CA1211058A - Binding nucleic acid to a support - Google Patents

Binding nucleic acid to a support

Info

Publication number
CA1211058A
CA1211058A CA000443141A CA443141A CA1211058A CA 1211058 A CA1211058 A CA 1211058A CA 000443141 A CA000443141 A CA 000443141A CA 443141 A CA443141 A CA 443141A CA 1211058 A CA1211058 A CA 1211058A
Authority
CA
Canada
Prior art keywords
nucleic acid
binding
support
organic solvent
alcohol
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Expired
Application number
CA000443141A
Other languages
French (fr)
Inventor
Suzanne S. Groet
Jonathan J. Ostman
Robert M. Wydro
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Integrated Genetics Inc
Original Assignee
Integrated Genetics Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Integrated Genetics Inc filed Critical Integrated Genetics Inc
Application granted granted Critical
Publication of CA1211058A publication Critical patent/CA1211058A/en
Expired legal-status Critical Current

Links

Classifications

    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07HSUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H21/00Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813Hybridisation assays
    • C12Q1/6834Enzymatic or biochemical coupling of nucleic acids to a solid phase

Abstract

Abstract of the Disclosure Method of binding nucleic acid to a nucleic acid-binding support comprising depositing the nucleic acid onto the support and then contacting the nucleic acid and the support with a liquid binding solution which is compatible with the support and which contains an organic solvent which is capable of binding the DNA to the support, for a period of time sufficient to effect the binding.

Description

~12-1410 Background of the Invention This invention relates to binding nucleic acids RAN and DNA) to supports, ego to carry out DNA hybridization assays.
Such assays have been used to detect specific DNA
sequences in samples for several years, and are described in the patent and technical literature, e.g. Fallow et at. US. Pat. No 4,35~,535. Such assays typically involve spotting a sample, e.g.
urine, suspected of containing a particular DOW sequence (in viruses or prokaryotic or eukaryotic cells in the sample) onto a DNA-binding support, e.g. a nitrocellulose membrane, lying the cells, if necessary, denaturing and neutralizing the DNA, and then affixing the DNA to the support prior to carrying out the hybrid ization assay. Affixation is typically carried out by air drying followed by drying in a vacuum oven for two hours, as described, e.g., in Gillespie et at. (1965) J. Mol. Blot. 12, 829.
Summary of the Invention In general, the invention features a method of binding nucleic acid EDNA ox RNA) to a nucleic acid-binding support including depositing the nucleic acid on the support and then contacting the nucleic acid and the support with a liquid binding solution which is compatible with the support and which contains an organic solvent capable of binding the nucleic acid to the support, for a period of time sufficient to effect binding.

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In preferred embodiments, the nucleic acid is included in a sample to be assayed by hybridization and the binding solution does not alter the DNA in a manner which interferes with hybridization; and the organic solvent contains fewer than 20 carbon atoms, makes up substantially all of the solvent, and is an alcohol, ether, aromatic compound, or kitten, most preferably ethanol, methanol, sec-bu~yl alcohol, iso-amyl alcohol, isopropyl alcohol, isobutyl alcohol r ethyl ether, or Tulane. In other preferred embodiments 9 the binding solution contains a mixture of more than one such organic solvent and the period of time during which the nucleic acid and the support are contacted with the binding solution is 1 second to 10 minutes, most preferably about 5 minutes.
The method of the invention permits nucleic immobilization in very short times; ire., in most instances on the order of five minutes or less. Thus the total time required Jo complete Dot blots, Southern blots, colony lifts, and any other technique requiring denatured nucleic acid immobilization on a support is greatly reduced.
Furthermore, the method obviates he use of expensive equipment such as vacuum pumps and vacuum ovens.
Other features and advantages of the invention will be apparent from the following description of tune preferred embodiments, and from the claims.

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so Description of the Preferred Embodiments A very wide range of organic solvents, in many different classes of organic compounds, can be used to bind nucleic acid to nuclei acid-binding membranes. The most preferred class of compounds are alcohols, which are generally less toxic and ! therefore easier to work with than other classes of compounds. Other classes of compounds which Jill bind nucleic acid, but which are less desirable than alcohols, are ethers, e.g. ethyl ether;
aromatic compounds, e.g. Tulane; and kittens, e.g.
acetone. Still other classes of organic solvents are alikeness, alikeness, alikeness, esters, and hetero-organic compounds such as halogenated alikeness, e.g. chloroform and carbon tetrachloride~
For all classes of organic solvents, considerations such as expense dictate a preferred size of fewer than 20 carbon atoms, and most preferably fewer than 10 carbon atoms.
The choice of solvent in a particular - instance will be dictated by several factors.
First, the binding solution containing the solvent should not alter the nucleic acid in a way which interferes with the intended purpose of the binding procedure e.g., if the nucleic acid it being immobilized for a hybridization assay, it must be capable of hybridizing after treatment with the solvent -Secondly, binding solution containing the solvent must be compatible with the support being used; i.e. the solvent should nut dissolve the support to an extent which interferes with the - ., .

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I

purpose of the binding procedure. Some nucleic acid-binding supports are more susceptible to being dissolved by organic solvents than others. Thus, practically any organic solvent can safely be used with the highly solvent-resistant nylon-based supports, while the choice is more limited for more easily dissolved supports such as nitrocellulose.
Thus, for example, absolute methanol and acetone are incompatible with nitrocellulose, since they cause a degree of softening of the membrane which is unacceptable in hybridization assays, but are compatible with nylon-based supports. Where the organic solvent and the support are incompatible, the nucleic acid binding solution can often be modified, ego by dilution with water or by combination with a milder organic solvent. Thus, for example, 90% methanol is an effective binding solution and is compatible with nitrocellulose, while absolute methanol is not.
20~ Finally, the binding solution should be a liquid at the temperature of use. In many case this will be room temperature buy in some instances may be higher or lower.
An example of the method, in which Hepatitis B viral DNA is detected in blood serum, is as follows. A 7 I sample of blood serum is spotted onto a 0.45 EM nitrocellulose membrane and allowed to air-dry. The DNA in the sample is denatured by immersing the membrane in 9.5M Noah, 1.5M Nail for 1 min., and then neutralized by immersing the membrane in loom Trip 1PH 7.5), EM
Nail for 1 min. The membrane is then allowed to air-dry and the DNA

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I

bound to -the membrane by immersing the membrane in an hydrous sea-bottle alcohol for 5 min. The membrane is then removed and air-dried.
The membrane, to which DNA is bound, is placed in a plastic bag, to which is then added hybridization solution of the composition 6X SKIP (0.9OM Nail, O.O90M Nay Citrate, 0.12M Pros-plate buffer pi 7.0), 2X Denhardt's solution (0.04% bovine serum albumin, 0.04% polyvinylpyrollidine, 0.04~ focal 500), 40%
formamide, 10% Dextran sulfite, 500 gel salmon sperm DNA, 1.6 mg/ml additional bovine serum albumin. Radioactively labeled Hepatitis B DNA probe (specific activity = 2-3X 108 cpm/~g) is then added, in an amount corresponding to 1~107 counts per ml hybridization solution.
The plastic bag is sealed and hybridization allowed to proceed for 2-3 hours at 37C. I've membrane is then removed and washed with 3mM tris-base for 20 min. to remove non-specifically bound probe. The washed membrane is placed under X-ray film and autoradiographed for 4-24 hours, to quantitatively determine Hope-tilts B DNA in the blood serum sample.
Other Embodiments . _ Other embodiments are within the following claims. For example, the nucleic acid binding technique can be used in conjunction with any suitable nucleic acid binding support, e.g., Pall Bedouin nylon membranes, and the sample and nucleic acid can be from any desired source (e.g. bacterial or eukaryotic DUN in urine of sputum samples, viral RAM in blood samples); and the nucleic acid can be purified prior to spotting.

Claims (18)

THE EMBODIMENTS OF THE INVENTION IN WHICH AN EXCLUSIVE
PROPERTY OR PRIVILEGE IS CLAIMED ARE DEFINED AS FOLLOWS:
1. A method of binding nucleic acid to a nucleic acid-binding support comprising depositing said nucleic acid onto said support and then contacting said nucleic acid and said support with a liquid binding solution which is compatible with said support and which contains an organic solvent which is capable of binding said nucleic acid to said support, for a period of time sufficient to effect said binding.
2. The method of claim 1 wherein said nucleic acid is included in a sample to be assayed by hybridization for a prede-termined type of nucleic acid, said sample being deposited on said nucleic acid-binding support.
3. The method of claim 2 wherein said nucleic acid is DNA
and, prior to said binding, said DNA is denatured and then neutralized for use in said hybridization assay.
4. The method of claim 1 wherein said nucleic acid and said support, after said depositing, are permitted to air-dry prior to being contacted with said nucleic acid-binding solution.
S. The method of claim 2 wherein said contacting with said nucleic acid-binding solution does not alter said nucleic acid in a manner which interferes with said hybridization.
6. The method of claim 1 wherein said organic solvent contains fewer than 20 carbon atoms.
7. The method of claim 1 wherein said nucleic acid binding solution is made up substantially entirely of said organic solvent.
8. The method of claim 6 wherein said organic solvent is an alcohol, an ether, an aromatic compound, or a ketone.
9. The method of claim 1 wherein said nucleic acid binding solution contains a mixture of more than one organic solvent, said mixture being capable of binding said nucleic acid to said nucleic acid-binding support.
10. The method of claim 9 wherein each said organic solvent contains fewer than 20 carbon atoms.
11. The method of claim 9 wherein each said organic solvent, independently, is an alcohol, an ether, an aromatic compound, or a ketone.
12. The method of claim 8 wherein said organic solvent is ethanol, methanol, sec-butyl alcohol, iso-amyl alcohol, isopropyl alcohol, isobutyl alcohol, ethyl ether, or toluene.
13. The method of claim 11 wherein each said organic solvent, independently, is ethanol, methanol, sec-butyl alcohol, iso-amyl alcohol, isopropyl alcohol, isobutyl alcohol ethyl ether, or toluene.
14. The method of claim 8 wherein said organic solvent is sec-butyl alcohol.
15. The method of claim 13 wherein one of said organic solvents is sec-butyl alcohol.
16. The method of claim 1 wherein said period of time is between 1 second and 10 minutes.
17. The method of claim 16 wherein said period of time is about 5 minutes.
18. The method of claim 1 wherein, following said contacting, said support and said nucleic acid are permitted to air-dry.
CA000443141A 1982-12-13 1983-12-13 Binding nucleic acid to a support Expired CA1211058A (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US06/448,979 US4588682A (en) 1982-12-13 1982-12-13 Binding nucleic acid to a support
US448,979 1982-12-13

Publications (1)

Publication Number Publication Date
CA1211058A true CA1211058A (en) 1986-09-09

Family

ID=23782403

Family Applications (1)

Application Number Title Priority Date Filing Date
CA000443141A Expired CA1211058A (en) 1982-12-13 1983-12-13 Binding nucleic acid to a support

Country Status (6)

Country Link
US (1) US4588682A (en)
EP (1) EP0111340B1 (en)
JP (1) JPS59122499A (en)
AT (1) ATE82330T1 (en)
CA (1) CA1211058A (en)
DE (1) DE3382639T2 (en)

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US4849077A (en) * 1984-08-06 1989-07-18 Akademie Der Wissenschaften Der Ddr Process for solid phase-sequencing of nucleic acid fragments
JPS61162752A (en) * 1985-01-11 1986-07-23 Sekisui Chem Co Ltd Detection of dna and/or rna
US4806546A (en) * 1985-09-30 1989-02-21 Miles Inc. Immobilization of nucleic acids on derivatized nylon supports
US4806631A (en) * 1985-09-30 1989-02-21 Miles Inc. Immobilization of nucleic acids on solvolyzed nylon supports
US5604099A (en) * 1986-03-13 1997-02-18 Hoffmann-La Roche Inc. Process for detecting specific nucleotide variations and genetic polymorphisms present in nucleic acids
CA1284931C (en) * 1986-03-13 1991-06-18 Henry A. Erlich Process for detecting specific nucleotide variations and genetic polymorphisms present in nucleic acids
GB8608269D0 (en) * 1986-04-04 1986-05-08 Brown J J Ice-maker
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EP0261955A3 (en) * 1986-09-26 1989-06-07 E.I. Du Pont De Nemours And Company Process for immobilization of dna
DE3717212A1 (en) * 1987-05-22 1988-12-08 Viktor Dr Dr Med Balazs METHOD FOR THE EXAMINATION OF A CELLULAR BIOLOGICAL LIQUID FOR CELLULAR ONCOGEN TRANScripts or THEIR FRAGMENTS
DE3721400A1 (en) * 1987-06-29 1989-01-12 Viktor Dr Dr Med Balazs METHOD FOR THE EXAMINATION OF A CELLULAR BIOLOGICAL LIQUID ON CELLULAR ONCOGEN DNA OR THEIR FRAGMENTS
US4942124A (en) * 1987-08-11 1990-07-17 President And Fellows Of Harvard College Multiplex sequencing
US5925525A (en) * 1989-06-07 1999-07-20 Affymetrix, Inc. Method of identifying nucleotide differences
US5800992A (en) 1989-06-07 1998-09-01 Fodor; Stephen P.A. Method of detecting nucleic acids
US5744101A (en) 1989-06-07 1998-04-28 Affymax Technologies N.V. Photolabile nucleoside protecting groups
US6955915B2 (en) * 1989-06-07 2005-10-18 Affymetrix, Inc. Apparatus comprising polymers
US6919211B1 (en) * 1989-06-07 2005-07-19 Affymetrix, Inc. Polypeptide arrays
US6416952B1 (en) 1989-06-07 2002-07-09 Affymetrix, Inc. Photolithographic and other means for manufacturing arrays
US6551784B2 (en) 1989-06-07 2003-04-22 Affymetrix Inc Method of comparing nucleic acid sequences
US5143854A (en) 1989-06-07 1992-09-01 Affymax Technologies N.V. Large scale photolithographic solid phase synthesis of polypeptides and receptor binding screening thereof
EP0405913B1 (en) * 1989-06-30 1998-12-23 Chiron Corporation Hydrophobic nucleic acid probe
DK0834576T3 (en) * 1990-12-06 2002-04-22 Affymetrix Inc A Delaware Corp Detection of nucleic acid sequences
US6943034B1 (en) 1991-11-22 2005-09-13 Affymetrix, Inc. Combinatorial strategies for polymer synthesis
US6864101B1 (en) 1991-11-22 2005-03-08 Affymetrix, Inc. Combinatorial strategies for polymer synthesis
GB9201073D0 (en) * 1992-01-18 1992-03-11 Cytocell Ltd Chromosome hybridisation methods
US7323298B1 (en) 1994-06-17 2008-01-29 The Board Of Trustees Of The Leland Stanford Junior University Microarray for determining the relative abundances of polynuceotide sequences
US7625697B2 (en) 1994-06-17 2009-12-01 The Board Of Trustees Of The Leland Stanford Junior University Methods for constructing subarrays and subarrays made thereby
ES2110916B1 (en) * 1996-05-24 1998-10-01 Ivia TARGET PREPARATION PROCEDURE FOR POLYMERASE CHAIN REACTION (PCR).
CN1148227A (en) * 1996-08-02 1997-04-23 韩苏 Application of analysis tech. of nucleic acid code used as counterfeit-proof method
US6703228B1 (en) 1998-09-25 2004-03-09 Massachusetts Institute Of Technology Methods and products related to genotyping and DNA analysis
EP1001037A3 (en) * 1998-09-28 2003-10-01 Whitehead Institute For Biomedical Research Pre-selection and isolation of single nucleotide polymorphisms
US6861214B1 (en) * 2000-10-23 2005-03-01 Beckman Coulter, Inc. Immobilization of biopolymers to aminated substrates by direct adsorption
US7189509B2 (en) * 2001-08-16 2007-03-13 Zhifeng Shao Analysis of gene expression profiles using sequential hybridization
EP1623996A1 (en) * 2004-08-06 2006-02-08 Deutsches Krebsforschungszentrum Stiftung des öffentlichen Rechts Improved method of selecting a desired protein from a library
US8524507B2 (en) * 2009-08-19 2013-09-03 The Cleveland Clinic Foundation Method for detecting a target molecule in a biological sample

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Also Published As

Publication number Publication date
EP0111340A3 (en) 1987-03-25
US4588682A (en) 1986-05-13
EP0111340A2 (en) 1984-06-20
EP0111340B1 (en) 1992-11-11
JPH0515438B2 (en) 1993-03-01
JPS59122499A (en) 1984-07-14
DE3382639D1 (en) 1992-12-17
ATE82330T1 (en) 1992-11-15
DE3382639T2 (en) 1993-07-15

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