WO2010015835A1 - Isolation of nucleic acid - Google Patents

Isolation of nucleic acid Download PDF

Info

Publication number
WO2010015835A1
WO2010015835A1 PCT/GB2009/001951 GB2009001951W WO2010015835A1 WO 2010015835 A1 WO2010015835 A1 WO 2010015835A1 GB 2009001951 W GB2009001951 W GB 2009001951W WO 2010015835 A1 WO2010015835 A1 WO 2010015835A1
Authority
WO
WIPO (PCT)
Prior art keywords
nucleic acid
buffer
solution
solid phase
buffering range
Prior art date
Application number
PCT/GB2009/001951
Other languages
French (fr)
Inventor
Yii Leng Chua
Allyson Victoria Ritchie
Original Assignee
Diagnostics For The Real World, Limited
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
Family has litigation
First worldwide family litigation filed litigation Critical https://patents.darts-ip.com/?family=39790526&utm_source=google_patent&utm_medium=platform_link&utm_campaign=public_patent_search&patent=WO2010015835(A1) "Global patent litigation dataset” by Darts-ip is licensed under a Creative Commons Attribution 4.0 International License.
Application filed by Diagnostics For The Real World, Limited filed Critical Diagnostics For The Real World, Limited
Priority to EP09784897.2A priority Critical patent/EP2329019B1/en
Priority to US13/057,947 priority patent/US9422543B2/en
Priority to ES09784897.2T priority patent/ES2469816T3/en
Priority to AU2009278915A priority patent/AU2009278915B2/en
Priority to JP2011521638A priority patent/JP6125752B2/en
Publication of WO2010015835A1 publication Critical patent/WO2010015835A1/en
Priority to US15/207,091 priority patent/US20170037394A1/en

Links

Classifications

    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/10Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1003Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor
    • C12N15/1006Extracting 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
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/10Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1003Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor

Definitions

  • This invention relates to improved methods for isolation of nucleic acid, and to soiutions, compositions, and kits for use in the methods.
  • chaotropic agents such as guanidinium thiocyanate
  • organic solvents to iyse cells
  • denature proteins including nucleases, which would otherwise degrade the nucleic acid.
  • Boom et al. describes a method in which a sample containing human serum or urine is contacted with si ⁇ ca particles in the presence of a lysis/binding buffer containing guanidinium thiocyanate.
  • nucleic acid binds to the silica particles, which are then washed with a wash buffer containing guanidinium thiocyanate, then with ethanol, and then acetone.
  • the bound nucleic acid is subsequently eluted in an aqueous low salt buffer (Tris- HCI, EDTA, pH 8.0).
  • a disadvantage of such methods is that chaotropic agents and organic solvents are highly inhibitory to enzymatic reactions. Residual amounts of these substances carried over into the eiuted sample can interfere with subsequent enzymatic processing of the isolated nucleic acid, for example in nucleic acid sequencing or amplification.
  • Use of chaotropic agents and organic solvents is also undesirable because these reagents are toxic and difficult to handle, and require special provision for their disposal.
  • a further disadvantage of use of chaotropic agents is that they are required in high molarities and tend to precipitate out of solution during storage, especially refrigerated storage. Solutions containing these agents may require heating to re-dissolve the chaotropic agent before use.
  • Plasma sample is mixed with magnetic silica particles in the presence of a lysis/binding buffer containing a kosmotropic salt (ammonium sulphate) before addition of proteinase K.
  • a kosmotropic salt ammonium sulphate
  • the magnetic particles are washed with wash buffer containing proteinase K, and eluted in elution buffer (Tris-HCI, pH 8.5) at 80 0 C.
  • Tris-HCI Tris-HCI, pH 8.5
  • a method for isolating a nucleic acid which comprises:
  • wash solution comprises a buffer with a buffering range that encompasses a pH that is higher than the first pH, and the wash solution is at a pH that is within a buffering range of the binding buffer but lower than the buffering range of the buffer of the wash solution (i.e. the wash buffer).
  • methods of the invention provide surprising increases in the yield of nucleic acid obtained compared with prior art methods, for example the method described by Hourfar et al. It is believed that the improved yield obtained using methods of the invention is due to reduced amounts of nucleic acid being removed from the solid phase during the washing step, and/or increased amounts of nucleic acid being released from the solid phase during the elution step, compared with prior art methods.
  • the first pH is an acidic pH, preferably in the range pH 3-6, or pH 3-5.
  • the second pH is at least pH 6.5, preferably at least pH 7.0, or an alkaline pH.
  • the second pH is in the range pH 6.5-10, preferably pH 7-9, Such pH values are typical of those used with solid phases such as silica-based solid phases that are able to bind nucleic acid at a lower pH and release nucleic acid at a higher pH. Extremes of pH are avoided which might otherwise damage the nucleic acid.
  • the buffering range of the wash buffer is higher than the first pH (i.e. a lower end of the buffering range of the wash buffer is greater than the first pH).
  • the buffering range of the wash buffer is higher than pH 5.0.
  • the second pH is within the buffering range of the wash buffer. This is preferred because it is believed that the pH of residual wash solution present on the solid phase after the washing step may then be converted most efficiently to the second pH during the elution step thereby maximising the amount of nucleic acid that is released from the solid phase.
  • the pH of the wash solution is pH 6.3 or less, preferably pH 6.0 or less, more preferably from pH 3.0 to pH 6.0.
  • Use of wash solution at a pH within these preferred ranges is compatible with buffer ranges of preferred binding and wash buffers.
  • the first pH is within the buffering range of the binding buffer so that the pH of the binding step is controlled by the binding buffer.
  • a lower end of the buffering range of the binding buffer is at pH 3.0 or higher so that extremes of pH are avoided in the binding step.
  • the buffering ranges of buffers commonly used in lysis, binding, washing, and elution buffers are known to those of skill in the art.
  • the pKa value and buffering range of some important biological buffers, sorted by buffering range, is given in Table 1 beiow (taken from Sigma-Aldrich).
  • Methods of the invention may be carried out using conventional binding buffers and/or elution buffers for use with a solid phase that is able to bind the nucleic acid in the presence of binding buffer at the first pH, and from which the nucleic acid can be eiuted at the second pH.
  • the solid phase preferably comprises an ionisable group, which changes charge according to the ambient conditions.
  • the pKa of the ionisable group is appropriate to the conditions at which it is desired to bind nucleic acid to and release nucleic acid from the solid phase.
  • nucleic acid will bind to the solid phase at a pH below or roughly equal to the pKa, and will be released at a higher pH (usually above the pKa).
  • Suitable solid phases for binding a nucleic acid at a first pH, and elution of bound nucleic acid at a second pH that is higher than the first pH are well known to those of ordinary skill in the art.
  • the solid phase may comprise a positive charge, and at the second pH the solid phase may have a less positive, neutral, or negative charge.
  • the solid phase may comprise a neutral or less negative charge, and at the second pH the solid phase may have a negative or more negative charge.
  • the solid phase may comprise a negatively ionisable group with a pKa between the first and second pH. Nucleic acid will bind to the solid phase when the solid phase is neutral or less negatively charged, and wiil be released when the solid phase is negatively or more negatively charged.
  • the solid phase may comprise a positively ionisable group with a pKa between the first and second pH. Nucleic acid will bind to the solid phase when the solid phase is positively charged, and will be released when the solid phase is neutral or less positively charged.
  • inorganic oxides such as silica or glass (for example, as described in Boom et al, or Hourfar et a!), or aluminium oxide, sugar polymers, or charge-switch materials (for example, as described in WO 02/48164).
  • the solid phase may be in any suitable form, for example comprising a membrane, gel, or particles, for example magnetic particles.
  • Silica membrane or gel, and magnetic siiica particles are preferred examples.
  • Silica membrane is particularly preferred. This is less expensive than magnetic silica particles (used for example by Hourfar, et al.) and does not require refrigerated storage, unlike magnetic silica particles.
  • binding of nucleic acid to the solid phase may be enhanced by the presence of a chaotropic agent, residual amounts of such agents inhibit enzymatic processing of the isolated nucleic acid and are toxic, so it is preferred that methods of the invention are carried out in the absence of a chaotropic agent.
  • the solid phase is a solid phase to which binding of nucleic acid is enhanced by the presence of a kosmotropic agent.
  • binding of the nucleic acid to the solid phase is carried out in the presence of a kosmotropic agent.
  • a kosmotropic agent Such agents are known to enhance binding of nucleic acid to solid phases such as silica- based solid phases.
  • chaotropic and kosmotropic agent originate from the Hofmeister series (Cacace ef a/., Q Rev Biophys 1997;30:241-77), which divides these agents depending on their influence on the structure of macromolecules and water.
  • a chaotrope may be defined as a substance that breaks solvent structure, and a kosmotrope as a substance that enhances solvent structure.
  • Figure 1 of Cacace etal shows the Hofmeister series and commonly occurring organic solutes with effects on protein structure/function.
  • Examples of chaotropic agents are known to those in the art, and include sodium iodide, sodium perchlorate, guanidinium thiocyanate and guanidinium hydrochloride.
  • kosmotropic agents are known to those in the art, and include ammonium sulphate and lithium chloride.
  • a method for isolating a nucleic acid from a cell which comprises lysing the cell to release the nucleic acid from the cell, and isolating the released nucleic acid using a method of the invention.
  • Lysis is preferably carried out using the binding buffer.
  • Binding buffers that may be used for cell iysis are known to those of ordinary skill in the art.
  • the lysis buffer used by Boom et al comprises guanidinium thiocyanate, Tris hydrochloride, pH 6.4, EDTA (adjusted to pH 8), and Triton X-100.
  • the lysis buffer does not include a chaotropic agent.
  • Preferred lysis/binding buffers for use according to the invention comprise a kosmotropic agent.
  • the buffer is an acidic buffer, suitably a strong acidic buffer with a pKa (25 0 C) in the range 3-5.
  • nucleic acid may be obtained by elution of the nucleic acid from the solid phase at a temperature above ambient temperature, for example 50- 90 0 C, 60"85 0 C, or 70-80 0 C.
  • the nucleic acid is eluted from the solid phase in the presence of an elution buffer.
  • the second pH is within a buffering range of the elution buffer so that the pH of elution is controlled by the elution buffer.
  • the buffering range of the elution buffer overlaps with, encompasses, or is encompassed by the buffering range of the wash buffer. This helps to ensure that the pH of residual wash solution on the solid phase after the washing step is readily increased towards the second pH during elution.
  • a solution comprising a buffer for washing a solid phase to which a nucleic acid is bound at a first pH and eiuted at a second, higher pH, wherein the pH of the solution is pH 6.3 or less, preferably pH 6.0 or less, more preferably from pH 3.0 to pH 6.0, and is lower than a buffering range of the buffer.
  • the solution of the invention does not include a chaotropic agent.
  • the solution does not include an organic solvent.
  • the or each buffering range of the buffer is higher than pH 5.0, preferably higher than pH 6.0, Preferably the buffering range of the buffer overlaps with, is encompassed by, or encompasses the range pH 6.5-10. In some preferred embodiments the buffering range of the buffer is higher than pH 7.0.
  • the pH of a solution of the invention is pH 5.0 or less, preferably from pH 3.5 to 5.
  • Examples of preferred buffers for the wash solution or solution of the invention include a Tris buffer, preferably Tris-HCI, and a 2-(f ⁇ l-morpho!ino)ethanesulfonic acid (MES) buffer.
  • the buffering range for Tris-HCI buffer is pH 7.1 to 9.
  • the buffering range for MES buffer is pH 5.5-6.7.
  • compositions in dry form that when dissolved in a liquid provides a solution according to the invention.
  • the composition may be a iyophilisate.
  • Such compositions can be prepared, for example, by providing a solution of the invention and lyophilising the solution to form the composition in dry form.
  • the wash solution or solution of the invention further comprises a detergent Detergent may assist in removing inhibitors that may interfere with subsequent processing of the isolated nucleic acid.
  • a detergent Detergent may assist in removing inhibitors that may interfere with subsequent processing of the isolated nucleic acid.
  • ionic detergents such as lithium dodecyl sulphate (LDS), or non-ionic detergents such as NP-40 and Triton-X.
  • detergent will not be present in a dry composition of the invention. If it is desired to include a detergent in a solution prepared using a composition in dry form, this may be added after the composition has been dissolved in aqueous solution.
  • Improved yieid of nucleic acid may be obtained using methods of the invention even without inclusion of a protease in the wash solution.
  • the wash solution or solution of the invention does not include a protease.
  • kits for isolation of a nucleic acid which comprises:
  • a binding buffer for binding the nucleic acid to a solid phase at a first pH
  • wash solution that comprises a buffer with a buffering range that encompasses a phi that is higher than the first pH, wherein the wash solution is at a pH that is within a buffering range of the binding buffer but lower than the buffering range of the buffer of the wash solution;
  • a solution for eluting the nucleic acid from the solid phase wherein the solution is at a second pH that is higher than the first pH.
  • kits for isolation of a nucleic acid which comprises:
  • a binding buffer for binding the nucleic acid to a solid phase at a first pH
  • composition in dry form that when dissolved in a liquid provides a wash soiution that comprises a buffer with a buffering range that encompasses a pH that is higher than the first pH, wherein the wash solution Is at a pH that is within a buffering range of the binding buffer but lower than the buffering range of the buffer of the wash solution;
  • kits may be used to carry out a method of the invention.
  • the binding buffer may be provided as a solution or in dry form (for example as a lyophilisate) for dissolving in a liquid.
  • composition in dry form that when dissolved in a liquid provides a wash solution and/or the composition in dry form that when dissolved in a liquid provides an elution solution, may be a lyophilisate.
  • the lyophilisate may be prepared, for example, by providing the wash solution or the elution solution and lyophilising the solution to form the composition in dry form.
  • the liquid for dissolving the binding buffer, or a composition of the invention is suitably water, or an aqueous solution.
  • the wash solution of a kit of the invention is preferably a solution of the invention.
  • composition in dry form for providing the wash solution is preferably a composition of the invention.
  • the kit does not comprise a chaotropic agent, nor an organic solvent.
  • the binding buffer of the kit comprises a kosmotropic agent.
  • suitable kosmotropic agents include ammonium sulphate and lithium chloride. Ammonium sulphate is preferred.
  • a kit of the invention may further comprise a solid phase to which the nucleic acid is able to bind.
  • Suitable solid phases are discussed above.
  • a preferred solid phase comprises a negatively ionisabie group with a pKa between a first pH at which the nucleic acid is able to bind to the solid phase, and a second pH at which the nucleic acid can be eluted from the solid phase.
  • the solid phase comprises an inorganic oxide, preferably silica.
  • a kit of the invention may further comprise a protease for use with the binding buffer.
  • the protease is in lyophilised form, separate from the binding buffer ⁇ and separate from the other components of the kit).
  • a kit of the invention may include instructions for carrying out nucleic acid isolation using the components of the kit.
  • a kit of the invention may further comprise reagents required for amplification and/or detection of nucleic acid once isolated.
  • kits of the invention will typically be provided with the components of the kit (i.e. the binding buffer, the wash solution (or the composition in dry form that when dissolved in a liquid provides the wash solution), and (if present) the elution solution (or the composition in dry form that when dissolved in a liquid provides the elution solution) separately packaged, or stored in separate compartments of a container in which the kit is provided.
  • the components of the kit i.e. the binding buffer, the wash solution (or the composition in dry form that when dissolved in a liquid provides the wash solution), and (if present) the elution solution (or the composition in dry form that when dissolved in a liquid provides the elution solution) separately packaged, or stored in separate compartments of a container in which the kit is provided.
  • the wash buffer should remain close to the first pH when mixed with residual binding buffer retained on the solid phase, so that nucleic acid remains bound to the solid phase and is not washed away.
  • residual wash buffer should change towards the second pH when mixed with elution solution for effective release of nucleic acid from the solid phase.
  • the improved yield obtainable using methods of the invention arises because: (i) the wash solution does not remove significant amounts of nucleic acid from the solid phase during the washing step (because the pH of the washing solution is within the buffering range of the binding buffer); and (ii) the pH of residual wash buffer retained on the solid phase readily changes towards the second pH when mixed with elution solution (due to the buffering range of the wash buffer).
  • methods of the invention are capable of extracting as few as 25 copies of nucleic acid, in particular viral RNA, from a biological sample.
  • nucleic acid in particular viral RNA
  • the yield of nucieic acid obtained using methods of the invention is as good as, if not more reproducible, than that of a typical nucleic acid extraction method, which uses chaotropic salts and organic solvents.
  • Methods of the invention can be performed with buffer formulations that are non- hazardous and do not require special disposal, unlike some conventional nucleic acid extraction methods that use chaotropic salts and/or organic solvents.
  • the buffer formulations used are stable and do not require refrigeration or heating before use to re-dissolve components that have precipitated during storage.
  • the methods may be used in nucleic acid isolation and testing in hospitals and laboratories, and are especially important for on-site nucleic acid testing in the field and for point-of-care nucleic acid testing.
  • Figure 1 shows a comparison of yield of nucleic acid obtained using acidic and alkaline wash buffers at pH 4 and pH 5;
  • Figure 2 shows the effect of residual (ysis buffer on wash buffer pH, and the effect of residual wash buffer on eiution buffer pH;
  • Figure 3 shows a comparison of yield of nucleic acid obtained at different wash buffer pH ⁇ using wash buffer comprising MES).
  • Figure 4 shows the results of RNA recovery obtained using a method of the invention compared with a Qiagen method of nucleic acid isolation.
  • HIV viral RNA was isolated using an aqueous-based lysis buffer (comprising Tris Acetate, pH 4.0), bound to a silica-based solid phase and washed with wash buffers comprising 1OmM Tris-HCI (buffering range, pH 7.1 to 9), at pH 4 or 5, 1OmM sodium citrate (buffering range, pH 3.0 to 6.2), at pH 4 or 5, or 1 OmM Tris Acetate (buffering range, pH 3.6-5.6), at pH 4 or 5.
  • the 1OmM Tris-HCi solutions at pH 4 and 5 are embodiments of a solution of the invention.
  • Washed nucleic acid bound to the solid phase was eluted with eiution buffer (comprising Tris-HCI, pH 8.5).
  • eiution buffer comprising Tris-HCI, pH 8.5.
  • the isolated nucleic acid was amplified and detected.
  • Figure 1 shows the average detection signal strength, error bars indicate the standard error of the mean.
  • Figure 1 shows that the yield of nucleic acids obtained with 10 mM Tris-HCI, pH 4 and pH 5 was significantly higher than with 1OmM sodium citrate, pH 4 and 5, and with 1OmM Tris Acetate, pH 4 and 5. It is believed that the acidic wash buffers were not as effective as 10 mM Tris- HCI, pH 4 or 5, because residual buffer left on the solid phase lowers the pH of the elution buffer, making elution of nucleic acid less efficient and so reducing yield.
  • HIV viral RNA was isolated using an aqueous-based lysis buffer (comprising Tris Acetate, pH 4.0), bound to a silica-based solid phase and washed with 10mM MES (buffering range, pH 5.5 to 6.7), pH 4, 5 or 6. Nucleic acid was eiuted with elution buffer (1OmM Tris-HCI, pH 8.5). The isolated nucleic acid was amplified and detected.
  • Figure 3 shows the average detection signal strength, error bars indicate the standard error of the mean. The results show that the yield of nucleic acid obtained at pH 4 and 5 (lower than the buffering range of MES buffer) is significantly higher than at pH 6 (within the buffering range of MES buffer).
  • RNA recovery obtained using a method of the invention compared with a Qiaqen method of nucleic acid isolation.
  • Viral RNA was isolated from HIV positive plasma samples using a method of the invention, and a Qiagen method of nucleic acid isolation. The isolated nucleic acid was then amplified and detected.
  • Lysis buffer (comprising sodium citrate, pH 4.5) was mixed with a plasma sample and incubated before adding proteinase K. The mixture was incubated, then loaded onto a silica or glass fibre solid phase. Bound nucleic acid was washed with wash buffer (Tris-HCI, pH 3.8), and eluted with elution buffer (comprising Tris-HCI, 8.5) at 75- 8O 0 C.
  • Figure 4 shows the average signal strength
  • error bars show the standard error of the mean.
  • the results for the method according to an embodiment of the invention are shown by the black columns, and the results for the Qiagen method are shown by the white columns.
  • the results shown in Figure 4 demonstrate that methods of the invention are capable of extracting as few as 25 copies of nucleic acid, in particular viral RNA, from a biological sample.
  • the yield of nucleic acid obtained using the method according to an embodiment of the invention is as good as, if not more reproducible, than that of a typical nucleic acid extraction method, which uses chaotropic salts and organic solvents.
  • the buffer formulations used are non-hazardous and do not require special disposal, unlike some conventional nucleic acid extraction methods that use chaotropic salts and/or organic solvents.
  • the buffer formulations used are stable and do not require refrigeration.
  • the methods may be used in nucleic acid isolation and testing in hospitals and laboratories, and are especially important for on-site nucleic acid testing in the field and for point-of-care nucleic acid testing.

Landscapes

  • Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Biomedical Technology (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Genetics & Genomics (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)
  • Analytical Chemistry (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Preparation Of Compounds By Using Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)

Abstract

A method for isolating a nucleic acid comprises: binding the nucleic acid to a solid phase at a first pH in the presence of a binding buffer, washing the bound nucleic acid with a wash solution, and eluting the nucleic acid from the solid phase at a second pH which is higher than the first pH. The wash solution comprises a buffer with a buffering range that encompasses a pH that is higher than the first pH, and the wash solution is at a pH that is within a buffering range of the binding buffer but lower than the buffering range of the buffer of the wash solution. Solutions, compositions, and kits for use in the methods are described.

Description

isolation of Nucleic Acid
This invention relates to improved methods for isolation of nucleic acid, and to soiutions, compositions, and kits for use in the methods.
Conventionai methods for isolation of nucleic acid use chaotropic agents, such as guanidinium thiocyanate, and organic solvents to iyse cells, and denature proteins (including nucleases, which would otherwise degrade the nucleic acid). For example, Boom et al. (Journal of Clinical Microbiology, 1990, Vol. 28(3): 495-503) describes a method in which a sample containing human serum or urine is contacted with siϋca particles in the presence of a lysis/binding buffer containing guanidinium thiocyanate. Released nucleic acid binds to the silica particles, which are then washed with a wash buffer containing guanidinium thiocyanate, then with ethanol, and then acetone. The bound nucleic acid is subsequently eluted in an aqueous low salt buffer (Tris- HCI, EDTA, pH 8.0).
A disadvantage of such methods, however, is that chaotropic agents and organic solvents are highly inhibitory to enzymatic reactions. Residual amounts of these substances carried over into the eiuted sample can interfere with subsequent enzymatic processing of the isolated nucleic acid, for example in nucleic acid sequencing or amplification. Use of chaotropic agents and organic solvents is also undesirable because these reagents are toxic and difficult to handle, and require special provision for their disposal. A further disadvantage of use of chaotropic agents is that they are required in high molarities and tend to precipitate out of solution during storage, especially refrigerated storage. Solutions containing these agents may require heating to re-dissolve the chaotropic agent before use.
The requirement for chaotropic salts and organic solvents is avoided in a method described by Hourfar et al, (Clinical Chemistry, 2005, 51 (7): 1217-1222). Plasma sample is mixed with magnetic silica particles in the presence of a lysis/binding buffer containing a kosmotropic salt (ammonium sulphate) before addition of proteinase K. Following separation, the magnetic particles are washed with wash buffer containing proteinase K, and eluted in elution buffer (Tris-HCI, pH 8.5) at 800C. Whilst nucleic acid can be obtained in reasonable yields using such methods, it is desired to obtain even greater yield of nucleic acid. It is also desired to provide methods that can be carried out without any requirement for enzymes, such as proteinase K. Use of enzymes increases the cost of carrying out the methods, and it is necessary to store the enzymes separately under special conditions (for example, at reduced temperature, or in Iyophilised form) to maintain their stability.
According to the invention there is provided a method for isolating a nucleic acid, which comprises:
(i) binding the nucleic acid to a solid phase at a first pH in the presence of a binding buffer;
(ii) washing the bound nucleic acid with a wash solution; and
(iii) eluting the nucleic acid from the solid phase at a second pH which is higher than the first pH;
wherein the wash solution comprises a buffer with a buffering range that encompasses a pH that is higher than the first pH, and the wash solution is at a pH that is within a buffering range of the binding buffer but lower than the buffering range of the buffer of the wash solution (i.e. the wash buffer).
We have found that methods of the invention provide surprising increases in the yield of nucleic acid obtained compared with prior art methods, for example the method described by Hourfar et al. It is believed that the improved yield obtained using methods of the invention is due to reduced amounts of nucleic acid being removed from the solid phase during the washing step, and/or increased amounts of nucleic acid being released from the solid phase during the elution step, compared with prior art methods.
Improved yields of nucleic acid may be obtained using methods of the invention without any requirement for enzyme (such as protease) to be present in the wash solution, or for use of organic solvents or chaotropic agents. The wash solution is thereby simplified compared, for example, with the wash solution required for the method of Hourfar ef al, and there is no requirement for separate storage of protease or other enzyme. Because there is no requirement for chaotropic agents or organic solvents, inhibition of subsequent enzymatic processing of the isolated nucleic acid by such agents or solvents can be avoided. Preferably the first pH is an acidic pH, preferably in the range pH 3-6, or pH 3-5. Preferably the second pH is at least pH 6.5, preferably at least pH 7.0, or an alkaline pH. Suitably the second pH is in the range pH 6.5-10, preferably pH 7-9, Such pH values are typical of those used with solid phases such as silica-based solid phases that are able to bind nucleic acid at a lower pH and release nucleic acid at a higher pH. Extremes of pH are avoided which might otherwise damage the nucleic acid.
Preferably the buffering range of the wash buffer is higher than the first pH (i.e. a lower end of the buffering range of the wash buffer is greater than the first pH). Preferably the buffering range of the wash buffer is higher than pH 5.0. Preferably the second pH is within the buffering range of the wash buffer. This is preferred because it is believed that the pH of residual wash solution present on the solid phase after the washing step may then be converted most efficiently to the second pH during the elution step thereby maximising the amount of nucleic acid that is released from the solid phase.
Preferably the pH of the wash solution is pH 6.3 or less, preferably pH 6.0 or less, more preferably from pH 3.0 to pH 6.0. Use of wash solution at a pH within these preferred ranges is compatible with buffer ranges of preferred binding and wash buffers.
Preferably the first pH is within the buffering range of the binding buffer so that the pH of the binding step is controlled by the binding buffer. Preferably a lower end of the buffering range of the binding buffer is at pH 3.0 or higher so that extremes of pH are avoided in the binding step.
The buffering ranges of buffers commonly used in lysis, binding, washing, and elution buffers are known to those of skill in the art. The pKa value and buffering range of some important biological buffers, sorted by buffering range, is given in Table 1 beiow (taken from Sigma-Aldrich).
Table 1
Figure imgf000004_0001
Figure imgf000005_0001
Figure imgf000006_0001
Methods of the invention may be carried out using conventional binding buffers and/or elution buffers for use with a solid phase that is able to bind the nucleic acid in the presence of binding buffer at the first pH, and from which the nucleic acid can be eiuted at the second pH.
The solid phase preferably comprises an ionisable group, which changes charge according to the ambient conditions. The pKa of the ionisable group is appropriate to the conditions at which it is desired to bind nucleic acid to and release nucleic acid from the solid phase. Generally, nucleic acid will bind to the solid phase at a pH below or roughly equal to the pKa, and will be released at a higher pH (usually above the pKa). Suitable solid phases for binding a nucleic acid at a first pH, and elution of bound nucleic acid at a second pH that is higher than the first pH, are well known to those of ordinary skill in the art. For example, at the first pH the solid phase may comprise a positive charge, and at the second pH the solid phase may have a less positive, neutral, or negative charge. Alternatively or additionally, at the first pH the solid phase may comprise a neutral or less negative charge, and at the second pH the solid phase may have a negative or more negative charge. Such changes in charge aliow the nucleic acid to be adsorbed to the solid phase at the first pH, and released at the second pH.
For example, the solid phase may comprise a negatively ionisable group with a pKa between the first and second pH. Nucleic acid will bind to the solid phase when the solid phase is neutral or less negatively charged, and wiil be released when the solid phase is negatively or more negatively charged.
Alternatively, or additionally, the solid phase may comprise a positively ionisable group with a pKa between the first and second pH. Nucleic acid will bind to the solid phase when the solid phase is positively charged, and will be released when the solid phase is neutral or less positively charged.
Examples of solid phases that may be used in accordance with the invention include solid phases that comprise inorganic oxides, such as silica or glass (for example, as described in Boom et al, or Hourfar et a!), or aluminium oxide, sugar polymers, or charge-switch materials (for example, as described in WO 02/48164).
The solid phase may be in any suitable form, for example comprising a membrane, gel, or particles, for example magnetic particles. Silica membrane or gel, and magnetic siiica particles are preferred examples. Silica membrane is particularly preferred. This is less expensive than magnetic silica particles (used for example by Hourfar, et al.) and does not require refrigerated storage, unlike magnetic silica particles.
Whilst binding of nucleic acid to the solid phase may be enhanced by the presence of a chaotropic agent, residual amounts of such agents inhibit enzymatic processing of the isolated nucleic acid and are toxic, so it is preferred that methods of the invention are carried out in the absence of a chaotropic agent.
Preferably the solid phase is a solid phase to which binding of nucleic acid is enhanced by the presence of a kosmotropic agent. Preferably binding of the nucleic acid to the solid phase is carried out in the presence of a kosmotropic agent. Such agents are known to enhance binding of nucleic acid to solid phases such as silica- based solid phases.
The terms "chaotropic" and "kosmotropic" agent originate from the Hofmeister series (Cacace ef a/., Q Rev Biophys 1997;30:241-77), which divides these agents depending on their influence on the structure of macromolecules and water. A chaotrope may be defined as a substance that breaks solvent structure, and a kosmotrope as a substance that enhances solvent structure. Figure 1 of Cacace etal shows the Hofmeister series and commonly occurring organic solutes with effects on protein structure/function. Examples of chaotropic agents are known to those in the art, and include sodium iodide, sodium perchlorate, guanidinium thiocyanate and guanidinium hydrochloride. Examples of kosmotropic agents are known to those in the art, and include ammonium sulphate and lithium chloride.
According to the invention there is also provided a method for isolating a nucleic acid from a cell, which comprises lysing the cell to release the nucleic acid from the cell, and isolating the released nucleic acid using a method of the invention.
Lysis is preferably carried out using the binding buffer. Binding buffers that may be used for cell iysis are known to those of ordinary skill in the art. The lysis buffer used by Boom et al comprises guanidinium thiocyanate, Tris hydrochloride, pH 6.4, EDTA (adjusted to pH 8), and Triton X-100. However, it is preferred that the lysis buffer does not include a chaotropic agent. Preferred lysis/binding buffers for use according to the invention comprise a kosmotropic agent. Preferably the buffer is an acidic buffer, suitably a strong acidic buffer with a pKa (250C) in the range 3-5.
Further improved yield of nucleic acid may be obtained by elution of the nucleic acid from the solid phase at a temperature above ambient temperature, for example 50- 900C, 60"850C, or 70-800C.
Preferably the nucleic acid is eluted from the solid phase in the presence of an elution buffer. Preferably the second pH is within a buffering range of the elution buffer so that the pH of elution is controlled by the elution buffer.
In a preferred embodiment, the buffering range of the elution buffer overlaps with, encompasses, or is encompassed by the buffering range of the wash buffer. This helps to ensure that the pH of residual wash solution on the solid phase after the washing step is readily increased towards the second pH during elution.
There is further provided according to the invention a solution for use as a wash solution in a method of the invention,
According to the invention there is aiso provided a solution comprising a buffer for washing a solid phase to which a nucleic acid is bound at a first pH and eiuted at a second, higher pH, wherein the pH of the solution is pH 6.3 or less, preferably pH 6.0 or less, more preferably from pH 3.0 to pH 6.0, and is lower than a buffering range of the buffer.
Preferably the solution of the invention does not include a chaotropic agent. Preferably the solution does not include an organic solvent.
Preferably the or each buffering range of the buffer is higher than pH 5.0, preferably higher than pH 6.0, Preferably the buffering range of the buffer overlaps with, is encompassed by, or encompasses the range pH 6.5-10. In some preferred embodiments the buffering range of the buffer is higher than pH 7.0.
Preferably the pH of a solution of the invention is pH 5.0 or less, preferably from pH 3.5 to 5.
Examples of preferred buffers for the wash solution or solution of the invention include a Tris buffer, preferably Tris-HCI, and a 2-(f\l-morpho!ino)ethanesulfonic acid (MES) buffer. The buffering range for Tris-HCI buffer is pH 7.1 to 9. The buffering range for MES buffer is pH 5.5-6.7.
There is further provided according to the invention a composition in dry form that when dissolved in a liquid provides a solution according to the invention. The composition may be a iyophilisate. Such compositions can be prepared, for example, by providing a solution of the invention and lyophilising the solution to form the composition in dry form.
In a preferred embodiment, the wash solution or solution of the invention further comprises a detergent Detergent may assist in removing inhibitors that may interfere with subsequent processing of the isolated nucleic acid. Suitable examples are ionic detergents such as lithium dodecyl sulphate (LDS), or non-ionic detergents such as NP-40 and Triton-X.
It will be appreciated that detergent will not be present in a dry composition of the invention. If it is desired to include a detergent in a solution prepared using a composition in dry form, this may be added after the composition has been dissolved in aqueous solution.
Improved yieid of nucleic acid may be obtained using methods of the invention even without inclusion of a protease in the wash solution. Preferably the wash solution or solution of the invention does not include a protease.
According to the invention, there is also provided a kit for isolation of a nucleic acid, which comprises:
i) a binding buffer for binding the nucleic acid to a solid phase at a first pH;
ii) a wash solution that comprises a buffer with a buffering range that encompasses a phi that is higher than the first pH, wherein the wash solution is at a pH that is within a buffering range of the binding buffer but lower than the buffering range of the buffer of the wash solution; and optionally
iii) a solution for eluting the nucleic acid from the solid phase, wherein the solution is at a second pH that is higher than the first pH.
According to the invention, there is also provided a kit for isolation of a nucleic acid, which comprises:
i) a binding buffer for binding the nucleic acid to a solid phase at a first pH;
ii) a composition in dry form that when dissolved in a liquid provides a wash soiution that comprises a buffer with a buffering range that encompasses a pH that is higher than the first pH, wherein the wash solution Is at a pH that is within a buffering range of the binding buffer but lower than the buffering range of the buffer of the wash solution; and optionally
iii) a composition in dry form that when dissolved in a liquid provides a solution for eiuting the nucleic acid from the solid phase, wherein the solution is at a second pH that is higher than the first pH. Such kits may be used to carry out a method of the invention.
The binding buffer may be provided as a solution or in dry form (for example as a lyophilisate) for dissolving in a liquid.
The composition in dry form that when dissolved in a liquid provides a wash solution, and/or the composition in dry form that when dissolved in a liquid provides an elution solution, may be a lyophilisate. The lyophilisate may be prepared, for example, by providing the wash solution or the elution solution and lyophilising the solution to form the composition in dry form.
The liquid for dissolving the binding buffer, or a composition of the invention is suitably water, or an aqueous solution.
The wash solution of a kit of the invention is preferably a solution of the invention.
The composition in dry form for providing the wash solution is preferably a composition of the invention.
Preferably the kit does not comprise a chaotropic agent, nor an organic solvent. Preferably the binding buffer of the kit comprises a kosmotropic agent. Examples of suitable kosmotropic agents include ammonium sulphate and lithium chloride. Ammonium sulphate is preferred.
A kit of the invention may further comprise a solid phase to which the nucleic acid is able to bind. Suitable solid phases are discussed above. A preferred solid phase comprises a negatively ionisabie group with a pKa between a first pH at which the nucleic acid is able to bind to the solid phase, and a second pH at which the nucleic acid can be eluted from the solid phase. Preferably the solid phase comprises an inorganic oxide, preferably silica.
A kit of the invention may further comprise a protease for use with the binding buffer. Preferably the protease is in lyophilised form, separate from the binding buffer {and separate from the other components of the kit).
A kit of the invention may include instructions for carrying out nucleic acid isolation using the components of the kit. A kit of the invention may further comprise reagents required for amplification and/or detection of nucleic acid once isolated.
A kit of the invention will typically be provided with the components of the kit (i.e. the binding buffer, the wash solution (or the composition in dry form that when dissolved in a liquid provides the wash solution), and (if present) the elution solution (or the composition in dry form that when dissolved in a liquid provides the elution solution) separately packaged, or stored in separate compartments of a container in which the kit is provided.
The Applicant has appreciated that during the washing step, the wash buffer should remain close to the first pH when mixed with residual binding buffer retained on the solid phase, so that nucleic acid remains bound to the solid phase and is not washed away. However, during the elution step, residual wash buffer should change towards the second pH when mixed with elution solution for effective release of nucleic acid from the solid phase. Without being bound by theory, it is believed that the improved yield obtainable using methods of the invention arises because: (i) the wash solution does not remove significant amounts of nucleic acid from the solid phase during the washing step (because the pH of the washing solution is within the buffering range of the binding buffer); and (ii) the pH of residual wash buffer retained on the solid phase readily changes towards the second pH when mixed with elution solution (due to the buffering range of the wash buffer).
There is also provided according to the invention use of a solution or composition of the invention, or use of a kit of the invention for isolation of a nucleic acid.
We have found that methods of the invention are capable of extracting as few as 25 copies of nucleic acid, in particular viral RNA, from a biological sample. At low concentrations of virus the yield of nucieic acid obtained using methods of the invention is as good as, if not more reproducible, than that of a typical nucleic acid extraction method, which uses chaotropic salts and organic solvents.
Methods of the invention can be performed with buffer formulations that are non- hazardous and do not require special disposal, unlike some conventional nucleic acid extraction methods that use chaotropic salts and/or organic solvents. The buffer formulations used are stable and do not require refrigeration or heating before use to re-dissolve components that have precipitated during storage. The methods may be used in nucleic acid isolation and testing in hospitals and laboratories, and are especially important for on-site nucleic acid testing in the field and for point-of-care nucleic acid testing.
Embodiments of the invention are now described, by way of example only, with reference to the accompanying drawings in which:
Figure 1 shows a comparison of yield of nucleic acid obtained using acidic and alkaline wash buffers at pH 4 and pH 5;
Figure 2 shows the effect of residual (ysis buffer on wash buffer pH, and the effect of residual wash buffer on eiution buffer pH;
Figure 3 shows a comparison of yield of nucleic acid obtained at different wash buffer pH {using wash buffer comprising MES); and
Figure 4 shows the results of RNA recovery obtained using a method of the invention compared with a Qiagen method of nucleic acid isolation.
Example 1
Comparison of yield of nucleic acid obtained using acidic and alkaline wash buffers at pH 4 and PH 5
HIV viral RNA was isolated using an aqueous-based lysis buffer (comprising Tris Acetate, pH 4.0), bound to a silica-based solid phase and washed with wash buffers comprising 1OmM Tris-HCI (buffering range, pH 7.1 to 9), at pH 4 or 5, 1OmM sodium citrate (buffering range, pH 3.0 to 6.2), at pH 4 or 5, or 1 OmM Tris Acetate (buffering range, pH 3.6-5.6), at pH 4 or 5. The 1OmM Tris-HCi solutions at pH 4 and 5 are embodiments of a solution of the invention.
Washed nucleic acid bound to the solid phase was eluted with eiution buffer (comprising Tris-HCI, pH 8.5). The isolated nucleic acid was amplified and detected. Figure 1 shows the average detection signal strength, error bars indicate the standard error of the mean.
Figure 1 shows that the yield of nucleic acids obtained with 10 mM Tris-HCI, pH 4 and pH 5 was significantly higher than with 1OmM sodium citrate, pH 4 and 5, and with 1OmM Tris Acetate, pH 4 and 5. It is believed that the acidic wash buffers were not as effective as 10 mM Tris- HCI, pH 4 or 5, because residual buffer left on the solid phase lowers the pH of the elution buffer, making elution of nucleic acid less efficient and so reducing yield.
Example 2
Effect of residual lysis buffer on wash buffer pH, and effect of residual wash buffer on elution buffer pH
The interactions between residual lysis buffer and wash buffer, and between residual wash buffer and elution buffer, were investigated by mixing these buffers. 20μl of iysis buffer (comprising Tris Acetate, pH 4), was mixed with 500μl of wash buffer
(1OmM Tris-HCI, pH 4, 1 OmM Tris-HCi, pH 6, or 1OmM sodium citrate, pH 4), and
20μl of wash buffer (1OmM Tris-HCI, pH 4, 1OmM Tris-HCI, pH 6, or 1 OmM sodium citrate, pH 4) was mixed with 120μl of elution buffer (comprising Tris-HCI, pH 8.5), to illustrate the interactions of the various buffers. The pH of the mixtures was measured with pH paper. The results are shown in Figure 2.
The results show that 1OmM Tris-HGI, pH 4, and 1OmM Tris-HCI, pH 6, remains acidic when mixed with lysis buffer. When Tris-HCI, pH 4, or Tris-HCI, pH 6, was mixed with elution buffer, the mixture remained at pH 8.5. However, when 1 OmM sodium citrate was mixed with elution buffer, the resulting solution has an acidic pH.
Example 3
Comparison of yield of nucleic acid obtained at different wash buffer pH (using wash buffer comprising MES)
HIV viral RNA was isolated using an aqueous-based lysis buffer (comprising Tris Acetate, pH 4.0), bound to a silica-based solid phase and washed with 10mM MES (buffering range, pH 5.5 to 6.7), pH 4, 5 or 6. Nucleic acid was eiuted with elution buffer (1OmM Tris-HCI, pH 8.5). The isolated nucleic acid was amplified and detected. Figure 3 shows the average detection signal strength, error bars indicate the standard error of the mean. The results show that the yield of nucleic acid obtained at pH 4 and 5 (lower than the buffering range of MES buffer) is significantly higher than at pH 6 (within the buffering range of MES buffer).
It is concluded that improved yield is obtained by use of a wash buffer at an acidic pH that is lower than the buffering range of the wash buffer.
Example 4
Comparison of RNA recovery obtained using a method of the invention compared with a Qiaqen method of nucleic acid isolation.
Viral RNA was isolated from HIV positive plasma samples using a method of the invention, and a Qiagen method of nucleic acid isolation. The isolated nucleic acid was then amplified and detected.
The method according to an embodiment of the invention was as follows:
Lysis buffer (comprising sodium citrate, pH 4.5) was mixed with a plasma sample and incubated before adding proteinase K. The mixture was incubated, then loaded onto a silica or glass fibre solid phase. Bound nucleic acid was washed with wash buffer (Tris-HCI, pH 3.8), and eluted with elution buffer (comprising Tris-HCI, 8.5) at 75- 8O0C.
Figure 4 shows the average signal strength, error bars show the standard error of the mean. The results for the method according to an embodiment of the invention are shown by the black columns, and the results for the Qiagen method are shown by the white columns.
The results shown in Figure 4 demonstrate that methods of the invention are capable of extracting as few as 25 copies of nucleic acid, in particular viral RNA, from a biological sample. At low concentrations of virus the yield of nucleic acid obtained using the method according to an embodiment of the invention is as good as, if not more reproducible, than that of a typical nucleic acid extraction method, which uses chaotropic salts and organic solvents. The buffer formulations used are non-hazardous and do not require special disposal, unlike some conventional nucleic acid extraction methods that use chaotropic salts and/or organic solvents. The buffer formulations used are stable and do not require refrigeration. The methods may be used in nucleic acid isolation and testing in hospitals and laboratories, and are especially important for on-site nucleic acid testing in the field and for point-of-care nucleic acid testing.

Claims

Claims
1. A method for isolating a nucleic acid, which comprises:
(i) binding the nucleic acid to a solid phase at a first pH in the presence of a binding buffer;
(ii) washing the bound nucleic acid with a wash solution; and
(Hi) eluting the nucleic acid from the solid phase at a second pH which is higher than the first pH;
wherein the wash solution comprises a buffer with a buffering range that encompasses a pH that is higher than the first pH, and the wash solution is at a pH that is within a buffering range of the binding buffer but lower than the buffering range of the buffer of the wash solution.
2 A method according to claim 1 , wherein the buffering range of the wash buffer is higher than the first pH.
3. A method according to claim 1 or 2, wherein the second pH is within the buffering range of the wash buffer.
4. A method according to any preceding claim, wherein the buffering range of the wash buffer is higher than pH 5.0.
5. A method according to any preceding claim, wherein the first pH is in the range pH 3-6, or pH 3-5.
6. A method according to any preceding claim, wherein the second pH is in the range pH 6.5-10, preferably pH 7-9.
7. A method according to any preceding claim, wherein the pH of the wash solution is pH 6.0 or less, preferably from pH 3.0 to pH 6.0.
8. A method according to any preceding claim, wherein the first pH is within the buffering range of the binding buffer.
9. A method according to any preceding claim, wherein a lower end of the buffering range of the binding buffer is at pH 3.0 or higher.
10. A method according to any preceding claim that is carried out in the absence of a chaotropic agent and an organic solvent.
11. A method according to any preceding claim, wherein binding of the nucleic acid to the solid phase is carried out in the presence of a kosmotropic agent.
12. A method according to claim 11 , wherein the kosmotropic agent is ammonium sulphate.
13. A method according to any preceding ciaim, wherein the soϋd phase comprises a negatively ionisable group with a pKa between the first and second pH.
14. A method according to any preceding ciaim, wherein the solid phase comprises an inorganic oxide, preferably silica.
15. A method for isolating a nucleic acid from a cell, which comprises lysing the ceil to release the nucleic acid from the cell, and isolating the released nucleic acid using a method according to any preceding claim.
16. A method according to claim 15, wherein lysis is carried out using the binding buffer.
17. A method according to any preceding claim, wherein the binding buffer comprises a kosmotropic agent.
18. A method according to any preceding claim, wherein the nucleic acid is eluted from the solid phase at a temperature above ambient temperature.
19. A method according to any preceding claim wherein the nucleic acid is eluted from the solid phase in the presence of an elution buffer, wherein the second pH is within a buffering range of the elution buffer.
20. A method according to claim 19, wherein the buffering range of the elution buffer overlaps with or is encompassed by the buffering range of the wash buffer.
21. A solution comprising a buffer for washing a solid phase to which a nucleic acid is bound at a first pH and eluted at a second, higher pH, wherein the pH of the solution is pH 6.0 or less, preferably from pH 3.0 to pH 6.0, and the or each buffering range of the buffer is higher than pH 6.0.
22. A solution according to claim 21 , which does not include a chaotropic agent.
23. A solution according to claim 21 or 22, which does not include an organic solvent.
24. A solution according to any of claims 21 to 23, wherein the pH of the solution is pH 5.0 or less.
25. A solution according to any of claims 21 to 24, wherein the buffering range of the buffer overlaps with, is encompassed by, or encompasses the range pH 6.5-10.
26. A solution according to any of claims 21 to 25, wherein the buffer comprises a Tris buffer, preferably Tris-HCI.
27. A solution according to any of claims 21 to 26, which does not include a protease.
28. A solution according to any of claims 21 to 27, which further comprises a detergent.
29. A composition in dry form that when dissolved in a liquid provides a solution according to any of claims 21 to 27.
30. A kit for isolation of a nucleic acid, which comprises:
i) a binding buffer for binding the nucleic acid to a solid phase at a first pH;
ii) a wash solution that comprises a buffer with a buffering range that encompasses a pH that is higher than the first pH, wherein the wash solution is at a pH that is within a buffering range of the binding buffer but lower than the buffering range of the wash buffer; and optionally
iii) a solution for eluting the nucleic acid from the solid phase, wherein the solution is at a second pH that is higher than the first pH.
31. A kit for isolation of a nucleic acid, which comprises:
i) a binding buffer for binding the nucleic acid to a solid phase at a first pH;
ii) a composition in dry form that when dissolved in a liquid provides a wash solution that comprises a buffer with a buffering range that encompasses a pH that is higher than the first pH, wherein the wash solution is at a pH that is within a buffering range of the binding buffer but lower than the buffering range of the buffer of the wash solution; and optionally
iii) a composition in dry form that when dissolved in a liquid provides a solution for eluting the nucleic acid from the solid phase, wherein the solution is at a second pH that is higher than the first pH.
32. A kit according to claim 30, wherein the wash solution is a solution according to any of claims 21 to 28.
33. A kit according to claim 31 , wherein the composition in dry form that when dissolved in a liquid provides a wash solution is a composition according to claim 29.
34. A kit according to any of claims 30 to 33, wherein the kit does not comprise a chaotropic agent, and the kit does not comprise an organic solvent.
35. A kit according to any of claims 30 to 34, wherein the binding buffer comprises a kosmotropic agent.
36. A kit according to any of claims 30 to 35, which further comprises a solid phase to which the nucleic acid is able to bind in the presence of the binding buffer at the first pH, and from which the nucleic acid can be eluted at the second pH.
37. A kit according to claim 36, wherein the solid phase comprises a negatively ionisable group with a pKa between a first pH at which the nucleic acid is able to bind to the solid phase, and a second pH at which the nucleic acid can be eluted from the solid phase.
38. A kit according to claim 36 or 37, wherein the solid phase comprises an inorganic oxide, preferably silica.
39. A kit according to any of claims 30 to 38, which further comprises a protease, preferably in lyophilised form, separate from the binding buffer.
40. Use of a solution according to any of claims 21 to 28, a composition according to claim 29, or a kit according to any of claims 30 to 39, for isolation of a nucleic acid.
PCT/GB2009/001951 2008-08-08 2009-08-07 Isolation of nucleic acid WO2010015835A1 (en)

Priority Applications (6)

Application Number Priority Date Filing Date Title
EP09784897.2A EP2329019B1 (en) 2008-08-08 2009-08-07 Isolation of nucleic acid
US13/057,947 US9422543B2 (en) 2008-08-08 2009-08-07 Isolation of nucleic acid
ES09784897.2T ES2469816T3 (en) 2008-08-08 2009-08-07 Nucleic acid isolation
AU2009278915A AU2009278915B2 (en) 2008-08-08 2009-08-07 Isolation of nucleic acid
JP2011521638A JP6125752B2 (en) 2008-08-08 2009-08-07 Nucleic acid isolation
US15/207,091 US20170037394A1 (en) 2008-08-08 2016-07-11 Isolation of nucleic acid

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
GBGB0814570.8A GB0814570D0 (en) 2008-08-08 2008-08-08 Isolation of nucleic acid
GB0814570.8 2008-08-08

Related Child Applications (2)

Application Number Title Priority Date Filing Date
US13/057,947 A-371-Of-International US9422543B2 (en) 2008-08-08 2009-08-07 Isolation of nucleic acid
US15/207,091 Continuation US20170037394A1 (en) 2008-08-08 2016-07-11 Isolation of nucleic acid

Publications (1)

Publication Number Publication Date
WO2010015835A1 true WO2010015835A1 (en) 2010-02-11

Family

ID=39790526

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/GB2009/001951 WO2010015835A1 (en) 2008-08-08 2009-08-07 Isolation of nucleic acid

Country Status (7)

Country Link
US (2) US9422543B2 (en)
EP (1) EP2329019B1 (en)
JP (3) JP6125752B2 (en)
AU (2) AU2009278915B2 (en)
ES (1) ES2469816T3 (en)
GB (1) GB0814570D0 (en)
WO (1) WO2010015835A1 (en)

Cited By (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2013035062A1 (en) * 2011-09-06 2013-03-14 North-West University A method of preparing biological material
US20130274454A1 (en) * 2012-03-16 2013-10-17 Cambridge Enterprise Limited Methods for obtaining liquid from a solid phase
WO2013181651A1 (en) * 2012-06-01 2013-12-05 Omega Bio-Tek, Inc. Selective nucleic acid fragment recovery
US10184950B2 (en) 2013-03-15 2019-01-22 Diagnostics For The Real World, Ltd HIV viral load testing
WO2020117769A1 (en) 2018-12-03 2020-06-11 Diagnostics For The Real World, Ltd Hcv detection
WO2021186361A1 (en) 2020-03-17 2021-09-23 Diagnostics For The Real World, Ltd Sample collection device
WO2021191795A1 (en) 2020-03-23 2021-09-30 Diagnostics For The Real World, Ltd Coronavirus detection
WO2023150708A1 (en) * 2022-02-05 2023-08-10 Becton, Dickinson And Company Method for separating genomic dna for amplification of short nucleic acid targets

Families Citing this family (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20170342399A1 (en) * 2014-11-07 2017-11-30 The Johns Hopkins University Chaotrope- and volatile-free method for purifying nucleic acids from plasma
AU2016306451B2 (en) * 2015-08-11 2022-03-31 Stem Arts Projects, Llc Portable nucleic acid extraction apparatus and method of using the same
EP3397763B1 (en) * 2015-12-28 2020-10-28 Koninklijke Philips N.V. Nucleic acid purification system using a single wash and elution buffer solution
CN110621791A (en) * 2017-02-27 2019-12-27 医学诊断公司 Systems and methods for purifying and amplifying nucleic acids
WO2019135800A2 (en) * 2017-09-14 2019-07-11 California Institute Of Technology Purification and detection of analytes
WO2019217570A1 (en) * 2018-05-08 2019-11-14 Waters Technologies Corporation Methods, compositions and kits useful for ph gradient cation exchange chromatography
US11866695B2 (en) 2019-12-23 2024-01-09 California Institute Of Technology Methods and systems and related compositions for mixtures separation with a solid matrix
CN114317527A (en) * 2022-02-18 2022-04-12 欧蒙医学诊断(中国)有限公司 Method and kit for extracting nucleic acid from sample

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2000069872A2 (en) * 1999-05-14 2000-11-23 Promega Corporation pH DEPENDENT ION EXCHANGE MATRIX AND METHOD OF USE IN THE ISOLATION OF NUCLEIC ACIDS
US20010018513A1 (en) * 1997-12-06 2001-08-30 Baker Matthew John Isolation of nucleic acids
WO2004055207A1 (en) * 2002-12-13 2004-07-01 Merck Patent Gmbh Method for purifying nucleic acids

Family Cites Families (35)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5955261A (en) 1984-09-04 1999-09-21 Gen-Probe Incorporated Method for detecting the presence of group-specific viral mRNA in a sample
US5714380A (en) 1986-10-23 1998-02-03 Amoco Corporation Closed vessel for isolating target molecules and for performing amplification
CA1340843C (en) 1987-07-31 1999-12-07 J. Lawrence Burg Selective amplification of target polynucleotide sequences
US6090591A (en) 1987-07-31 2000-07-18 The Board Of Trustees Of The Leland Stanford Junior University Selective amplification of target polynucleotide sequences
JP2650159B2 (en) 1988-02-24 1997-09-03 アクゾ・ノベル・エヌ・ベー Nucleic acid amplification method
CA1340807C (en) 1988-02-24 1999-11-02 Lawrence T. Malek Nucleic acid amplification process
US5130238A (en) 1988-06-24 1992-07-14 Cangene Corporation Enhanced nucleic acid amplification process
AU2684488A (en) 1988-06-27 1990-01-04 Carter-Wallace, Inc. Test device and method for colored particle immunoassay
CA2020958C (en) 1989-07-11 2005-01-11 Daniel L. Kacian Nucleic acid sequence amplification methods
CA2067711C (en) * 1991-05-03 2000-08-08 Daniel Lee Woodard Solid phase extraction purification of dna
DE69327326T2 (en) 1992-07-24 2001-08-16 Diatech Pty. Ltd., Brisbane REPLACEMENT AND DETECTION PROCESS
ZA936016B (en) 1992-08-24 1994-03-10 Akzo Nv Method for nucleic acid amplification
JP4108118B2 (en) 1993-03-26 2008-06-25 ジェン−プローブ・インコーポレイテッド Detection of human immunodeficiency virus type 1
US5556771A (en) 1995-02-10 1996-09-17 Gen-Probe Incorporated Stabilized compositions of reverse transcriptase and RNA polymerase for nucleic acid amplification
DE69734263T2 (en) 1996-07-12 2006-07-13 Toyo Boseki K.K. Process for isolating ribonucleic acids.
JP3082908B2 (en) * 1996-07-12 2000-09-04 東洋紡績株式会社 Method for isolating ribonucleic acid
US5981254A (en) 1997-10-30 1999-11-09 Haemacure Corporation Process for producing thrombin from plasma
GB9725839D0 (en) 1997-12-06 1998-02-04 Baker Matthew J Isolation of nucleic acids
DE69839133T2 (en) 1997-12-06 2009-02-05 Invitrogen Corp., Carlsbad Isolation of nucleic acids
DE59912604D1 (en) * 1998-02-04 2005-11-03 Merck Patent Gmbh PROCESS FOR THE ISOLATION AND PURIFICATION OF NUCLEIC ACIDS
US6203989B1 (en) 1998-09-30 2001-03-20 Affymetrix, Inc. Methods and compositions for amplifying detectable signals in specific binding assays
DE19851156C1 (en) * 1998-11-06 2000-04-27 Merck Patent Gmbh Isolation of plasmid DNA from a microbial culture comprises acidification and using particles to separate microbial cells from the culture
DE19856064C2 (en) * 1998-12-04 2000-11-30 Invitek Gmbh Universal method for the isolation of DNA from any starting material
US6803196B1 (en) 2000-10-13 2004-10-12 Affymetrix, Inc. Methods and compositions for detecting signals in binding assays using microparticles
WO2004042058A2 (en) * 2002-11-08 2004-05-21 InViTek Gesellschaft für Biotechnik & Biodesign mbH Novel buffer formulations for isolating, purifying and recovering long-chain and short-chain nucleic acids
EP1603674B1 (en) 2003-02-05 2016-01-06 Iquum, Inc. Sample processing
EP1498133A1 (en) 2003-07-18 2005-01-19 Aventis Pharma Deutschland GmbH Use of a pak inhibitor for the treatment of a joint disease
EP1529840A1 (en) * 2003-11-04 2005-05-11 Qiagen GmbH A rapid and low cost method for isolating nucleic acid
JP5112064B2 (en) 2004-05-21 2013-01-09 エムオー バイオ ラボラトリーズ インコーポレイテッド Kits and methods for removing contaminants from nucleic acids in environmental and biological samples
DE102004063265B4 (en) * 2004-12-29 2012-02-02 Biontech Ag Method for determining the function of nucleic acid sequences and the expression products encoded thereby
US20070184472A1 (en) * 2005-06-08 2007-08-09 Toagosei Co., Ltd Method of purifying environmental dna and method of efficiently screening for protein-encoding gene from environmental dna
EP1963352B1 (en) * 2005-12-14 2010-09-08 Roche Diagnostics GmbH New method for bisulfite treatment
JP2007244375A (en) * 2006-02-14 2007-09-27 Toyobo Co Ltd Method for separation and purification of ribonucleic acid
WO2008035991A2 (en) 2006-09-19 2008-03-27 Michael Ronald Cook A nucleic acid extraction method
JP5268963B2 (en) 2010-02-10 2013-08-21 アズビル株式会社 Pressure measuring system and pressure measuring method

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20010018513A1 (en) * 1997-12-06 2001-08-30 Baker Matthew John Isolation of nucleic acids
WO2000069872A2 (en) * 1999-05-14 2000-11-23 Promega Corporation pH DEPENDENT ION EXCHANGE MATRIX AND METHOD OF USE IN THE ISOLATION OF NUCLEIC ACIDS
WO2002048164A2 (en) 2000-12-14 2002-06-20 Dna Research Innovations Limited Isolation of nucleic acids
WO2004055207A1 (en) * 2002-12-13 2004-07-01 Merck Patent Gmbh Method for purifying nucleic acids

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
CACACE ET AL., Q REV BIOPHYS, vol. 30, 1997, pages 241 - 77
HOURFAR MICHAEL K ET AL: "High-throughput purification of viral RNA based on novel aqueous chemistry for nucleic acid isolation", July 2005, CLINICAL CHEMISTRY, VOL. 51, NR. 7, PAGE(S) 1217-1222, ISSN: 0009-9147, XP002552471 *

Cited By (14)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10308929B2 (en) 2011-09-06 2019-06-04 North-West University Method of preparing biological material
WO2013035062A1 (en) * 2011-09-06 2013-03-14 North-West University A method of preparing biological material
CN103890176A (en) * 2011-09-06 2014-06-25 西北大学 A method of preparing biological material
CN103890176B (en) * 2011-09-06 2016-10-26 西北大学 The method preparing biomaterial
US20130274454A1 (en) * 2012-03-16 2013-10-17 Cambridge Enterprise Limited Methods for obtaining liquid from a solid phase
US9821248B2 (en) * 2012-03-16 2017-11-21 Cambridge Enterprise Limited Methods for obtaining liquid from a solid phase
US9624252B2 (en) 2012-06-01 2017-04-18 Omega Bio-Tek, Inc. Selective nucleic acid fragment recovery
CN104350152A (en) * 2012-06-01 2015-02-11 欧米伽生物技术公司 Selective nucleic acid fragment recovery
WO2013181651A1 (en) * 2012-06-01 2013-12-05 Omega Bio-Tek, Inc. Selective nucleic acid fragment recovery
US10184950B2 (en) 2013-03-15 2019-01-22 Diagnostics For The Real World, Ltd HIV viral load testing
WO2020117769A1 (en) 2018-12-03 2020-06-11 Diagnostics For The Real World, Ltd Hcv detection
WO2021186361A1 (en) 2020-03-17 2021-09-23 Diagnostics For The Real World, Ltd Sample collection device
WO2021191795A1 (en) 2020-03-23 2021-09-30 Diagnostics For The Real World, Ltd Coronavirus detection
WO2023150708A1 (en) * 2022-02-05 2023-08-10 Becton, Dickinson And Company Method for separating genomic dna for amplification of short nucleic acid targets

Also Published As

Publication number Publication date
AU2016203697A1 (en) 2016-06-23
US9422543B2 (en) 2016-08-23
GB0814570D0 (en) 2008-09-17
AU2009278915A1 (en) 2010-02-11
JP2011530278A (en) 2011-12-22
EP2329019A1 (en) 2011-06-08
JP2016082980A (en) 2016-05-19
JP6571544B2 (en) 2019-09-04
US20170037394A1 (en) 2017-02-09
EP2329019B1 (en) 2014-03-12
US20110257386A1 (en) 2011-10-20
JP6125752B2 (en) 2017-05-10
AU2009278915B2 (en) 2016-03-03
JP2018042565A (en) 2018-03-22
ES2469816T3 (en) 2014-06-20

Similar Documents

Publication Publication Date Title
AU2016203697A1 (en) Isolation of nucleic acid
US20190345480A1 (en) Compositions and methods for purifying nucleic acids from stabilization reagents
US9062303B2 (en) Methods and compositions for the rapid isolation of small RNA molecules
US10273470B2 (en) Method for isolating RNA from a RNA and DNA containing sample
EP2094846B1 (en) Use of tde for the isolation of nucleic acids
US20090176296A1 (en) Process for isolating nucleic acids
WO2008035991A2 (en) A nucleic acid extraction method
US20090253903A1 (en) Method for parallel isolation of viral nucleic acids
JP6024266B2 (en) DNA extraction method
EP1487977B1 (en) Method to isolate dna

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 09784897

Country of ref document: EP

Kind code of ref document: A1

ENP Entry into the national phase

Ref document number: 2011521638

Country of ref document: JP

Kind code of ref document: A

NENP Non-entry into the national phase

Ref country code: DE

WWE Wipo information: entry into national phase

Ref document number: 2009278915

Country of ref document: AU

WWE Wipo information: entry into national phase

Ref document number: 1558/DELNP/2011

Country of ref document: IN

WWE Wipo information: entry into national phase

Ref document number: 2009784897

Country of ref document: EP

ENP Entry into the national phase

Ref document number: 2009278915

Country of ref document: AU

Date of ref document: 20090807

Kind code of ref document: A

WWE Wipo information: entry into national phase

Ref document number: 13057947

Country of ref document: US