid phase to form an RNA-containing solid phase
- each component of the kit may be supplied in a separate container.
- components of the kit may be supplied in a manner to be used with appropriate apparatus.
- the kit is supplied with solid phases in the form of magnetic particles.
- the components may be supplied in a plurality of containers forming a cartridge for use in the apparatus.
- the lysis solution may be supplied in a separate container, if required.
- cartridges are made of disposable plastics and the user of the apparatus uses one cartridge for each biological sample.
- non-ionic solid phase comprises magnetic particles
- they may be supplied together with the lower alcohol in the same container.
- first solid phase and salt solution may be supplied together in the same container where the first solid phase comprises magnetic particles.
- combining a solid phase with its associated solution allows the solid phase and solution to be aspirated together from an individual container.
- FIGURE 1 shows the results of agarose gel electrophoresis on samples to compare solid phase ability to precipitate DNA
- FIGURE 2 shows the results of agarose gel electrophoresis on samples to compare solid phase ability to precipitate RNA
- FIGURE 3 shows the results of agarose gel electrophoresis on samples to compare aminated solid phase ability to precipitate DNA.
- Figure 1 shows a gel following the experimental procedure.
- the preparations that have been subjected to electrophoresis have been through all of the steps of the complete isolation method. They have therefore been through the non-ionic precipitation step (iv) that shows preference for RNA as well. All samples have been treated in the same way except for the different beads in the salt precipitation.
- the results demonstrate that some solid phases can selectively remove more DNA than others at the salt precipitation step.
- the negatively charged carboxylated beads do not remove as much DNA at the salt precipitation step (ii) as the positively-charged aminated beads do.
- RNA precipitation step (iv) has a specificity that depends on the surface of the solid phase.
- Figure 2 shows a gel following the experimental procedure.
- the preparations that have been subjected to electrophoresis have been through all of the steps of the complete isolation method. They have therefore been through the salt precipitation step (ii) that removes some of the DNA. All samples have been treated in the same way except for the different beads in the RNA precipitation step (iv).
- Lanes 3, 4 and 5 correspond respectively to RNA preparations obtained in the above procedure in which the RNA precipitation step used: carboxylated beads (3), unfunctionalised PVA beads (4) and aminated beads (5).
- the results demonstrate that solid phases can exhibit specificity for RNA: the unfunctionalized beads yield RNA without contaminating DNA being detectable on the gel.
- This example relates to a preferred embodiment of the invention.
- Optical Density (OD) at 260 nm and 280nm wavelength was measured using a Perkin Elmer Lambda spectrophotometer. A ratio of approximately 2.1 between OD at 260 nm and at 280 nm is an indication of pure RNA
- Ct values were obtained using an Applied Bio systems 7300 with Hs_ACTB_SG_l QuantiTect Primer Assay and Quantitect SYBR Green RT- PCR Kit, one step, both kits from QIAGEN NV according to the manufacturer's instructions.
- Ct is the number of PCR cycles necessary to produce a threshold level of product.
- Delta Ct is the difference in Ct between a reaction based on RNA and DNA in the isolate. The data in Table 1 indicate that there is a 16 000 fold excess of RNA templates compared to DNA templates in the isolations.
- Test bead 1 amine functionalized PVA
- Test bead 2 amine functionalized iron oxide
- Test bead 3 chitosan beads
- Test bead 4 negative control (bead that does not bind DNA) Mix 10 cycles, leave alone for 5 min
- Figure 3 shows the results of the agarose gel electrophoresis.
- Table 1 Average data from 8 samples
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Abstract
Description
Claims
Priority Applications (1)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
GB1006994A GB2466419B (en) | 2007-09-28 | 2008-09-29 | RNA isolation method |
Applications Claiming Priority (2)
Application Number | Priority Date | Filing Date | Title |
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GB0719022.6 | 2007-09-28 | ||
GBGB0719022.6A GB0719022D0 (en) | 2007-09-28 | 2007-09-28 | Isolation method |
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WO2009040444A1 true WO2009040444A1 (en) | 2009-04-02 |
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Family Applications (1)
Application Number | Title | Priority Date | Filing Date |
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PCT/EP2008/063039 WO2009040444A1 (en) | 2007-09-28 | 2008-09-29 | Rna isolation method |
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GB (2) | GB0719022D0 (en) |
WO (1) | WO2009040444A1 (en) |
Cited By (3)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
EP2391725A1 (en) * | 2009-01-30 | 2011-12-07 | The United States Of America, As Represented By The Secretary, Department of Health and Human Services | Methods and systems for purifying transferring and/or manipulating nucleic acids |
WO2014019966A1 (en) | 2012-08-02 | 2014-02-06 | bioMérieux | Functionalisation methods and reagents used in such methods using an azaisatoic anhydride or one of the derivatives of same, biological molecules thereby treated, and kits |
EP3135769A1 (en) * | 2015-08-26 | 2017-03-01 | Qiagen GmbH | Kits and methods for extracting rna |
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WO2003033739A1 (en) * | 2001-10-12 | 2003-04-24 | Gentra Systems, Inc. | Compositions and methods for using a solid support to purify rna |
WO2003046146A2 (en) * | 2001-11-28 | 2003-06-05 | Applera Corporation | Compositions and methods of selective nucleic acid isolation |
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2007
- 2007-09-28 GB GBGB0719022.6A patent/GB0719022D0/en not_active Ceased
-
2008
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- 2008-09-29 WO PCT/EP2008/063039 patent/WO2009040444A1/en active Application Filing
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US5681946A (en) * | 1990-02-13 | 1997-10-28 | Amersham International Plc | Precipitating polymers |
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WO2003033739A1 (en) * | 2001-10-12 | 2003-04-24 | Gentra Systems, Inc. | Compositions and methods for using a solid support to purify rna |
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EP2391725A1 (en) * | 2009-01-30 | 2011-12-07 | The United States Of America, As Represented By The Secretary, Department of Health and Human Services | Methods and systems for purifying transferring and/or manipulating nucleic acids |
EP2391725A4 (en) * | 2009-01-30 | 2013-01-02 | Us Health | Methods and systems for purifying transferring and/or manipulating nucleic acids |
WO2014019966A1 (en) | 2012-08-02 | 2014-02-06 | bioMérieux | Functionalisation methods and reagents used in such methods using an azaisatoic anhydride or one of the derivatives of same, biological molecules thereby treated, and kits |
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EP3135769A1 (en) * | 2015-08-26 | 2017-03-01 | Qiagen GmbH | Kits and methods for extracting rna |
Also Published As
Publication number | Publication date |
---|---|
GB201006994D0 (en) | 2010-06-09 |
GB2466419A (en) | 2010-06-23 |
GB0719022D0 (en) | 2007-11-07 |
GB2466419B (en) | 2011-04-13 |
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