DK174784B1 - Quantification of nucleic acid molecules and reagent kits thereto - Google Patents
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Description
DK 174784 B1DK 174784 B1
Den foreliggende opfindelsen angår kvantificering af visse nukleinsyremolekyler, navnlig graden af forøgelse {amplification) af gener og/eller tilsvarende mes-senger-RNA molekyler under anvendelse af sandwich- el-5 ler opløsnings-hybridiseringsmetoden, samt et reagenssæt anvendt hertil.The present invention relates to the quantification of certain nucleic acid molecules, in particular the degree of amplification of genes and / or corresponding messenger RNA molecules using the sandwich or solution hybridization method, and a reagent kit used therefor.
Antallet af kopier af enkelte gener i genomet er som regel konstant. I nogle tilfælde er der kun ét gen pr. haploidt genom og i andre flere. Under visse omstæn-10 digheder kan antallet af kopier ændre sig. Forøgelsen af visse gener har fx vist sig at være forbundet med udvikling af kræft. Det er også kendt at ydre faktorer såsom farmaceutiske midler og metaller etc. bevirker at visse gener multipliceres. Til udvikling af en sygdom er det 15 forkerte eller forøgede ekspressionsniveau for et gen, fx et oncogen, dvs. mængden af messenger-RNA i cellen, af meget stor betydning. Forøget antal af nogle kromosomer er grund til visse arvelige sygdomme og andre forstyrrelser, mens nogle arvelige sygdomme kun behøver du-20 plikering af ét recessivt gen. I alle sådanne tilfælde er det vigtigt at bestemme antallet af tilstedeværende kromosomer eller gener.The number of copies of individual genes in the genome is usually constant. In some cases, there is only one gene per haploid genome and in others several. Under certain circumstances, the number of copies may change. For example, the increase of certain genes has been shown to be associated with the development of cancer. It is also known that external factors such as pharmaceuticals and metals etc. cause multiple genes to be multiplied. For the development of a disease, it is the wrong or increased expression level of a gene, eg an oncogene, ie. the amount of messenger RNA in the cell, of great importance. Increased numbers of some chromosomes are the cause of certain hereditary diseases and other disorders, while some hereditary diseases require only one replication of one recessive gene. In all such cases, it is important to determine the number of chromosomes or genes present.
Antallet af visse DNA-molekyler, fx graden af forøgelse af visse gener, bestemmes for tiden ved ned-25 brydning (digesting) af det ekstraheredes DNA som skal undersøges ved hjælp af restriktionsenzymer, og ved fra-skillelse af nukleotidfragmenterne i overensstemmelse med længden ved agarose-gelelektroforese. Derefter overføres det enkelt-strengede DNA og fæstnes til et nitro-30 cellulosefilter hvor hybridisering finder sted under anvendelse af det til undersøgelse værende gen eller en del af genet som sonde. Resultaterne fås ved autora-diografering (Southern, J. Mol. Biol. 98, pp. 503-517, 1975). Ved hver parallel analyse er mængden af cellulært 35 DNA den samme.The number of certain DNA molecules, for example the degree of increase of certain genes, is currently determined by digesting the extracted DNA to be examined by restriction enzymes and by separating the nucleotide fragments according to the length of agarose gel electrophoresis. Then, the single-stranded DNA is transferred and attached to a nitro cellulose filter where hybridization takes place using the gene or part of the gene as probe. The results are obtained by autoradiographing (Southern, J. Mol. Biol. 98, pp. 503-517, 1975). With each parallel analysis, the amount of cellular DNA is the same.
Intensiteterne af hybridiseringsbåndene, dvs. signalerne, sammenlignes og forholdene mellem kopiantal- 2 DK 174784 B1 lene af de til undersøgelse værende gener i testprøverne udledes. Metoden giver kun tilnærmede resultater. Ligeledes måles RNA ved hjælp af Northern-pletnings- eller prik-pletningsmetoder. Disse metoder er kvantitativt me-5 get unøjagtige (Thomas, Methods in Enzymol., 100, pp.The intensities of the hybridization bands, i.e. the signals are compared and the ratios of the copy number of the genes under study in the test samples are deduced. The method only gives approximate results. Likewise, RNA is measured by Northern staining or dot staining methods. These methods are quantitatively inaccurate (Thomas, Methods in Enzymol., 100, p.
255-266, 1983).255-266, 1983).
Kendte metoder såsom Southern- og Northern-plet-ningsmetoderne er langsomme og vanskelige at gennemføre. Eftersom de kun giver tilnærmede resultater er deres 10 diagnostiske værdi tvivlsom i tilfælde,hvor det er betydningsfuldt at kende antallet af visse nukleinsyre-molekyler pr. given enhed såsom en celle.Known methods such as the Southern and Northern staining methods are slow and difficult to implement. Since they only give approximate results, their diagnostic value is questionable in cases where it is important to know the number of certain nucleic acid molecules per cell. given unit such as a cell.
Sandwich- eller opløsnings-hybridiseringsmetoder-ne, beskrevet i US patentskrift nr. 4.486.539 og i bri-15 tisk offentliggjort patentansøgning nr. 2.169.403 er kvantitative (Virtanen et al.. Lancet, J_, side 381-383, 1983). Desuden fordrer fremgangsmåden ifølge den foreliggende opfindelse en standard-nukleinsyre hvis kopiantal er konstant og udgør bestemmelse af antallet af 20 relevante nukleinsyremolekyler pr. given enhed såsom en celle, en kerne, et ribosom eller et kromosom.The sandwich or solution hybridization methods described in U.S. Patent No. 4,486,539 and in British Patent Application No. 2,169,403 are quantitative (Virtanen et al., Lancet, J, pp. 381-383, 1983). . In addition, the method of the present invention requires a standard nucleic acid whose copy number is constant and constitutes the determination of the number of 20 relevant nucleic acid molecules per given unit such as a cell, nucleus, ribosome or chromosome.
Formålet med den foreliggende opfindelse er at tilvejebringe en nøjagtig og hurtig kvantitativ fremgangsmåde til bestemmelse af nukleinsyremolekyler, en 25 fremgangsmåde der også er hurtigere og simplere at gennemføre end den der bruges for tiden. Den kan bruges til kræft- og prenataldiagnose, til detektering af midler som bevirker genformering og til påvisning af udvikling af fx lægemiddelresistens såvel som til bestemmelse af 30 ekspressions-niveauet for messenger-RNA.The object of the present invention is to provide an accurate and rapid quantitative method for determining nucleic acid molecules, a method which is also faster and simpler to implement than the one currently used. It can be used for cancer and prenatal diagnosis, for detecting agents that cause reformation and for detecting the development of, for example, drug resistance as well as for determining the level of expression of messenger RNA.
Der behøves mindst to bestemmelser ved den foreliggende opfindelse. Den ene bestemmer nukleinsyremole-kylet, der kan være til stede i et antal kopier, test-nukleinsyre. Den anden bestemmer de konstitutive nuklein-35 syremolekyle som med fordel er til stede i konstant antal, standard-nukleinsyre. Ved fremgangsmåden ifølge opfindelsen menes der med et nukleinsyremolekyle en given 3 DK 174784 B1 nukleosidsekvens på 10-12 nukleotider eller et gen som indeholder flere tusinde nukleotider. Det kan også betyde et messenger-RNA eller en nukleotidsekvens som er betydelig længere end et enkelt gen, dvs. en ampiicon.At least two provisions are needed in the present invention. One determines the nucleic acid molecule which may be present in a number of copies, the test nucleic acid. The second determines the constitutive nucleic acid molecule which is advantageously present in a constant number of standard nucleic acids. By the method of the invention is meant by a nucleic acid molecule a given nucleotide sequence of 10-12 nucleotides or a gene containing several thousand nucleotides. It can also mean a messenger RNA or nucleotide sequence that is significantly longer than a single gene, i.e. an ampiicon.
5 Bestemmelsen af test- og standard-nukleinsyre gennemføres under anvendelse af den i øvrigt normale sandwich-hybridiseringsmetode som fx er beskrevet i US patentskrift nr. 4.486.539, eller en opløsnings-hybridi-seringsmetode som er beskrevet i offentliggjorte briti-10 ske patentansøgning nr. 2.169.403. Opfindelsen angår også et reagenssæt som indeholder nukleinsyrereagenser bestående af mindst ét testsondepar og mindst ét standardsondepar .The determination of test and standard nucleic acid is carried out using the otherwise normal sandwich hybridization method described, for example, in U.S. Patent No. 4,486,539, or a solution hybridization method disclosed in published British patent application. No. 2,169,403. The invention also relates to a reagent set containing nucleic acid reagents consisting of at least one test probe pair and at least one standard probe pair.
De reagenser, eller sonder, der bruges ved frem-15 gangsmåden fremstilles under anvendelse af rekombinant- DNA-teknikker ud fra nukleinsyrer som er tilstrækkelig ' homologe med test- og standard-nukleinsyrerne. Tilstrækkeligt homologe nukleinsyrer kan også fremstilles syntetisk eller halvsyntetisk.The reagents or probes used in the method are prepared using recombinant DNA techniques from nucleic acids sufficiently homologous to the test and standard nucleic acids. Sufficiently homologous nucleic acids may also be prepared synthetically or semi-synthetically.
20 Test- og standard-nukleinsyrerne kan isoleres di rekte fra celler og identificeres ved forskellige hybri-diseringsteknikker. Sådanne test- og standard-nuklein-syrer er imidlertid også kommercielt tilgængelige fra forskellige genbanker. Test- og standard-nukleinsyrerne 25 kan være enten DNA eller RNA.The test and standard nucleic acids can be isolated directly from cells and identified by various hybridization techniques. However, such test and standard nucleic acids are also commercially available from various gene banks. The test and standard nucleic acids 25 can be either DNA or RNA.
Sådanne par som egner sig til sandwich- eller op-løsnings-hybridiseringsmetoder fremstilles ud fra nukleinsyrer som er tilstrækkeligt homologe med test- og standard-nukleinsyrerne med rekombinant-DNA-teknikker. De re-30 levante nukleinsyrer nedbrydes (digested) ved hjælp af passende restriktionsenzymer; mindst to af de resultaterende restriktionsfragmenter, som befinder sig forholdsvis nær ved hinanden, klones til mindst to egnede vektorer.Such pairs suitable for sandwich or solution hybridization methods are prepared from nucleic acids sufficiently homologous to the test and standard nucleic acids with recombinant DNA techniques. The relevant nucleic acids are degraded (digested) by appropriate restriction enzymes; at least two of the resultant restriction fragments, which are relatively close to each other, are cloned into at least two suitable vectors.
Det ene af fragmenterne, detektorsonden, mærkes med en 35 egnet, detekterbar markering og den anden, fangersonden, fæstnes enten til en passende bærer, eller der fæstnes et stof dertil som muliggør adskillelse af den resulte- 4 DK 174784 B1 rende hybrid fra hybridiseringsblandingen ved hjælp af et yderligere stof såsom den komplementære komponent af et affinitetspar.One of the fragments, the detector probe, is labeled with a suitable, detectable marker and the other, the capture probe, is either attached to a suitable carrier or a substance is attached thereto which allows separation of the resulting hybrid from the hybridization mixture by using an additional substance such as the complementary component of an affinity pair.
Test- og standard-sondeparrene kan samles til pas-5 sende reagenssæt hvor test- og standard-sondeparrene begge er DNA eller RNA, eller hvor test-sondeparret er DNA og standard-sondeparret RNA eller omvendt. Forbehandlingen og den videre behandling af prøverne forud for hy-bridiseringen og hybridiseringsbetingelserne må derefter 10 stemme med disse andre par der bruges ved testen.The test and standard probe pairs can be assembled into appropriate reagent sets where the test and standard probe pairs are both DNA or RNA, or where the test probe pair is DNA and standard probe paired RNA or vice versa. The pretreatment and further processing of the samples prior to the hybridization and hybridization conditions must then be 10 with these other pairs used in the test.
Fremgangsmåden ifølge opfindelsen er særlig velegnet til bestemmelse af antallet af nukleinsyremoleky-ler direkte ud fra cellehomogenater. Fremgangsmåden kan naturligvis også bruges til bestemmelse af rensede el-15 ler rene nukleinsyrer. Før man gennemfører fremgangsmåden ifølge opfindelsen bør man imidlertid vælge den mest hensigtsmæssige forbehandling af nukleinsyreprøven.The process of the invention is particularly well suited for determining the number of nucleic acid molecules directly from cell homogenates. Of course, the process can also be used to determine purified or pure nucleic acids. However, before carrying out the method according to the invention, the most appropriate pretreatment of the nucleic acid sample should be chosen.
Det er muligt at udføre både DNA- og RNA-bestem-melser ved hjælp af fremgangsmåden ifølge opfindelsen.It is possible to perform both DNA and RNA assays by the method of the invention.
20 Deoxyribonukleinsyrer denatureres til opnåelse af enkelt strenge om nødvendigt. Enkeltstrengede messenger-RNA molekyler som potentielt måtte forstyrre hybridiserings-testen kan hydrolyseres, fx ved kogning med alkali. Prøven denatureres ikke i forbindelse med ribonukleinsyre-25 bestemmelser eftersom den dobbeltstrengede deoxyribonu-kleinsyre ikke indgriber i RNA-bestemmelsen. Det er naturligvis muligt at nedbryde DNA med deoxyribonuklease eller ændre det enten kemisk eller mekanisk så det ikke kan deltage i hybridiseringsreaktionen. Man må derfor i 30 forbindelse med DNA- og RNA-bestemmelser vælge en passende fremgangsmåde til yderligere behandling af prøven, eller man kan udlade denne yderligere behandling. Valget af en passende fremgangsmåde til viderebehandling afhænger naturligvis af den fremgangsmåde der bruges 35 til den preliminære behandling af nukleinsyreprøven. Der er beskrevet talrige fremgangsmåder til forbehandling og viderebehandling af nukleinsyreprøver i litteraturen, og 5 DK 174784 B1 herud fra kan man i hvert enkelt tilfælde vælge den mest hensigtsmæssige fremgangsmåde.20 Deoxyribonucleic acids are denatured to obtain single strands if necessary. Single-stranded messenger RNA molecules that could potentially interfere with the hybridization test can be hydrolyzed, for example, by boiling with alkali. The sample is not denatured for ribonucleic acid assays since the double-stranded deoxyribonucleic acid does not interfere with the RNA assay. Of course, it is possible to break down DNA with deoxyribonuclease or change it either chemically or mechanically so that it cannot participate in the hybridization reaction. Therefore, in connection with DNA and RNA assays, an appropriate method for further processing of the sample must be selected or this additional treatment may be discharged. The choice of a suitable method for further processing, of course, depends on the method used for the preliminary treatment of the nucleic acid sample. Numerous methods for pre-processing and further processing of nucleic acid samples have been described in the literature, and from this, the most appropriate method can be selected in each case.
Bestemmelser hvor både test- og standard-nuklein-syrerne er enten DNA eller RNA kan udføres ved anvendel-5 se af en udelt prøve. Bestemmelser hvor test-nukleinsyrer-ne er DNA og standard-nukleinsyrerne RNA eller omvendt, må udføres ved hjælp af en delt prøve eftersom forskellige fremgangsmåder til viderebehandlingen er nødvendige. Prøven kan naturligvis deles selv om test- og standard-nu-10 kleinsyrerne er af samme nukleinsyretype.Determinations in which both the test and standard nucleic acids are either DNA or RNA can be made using an undivided sample. Determinations in which the test nucleic acids are DNA and the standard nucleic acids RNA or vice versa must be carried out by means of a split sample, as different methods of further processing are necessary. Of course, the sample can be split even if the test and standard nu-10 small acids are of the same nucleic acid type.
Hybridiseringstesten selv udføres ved at man bringer den udelte prøveopløsning i kontakt samtidig med mindst ét test-sondepar og ét standard-sondepar. Hvis prøveopløsningen er delt, bringes den særskilt i kon-15 takt med mindst ét test-sondepar og ét standard-sondepar.The hybridization test itself is performed by contacting the undivided sample solution simultaneously with at least one test probe pair and one standard probe pair. If the sample solution is divided, it is contacted separately with at least one test probe pair and one standard probe pair.
I sådanne tilfælde bestemmes mængden af test-nukleinsyre i en reaktionsbeholder og mængden af standard-nuklein-syre i den anden.In such cases, the amount of test nucleic acid in one reaction vessel and the amount of standard nucleic acid in the other are determined.
Uanset om prøven deles eller ej, lader man hybri-20 diseringen finde sted under de mest fordelagtige betingelser og tidsrum i hvert enkelt tilfælde. Når reaktionen eller reaktionerne har fundet sted, skilles de resulterende test- og standard-hybrider fra hybridiserings-blandingen eller -blandingerne ved hjælp af bæreren og 25 vaskes, eller ved hjælp af et isoleringsmiddel såsom et komplementært medlem af et affinitetspar. Den markør som er knyttet til test- og standard-hybriderne måles og resultatet sammenlignes med standardkurver. På denne måde kan man bestemme antallet af til undersøgelse væ-30 rende nukleinsyremolekyler pr. valgt enhed.Whether or not the sample is split, the hybridization is allowed to take place under the most advantageous conditions and times in each case. When the reaction or reactions have taken place, the resulting test and standard hybrids are separated from the hybridization mixture or mixtures by the carrier and washed, or by an insulating agent such as a complementary member of an affinity pair. The marker associated with the test and standard hybrids is measured and the result is compared with standard curves. In this way, one can determine the number of nucleic acid molecules under study per cell. selected device.
Fremgangsmåden ifølge opfindelsen har praktisk diagnostisk værdi, navnlig ved konstatering af nogle typer kræft. I småcellede lungekarcinomer er c-myc-genet ofte multipliceret og dets ekspressionsniveau betydeligt 35 højere end i normalt væv. I tilfælde af neuroblastom er N-myc-genet multipliceret.The method of the invention has practical diagnostic value, especially in detecting some types of cancer. In small cell lung carcinomas, the c-myc gene is often multiplied and its expression level is significantly higher than in normal tissue. In the case of neuroblastoma, the N-myc gene is multiplied.
6 DK 174784 B16 DK 174784 B1
Fremgangsmåden ifølge opfindelsen kan også bruges til påvisning af mutagene eller karcinogene virkninger af visse midler eller udvikling af lægemiddelresistens. Det er kendt at ydre selektionstryk kan resulte-5 rer i forøget ekspression af et givet gen. Ved behandling af kræft udvikler celler resistens mod et givet lægemiddel ved multiplicering af genet, hvis ekspressionsprodukt inaktiverer lægemidlet. Et sådant tilfælde er methotrexat, der inducerer formering af genet for dihy-10 drofulatreduktase (DHFR). Et yderligere eksempel er formering af genet for metallothionin under indflydelse af cadmium.The method of the invention can also be used to detect the mutagenic or carcinogenic effects of certain agents or the development of drug resistance. It is known that external selection pressures may result in increased expression of a given gene. In the treatment of cancer, cells develop resistance to a given drug by multiplying the gene whose expression product inactivates the drug. One such case is methotrexate which induces the propagation of the dihydrofolate reductase (DHFR) gene. A further example is the propagation of the gene for metallothionine under the influence of cadmium.
Ekspressionsniveauet af et gen er betydningsfuldt ud fra synspunktet af cellens fenotype og funktion.The level of expression of a gene is significant from the standpoint of the phenotype and function of the cell.
15 Dette kan undersøges ved måling af mængden af messenger-RNA, der er korreleret med den mængde protein der podes af den. Transskriptionsproduktet af et oncogen bestemmer den måde på hvilken den endeligt vil blive udtrykt ( expressed).This can be investigated by measuring the amount of messenger RNA correlated with the amount of protein seeded by it. The transcription product of an oncogene determines the way in which it will be finally expressed.
20 Ekspressionsniveauerne fra oncogen varierer i af hængighed af celletypen, differentieringsniveauet og cellens udviklingsfase. Fx kopieres på et vist stadium af fosterudviklingen c-myc-oncogenet hurtigt, mens udviklingen på et andet stadium er meget langsom. Graden af 25 multiplicering eller formering (amplification) er ofte korreleret med ekspressionsniveauet for genet, om end sidstnævnte kan forøges signifikant uden førstnævnte. I sådanne tilfælde bestemmes et oncogens rolle bedst ved måling af dets ekspressionsniveau fremfor antallet af 30 kopier. I nogle tilfælde kan kvantitativ bestemmelse af messenger-RNA være simplere og lettere at håndterer end kvantificering af genproduktets celle. Som eksempel kan nævnes c-myc-oncogenet, et labilt protein som let koaguleres af varme.20 The levels of expression from oncogen vary in dependence on the cell type, the level of differentiation, and the developmental phase of the cell. For example, at a certain stage of fetal development, the c-myc oncogene is copied rapidly, while the development at another stage is very slow. The degree of multiplication or amplification is often correlated with the level of expression of the gene, although the latter can be significantly increased without the former. In such cases, the role of an oncogene is best determined by measuring its expression level rather than the number of 30 copies. In some cases, quantitative determination of messenger RNA may be simpler and easier to handle than quantification of the gene product cell. An example is the c-myc oncogene, a labile protein that is easily coagulated by heat.
35 Fremgangsmåden ifølge opfindelsen kan også bru ges til identificering af nummeriske kromosomale abnor-maliteter som Downs syndrom. Ved prænatal diagnostise- 7 DK 174784 B1 ring er det også muligt at bestemme om fosteret er defekt, dvs. homozygot med hensyn til et eller andet recessivt gen.The method of the invention may also be used to identify numerical chromosomal abnormalities such as Down syndrome. In prenatal diagnosis, it is also possible to determine if the fetus is defective, ie. homozygous for some recessive gene.
Fremgangsmåden ifølge opfindelsen og de nuklein-5 syrereagenser der bruges ved fremgangsmåden vil blive beskrevet mere udførligt i det følgende.The process of the invention and the nucleic acid reagents used in the process will be described in more detail below.
Eksempel 1 1 o Kvantificering af et multipliceret (amplified) oncogen a) Nukle i nsy rereagenser_02_ fremstil li n2_der;a.fExample 1 1 o Quantification of a Multiplied (Amplified) Oncogene a) Nucleic Acid Reagents_02_ Prepare Li n2_der; a.f
STANDARD SONDERSTANDARD WITHOUT
CeIle-standardnukleinsyre. c-Ki-rasI-genet er til stede i alle menneskeceller. Sondeparrene til sandwich-15 hybridisering blev fremstillet ved subkloning af Hindlll-fragmentet af c-Ki-rasI-genet, hvis længde er 3,8 kb, og -hvis restriktionskort er beskrevet af Chang et al., i PNAS 79_, side 4848-4852, 1982. Fragmentet er til rådighed, fx klonet ind i pBR322-plasmidet (ATCC 41032) og 20 kan erhverves fx fra ATCC-kultursamlingen.Standardnukleinsyre-T cell is intended. The c-Ki-rasI gene is present in all human cells. The probe pairs for sandwich hybridization were prepared by subcloning the HindIII fragment of the c-Ki rasI gene, whose length is 3.8 kb, and whose restriction map is described by Chang et al., In PNAS 79_, p. 4852, 1982. The fragment is available, for example, cloned into the pBR322 plasmid (ATCC 41032) and can be acquired, for example, from the ATCC culture collection.
Yderligere behandling af celle-standardnuklein-syre. Den ovenfor beskrevne pBR322 klon blev behandlet med Bglll og Hindlll restriktionsenzymer og de resulte-25 rende fragmenter isoleredes fra agarosegelen; rensede fragmenter lokaliseret tæt ved hinanden blev subklonet ind i to egnede vektorer til fremstilling af detektor og fangersonderne.Further treatment of standard cell nucleic acid. The above-described pBR322 clone was treated with BglII and HindIII restriction enzymes and the resulting fragments were isolated from the agarose gel; purified fragments located close to each other were subcloned into two suitable vectors to produce the detector and the capture probes.
30 Standard-dektorsonde. Et Bglll-BgIII fragment med en længde på ca. 1,1 kb blev subklonet ind på BamHI restriktionsenzymstedet på pBR322-plasmidet og mærket ved 1 25 indsnit-translatering med I-mærket dCTP.30 Standard detector probe. A BglII-BglII fragment having a length of approx. 1.1 kb was subcloned into the BamHI restriction enzyme site on the pBR322 plasmid and labeled by 1 25 incision translation with I-labeled dCTP.
35 Standard-fangersonde. Bglll-Hindlll-fragmentet på ca. 0,5 kb indsattes i M13 mp10 og mpl1 fag-vektorer mellem restriktionsstederne for BamHI-og Hindlll-restrik- tionsenzymerne og fæstnedes til et nitrocellulosefilter (150 ng DNA/dia 1 cm).35 Standard Prisoner Probe. The BglII-HindIII fragment of ca. 0.5 kb was inserted into M13 mp10 and mpl1 phage vectors between the restriction sites of the BamHI and HindIII restriction enzymes and attached to a nitrocellulose filter (150 ng DNA / dia 1 cm).
88
DK 174784 WDK 174784 W
TESTSONDERTEST ONDER
55
Test-nukleinsyre. Et sondepar til sandwich-hybri-disering fremstillet ud fra et klonet c-myc gen som fx kan fås fra ATCC-kultursamlingen (ATCC 41010). Genets restriktionskort er beskrevet af Watt et al., PNAS 80, 10 side 6307-6311, 1983.The test nucleic acid. A sandwich pair for sandwich hybridization prepared from a cloned c-myc gene which can be obtained, for example, from the ATCC culture collection (ATCC 41010). The gene restriction map is described by Watt et al., PNAS 80, pages 6307-6311, 1983.
Yderligere behandling af test-nukleinsyren. c-myc-genet behandledes med Hindlll, Xbal og PstI restriktionsenzymer og fragmenterne isoleredes fra agarosegelen, ren-15 sedes og subklonedes ind i passende vektorer for at fremstille detektor- og fangersonderne.Further treatment of the test nucleic acid. The c-myc gene was treated with HindIII, XbaI and PstI restriction enzymes and the fragments were isolated from the agarose gel, purified and subcloned into appropriate vectors to prepare the detector and capture probes.
Test-detektorsonde. De enkeltstrengede ender af Hindlll-Xbal-restriktionsfragmentet af c-myc-genet, med 20 en længde på 3,7 kb, blev gjort dobbeltstrenget ved hjælp af DNA-polymerase. Hindlll-koblerne blev indsat ved hjælp af T4-DNA ligase i de resulterende butendede-DNA-fragmenter; efter fenolekstraktion blev DNA behandlet med Hindlll-restriktionsenzymet. DNA-fragmentet blev der-25 efter klonet ind i pBR322-plasmidet på restriktionstedet for Hindlll-restriktionsenzymet og mærket ved indsnits- 125 translatering med I-mærket dCTP.Test-probe detector. The single-stranded ends of the HindIII-XbaI restriction fragment of the c-myc gene, with a length of 3.7 kb, were double-stranded by DNA polymerase. The HindIII couplers were inserted by T4 DNA ligase into the resultant but-terminated DNA fragments; after phenol extraction, DNA was treated with the HindIII restriction enzyme. The DNA fragment was then cloned into the pBR322 plasmid at the restriction site of the HindIII restriction enzyme and labeled by incision 125 translation with I-labeled dCTP.
Test-fangersonde. X-bal-Pstl-fragmentet på 1,1 kb 30 fra c-myc-genet klonedes ind i M13 mp1Q og mp11 fag-kloningsvektorer mellem restriktionsstederne for Xbal og PstI restriktionsenzymerne og fæstnedes til nitrocellulosefilteret (150 ng DNA/dia 1 cm).Test-capturing probe. The 1.1 kb x-bale PstI fragment of the c-myc gene was cloned into M13 mp1Q and mp11 phage cloning vectors between the restriction sites of XbaI and the PstI restriction enzymes and attached to the nitrocellulose filter (150 ng DNA / dia 1 cm).
35 b) §§§^Ξίϋ!££^§®_?^§£§ηά3Γά1ςηΓνθη35 b) §§§ ^ Ξίϋ! ££ ^ §® _? ^ § £ §ηά3Γά1ςηΓνθη
Den prøve der brugtes til bestemmelse af standardkurven bestod af en alkalidenatureret pBR322 klon af c- 9 DK 174784 B1 myc-genet. Den sandwich-hybridiseringsopløsning til hvilken ovennævnte testsonde blev sat bestod af 4 x SSC, 1 x Denhardt opløsning, 200 yg/ml sildesperma-DNA og 0,2% SDS. Hybridisering fandt sted ved 65°C i 17-19 timer, 5 hvorefter filtrene vaskedes i vaskeopløsningen (0,1 x SSC 0,2% SDS) ved 50°C. Den markør der var knyttet til sandwichhybriderne blev derefter talt i en gammatæller.The sample used to determine the standard curve consisted of an alkali-denatured pBR322 clone of the c- 9 DK 174784 B1 myc gene. The sandwich hybridization solution to which the above test probe was added consisted of 4 x SSC, 1 x Denhardt solution, 200 µg / ml herring sperm DNA and 0.2% SDS. Hybridization took place at 65 ° C for 17-19 hours, after which the filters were washed in the wash solution (0.1 x SSC 0.2% SDS) at 50 ° C. The marker associated with the sandwich hybrids was then counted in a gamma counter.
Tabel 1 10 'Table 1 10 '
Prøve, c-myc_ molekyler/test c-myc-filter 0 40 106 75 15 5 x 106 190 107 340 108 2200 C) Bestemmelse af antal qener 20Sample, c-myc_ molecules / test c-myc filter 0 40 106 75 15 5 x 106 190 107 340 108 2200 C) Determination of number of genes 20
Prøverne omfattede 1) celler fra et menneskes placenta og 2) Colo 320 celler, der kan fås fx fra ATCC kultursamlingen (ATCC-CCC220). DNA blev isoleret fra begge prøver, og der sattes samme mængde celle-DNA, denatu-25 reret ved kogning i alkali, til begge prøver. Denaturering med alkali hydrolyserede al RNA som var til stede i prøven.The samples included 1) cells from a human placenta and 2) Colo 320 cells obtainable, for example, from the ATCC culture collection (ATCC-CCC220). DNA was isolated from both samples and the same amount of cell DNA, denatured by boiling in alkali, was added to both samples. Denaturation with alkali hydrolyzed all the RNA present in the sample.
Testen udvalgtes ved at man til hver af prøverne satte både c-myc og c-Ki-rasI filtrene og de to mærkede 30 reagenser, hvilket gjorde det muligt at måle både standarden og test-DNA for hver prøves vedkommende. På basis af c-Ki-rasI bestemmelser viste hver test sig at indeholde samme mængde DNA, og det kan heraf udledes at c-myc-genet i Colo 320 celler er til stede i et omkring 35 16-20 højere kopiantal end i den normale situation. Re sultaterne fremgår af tabel 2.The test was selected by adding to each of the samples both the c-myc and c-Ki-rasI filters and the two labeled 30 reagents, which made it possible to measure both the standard and the test DNA for each sample. On the basis of c-Ki-rasI assays, each test was found to contain the same amount of DNA, and it can be deduced from this that the c-myc gene in Colo 320 cells is present in about 35 to 20-20 higher copies than in the normal situation. The results are shown in Table 2.
Tabel 2 10 DK 174784 B1Table 2 10 DK 174784 B1
Prøve c-Ki-rasI-filter c-myc filter cpm* cpm* antal - - 5 Human placentalceller 486 340 10Sample c-Ki-rasI filter c-myc filter cpm * cpm * number - - 5 Human placental cells 486 340 10
Colo 320 celler 432 3205 1,6 x 10® * Den aflæsning der er opnået fra blindfilteret er subtraheret fra aflæsningerne.Colo 320 cells 432 3205 1.6 x 10® * The reading obtained from the blank filter is subtracted from the readings.
^ Eksempel 2Example 2
Kvantificering af multipliceret gen a) NukleinsYrereagenser_og_fremstilling_derafQuantification of Multiplied Gene a) Nucleic Acid Reagents_and_production_of
STANDARD SONDERSTANDARD WITHOUT
1 51 5
Cellestandard-nukleinsyre. Kontrol-nukleinsyren blev udtaget fra promoterområdet af metallothionin-genet fra mus, dvs. MT-genet, og den DNA der var umiddelbart ovenfor den. Strukturen af MT-genet er beskrevet af Pav-lakis og Hamer, PNAS 8JD, side 397-401 , 1983. Reference- 20 nukleinsyrefragmentet er tilgængeligt, fx klonet ind i pBPV-MMTneo (432-12) vektoren (ATCC 37224) og kan fx fås fra ATCC-kultursamlingen.Standard cell nucleic acid. The control nucleic acid was taken from the promoter region of the mouse metallothionine gene, i. The MT gene, and the DNA immediately above it. The structure of the MT gene is described by Pav-lakis and Hamer, PNAS 8JD, pages 397-401, 1983. The reference nucleic acid fragment is available, for example, cloned into the pBPV-MMTneo (432-12) vector (ATCC 37224) and can eg from the ATCC culture collection.
Yderligere behandling af cellestandard-nukleinsyre.Further treatment of cell standard nucleic acid.
2 52 5
Det ovenfor beskrevne MT-gen behandledes med Kpnl, Bglll og EcorRI restriktionsenzymer til subkloning ind i pAT153 plasmid. KpnI-enden blev omdannet til en Hindlll-ende med en kobler.The MT gene described above was treated with KpnI, BglII and EcorRI restriction enzymes for subcloning into pAT153 plasmid. The KpnI end was converted to a HindIII end with a coupler.
Standarddetektorsonde. EcoRI-Kpnl-(Hindlll)-fragmentet med en størrelse på ca. 1,2 kb og lokaliseret ovenfor (upstream of) promotorområdet af metallothionin-genet blev klonet til pATI53-plasmidet mellem restriktionsstederne for EcoRI-og Hindlll-restriktionsenzymer- 35 32 ne og mærket ved indsnits-translatenng med P-mærket nukleosidtrifosfater.Standard Detector evil. The EcoRI-KpnI (HindIII) fragment having a size of ca. 1.2 kb and located above the (upstream of) promoter region of the metallothionine gene was cloned to the pATI53 plasmid between the restriction sites of the Eco RI and HindIII restriction enzymes 32 and labeled by incision translation with P-labeled nucleoside triphosphates.
11 DK 174784 B111 DK 174784 B1
Standard-fangersonde. Det 0,8 kb KpnI-BgIII fragment omfattende promotorområdet af metallothionin-genet og området ovenfor det blev klonet ind i Ml 3 mp18 og M13 mp19 fag-vektorer mellem restriktionsstederne for 5 Kpnl og BamHI restriktionsenzymer og fæstnet til nitrocellulosefilteret .Standard capturing probe. The 0.8 kb KpnI-BgIII fragment comprising the promoter region of the metallothionine gene and the region above it was cloned into M1 3 mp18 and M13 mp19 phage vectors between the restriction sites of 5 KpnI and BamHI restriction enzymes and attached to the nitrocellulose filter.
TESTSONDERTEST ONDER
10 Test-nukleinsyre. Sondeparrene for sandwich-hy- bridiseringstesten blev fremstillet ved hjælp af det i handlen gående pMTVdhfr plasmid (Bethesda Research Laboratories, produkt nr. 5369SS), hvis struktur er beskrevet af Lee et al., i Nature 294, side 228-232, 1981.10 Test nucleic acid. The probe pairs for the sandwich hybridization test were prepared using the commercially available pMTVdhfr plasmid (Bethesda Research Laboratories, Product No. 5369SS), whose structure is described by Lee et al., In Nature 294, pages 228-232, 1981.
1515
Yderligere behandling af test-nukleinsyren. ' pMTVdhfr-plasmidet indeholder cDNA fra dihydrofolatre-duktasegenet (DHFR) behandledes med Hindlll og Bglll restriktionsenzymer .Further treatment of the test nucleic acid. The pMTVdhfr plasmid contains cDNA from the dihydrofolate reductase gene (DHFR) treated with HindIII and BglII restriction enzymes.
2020
Test-detektorsonde. HindIII-BglII-fragmentet, der måler 0,75 kb og svarer til det område der koder for DHFR-genet i pMTVdhf-plasmidet blev indsat i plasmid pAT153-vektoren mellem restriktionsstederne for Hindlll 25 og BamHI restriktionsenzymerne og mærkedes ved indsnits- 32 translatering med P-roaerket nukleosidtrif osf ater.Test-probe detector. The HindIII-BglII fragment, measuring 0.75 kb and corresponding to the region encoding the DHFR gene in the pMTVdhf plasmid, was inserted into the plasmid pAT153 vector between the restriction sites of HindIII 25 and the BamHI restriction enzymes and labeled by section 32 translation with P-labeled nucleoside trip, etc.
Test-fangersonde. Et Hindlll fragment med en størrelse på 1,4 kb, taget fra MMTV-genområdet i pMTVdhfr-30 plasmidet klonedes ind i M13 mp18 og M13 mp19 fag-vektorerne .Test-capturing probe. A 1.4 kb HindIII fragment taken from the MMTV genome region of the pMTVdhfr plasmid was cloned into the M13 mp18 and M13 mp19 phage vectors.
b) §®§temmelse_af_standardkurvenb) §®§ void_of_standard curve
Den prøve der brugtes til testen var renset DNA 3 5 fra pMTVdhfr-plasmidet. Selve testen udførtes som beskrevet i eksempel Ib, med den forskel at der brugtes en væ-ske-scintillationstæller til tællingen. Den resulterende standardkurve fremgår af tabel 3.The sample used for the test was purified DNA from the pMTVdhfr plasmid. The test itself was performed as described in Example 1b, with the exception that a liquid scintillation counter was used for the count. The resulting standard curve is shown in Table 3.
12 DK 174784 B112 DK 174784 B1
Tabel 3 5 Prøve_ cmp_ molekyler/test DHRF-filter 0 17 1 06 45 3 x 106 79 10 7 υ 1θ' 210Table 3 5 Sample_ cmp_ molecules / test DHRF filter 0 17 1 06 45 3 x 106 79 10 7 υ 1θ '210
Cellelinier stammende fra musefibroblastcellen NIH 3T3, hvilken cellelinie kan erhverves fra ATCC-kul-15 tursamlingen og hvis nummer er CRL 1658, der var blevet transficeret med forskellige mængder cDNA svarende til mRNA i DHFR-genet, blev podet på cellekulturplader og brugtes som prøven. Cellerne blev lyseret ved hjælp af natriumdodecylsulfat og deres DNA blev fraskåret ved 20 presning fra en sprøjte gennem en fin injektionsnål. En prøve på 250 μΐ svarende til 10° celler, blev udtaget fra homogenisatet og der tilsattes 50 μΐ NaOH. Prøven kogtes og neutraliseredes med eddikesyre og hybridise-ringsblandingen. Det samlede rumfang var 0,5 ml. Alle de 25 ovenfor beskrevne sonder blev tilsat samtidig og der tilsattes et såkaldt blindfilter som baggrundskontrol. Hybridiserng, vask og markørtælling blev udført som i eksempel Ib, dog med den forskel at der brugtes en væ-skescintillationstæller til tællingen. Resultaterne frem-30 går af tabel 4.Cell lines derived from the mouse fibroblast cell NIH 3T3, which cell line can be acquired from the ATCC culture collection and whose number is CRL 1658, which had been transfected with different amounts of cDNA corresponding to mRNA in the DHFR gene, were seeded on cell culture plates and used as the sample. The cells were lysed by sodium dodecyl sulfate and their DNA was excised by pressing from a syringe through a fine injection needle. A 250 μΐ sample corresponding to 10 ° cells was taken from the homogenate and 50 μΐ NaOH was added. The sample was boiled and neutralized with acetic acid and the hybridization mixture. The total volume was 0.5 ml. All the 25 probes described above were added at the same time and a so-called blank filter was added as a background check. Hybridization, washing, and marker counting were performed as in Example 1b, with the exception that a liquid scintillation counter was used for the counting. The results are shown in Table 4.
3535
Tabel 4 13 DK 174784 B1Table 4 13 DK 174784 B1
Celle MT Antal cel- _DHFRCell MT Number of cell _DHFR
cpm* ler i prø- cpm* antal mole- antal 5 ven kyler i prø- kopier _ven_cpm * smiles in sample cpm * number of mole number 5 friend cool in samples _ven_
Kontrolcelle {ingen DHFR- , cDNA) 182 1,05 x 10 21 < 10° 1Q Linie I 138 0,9 x 106 80 3 x 106 3Control cell (no DHFR, cDNA) 182 1.05 x 10 21 <10 ° 1Q Line I 138 0.9 x 106 80 3 x 106 3
Linie II 210 1 ,25 x 106 732 5 x 107_40 * cpm: den aflæsning der gives af blindfilteret er fratrukket.Line II 210 1, 25 x 106 732 5 x 107_40 * cpm: the reading given by the blank filter is deducted.
15 MT-genet er en intern markør som måler antallet af celler som er til stede i en prøve. Resultaterne vi-ser at 10 -celler ved denne test gav et MT-specifikt signal på 165 + 20 cpm. DHFR-reagenserne måler mængden af DHFR-cDNA. Antallet af celler blev udledet af det MT-20 specifikke signal. Det var således muligt at bestemme antallet af DHFR-cDNA kopier i forskellige cellelinier som det fremgår af tabel 4,The MT gene is an internal marker that measures the number of cells present in a sample. The results show that 10 cells in this test gave an MT-specific signal of 165 + 20 cpm. The DHFR reagents measure the amount of DHFR cDNA. The number of cells was deduced by the MT-20 specific signal. Thus, it was possible to determine the number of DHFR cDNA copies in different cell lines as shown in Table 4.
Eksempel 3 25Example 3 25
Kvantificering af messenger-RNAQuantification of messenger RNA
a) Nukleinsyrerea2enser_og_fremstilling_derafa) Nucleic Acid Reagents and Preparation
Under anvendelse af de i eksempel 2 beskrevne testsonder er det også muligt at måle den mængde mRNA 30 som er afledet af DHFR-cDNA. Strukturen af pMTVdhfr- plasmidet er en sådan,at transkription af DHFR-genet begynder ved MMTV-promotoren. De resulterende messengers har en længde på ca. 1,0 kb. Heraf stammer ca. 0,25 kb fra MMTV-promotorområdet og resten af DHFR-cDNA (Lee et 35 al., Nature 2£4, side 228-232, 1981.Using the test probes described in Example 2, it is also possible to measure the amount of mRNA 30 derived from DHFR cDNA. The structure of the pMTVdhfr plasmid is such that transcription of the DHFR gene begins at the MMTV promoter. The resulting messengers have a length of approx. 1.0 kb. Of this, approx. 0.25 kb from the MMTV promoter region and the rest of the DHFR cDNA (Lee et al., Nature 2 £ 4, pages 228-232, 1981.
14 DK 174784 B114 DK 174784 B1
STANDARD-SONDERSTANDARD PROBES
Cellestandardnukleinsyre, standarddetektor og standardfangersonde var som beskrevet i eksempel 2.Cell standard nucleic acid, standard detector and standard capture probe were as described in Example 2.
55
TEST-SONDERTEST PROBES
Test-nukleinsyren, testdetektoren og test-fanger-sonden var som beskrevet i eksempel 2.The test nucleic acid, test detector, and test capture probe were as described in Example 2.
10 b) Bestemmelse af standardkurven10 b) Determination of the standard curve
Den prøve der brugtes til bestemmelse af standardkurven bestod af messenger-RNA svarende til dihydrofo- latreduktase-genet, frembragt ved transkription in vi-1 5 tro. Den DNA der behøves til transknptionen var fremstillet ved subkloning af 1,4 kb HindIII-fragmentet af MMTV-promotoren fra pMTVdhfr-plasmidet og 0,75 kb HindIII-BglII-fragmentet (DHFR-cDNA) ved siden af hinanden ind i pSP64-plasmidet (Progema Biotec) mellem re- 20 striktionsstederne for Hindlll og BanHI restriktionsenzymer. Prøven af RNA blev opbevaret i 0,2% SDS vandig opløsning.The sample used to determine the standard curve consisted of messenger RNA corresponding to the dihydrofolate reductase gene produced by transcription in vitro. The DNA required for transcription was prepared by subcloning the 1.4 kb HindIII fragment of the MMTV promoter from the pMTVdhfr plasmid and the 0.75 kb HindIII-BglII fragment (DHFR cDNA) side by side into the pSP64 plasmid (Progema Biotec) between the restriction sites of HindIII and BanHI restriction enzymes. The sample of RNA was stored in 0.2% SDS aqueous solution.
Sandwich-hybridiseringsforsøget udførtes som beskrevet i eksempel Ib og 2b, men denaturering blev ude- 25 1 ladt.The sandwich hybridization experiment was performed as described in Examples Ib and 2b, but denaturation was omitted.
Tabel 5Table 5
Prøve cmp 30 molekyler/test DHFR-filter 0 20 5 x 106 65 107 130 5 x 107 390 J D β 10B 653 15 DK 174784 B1 c) Bestemrnelse_af _antallet_af _messenger-RNA_rTiolekylerSample cmp 30 molecules / test DHFR filter 0 20 5 x 106 65 107 130 5 x 107 390 J D β 10B 653 15 DK 174784 B1 c) Determination_of_the_number_of_messenger RNA_riol
Det antal messenger-RNA molekyler som svarer til DHFR-genet blev bestemt fra de i eksempel 2 beskrevne cellelinier.The number of messenger RNA molecules corresponding to the DHFR gene was determined from the cell lines described in Example 2.
5 Cellerne blev analyseret ved hjælp af natriumdo- decylsulfat og deres DNA blev afskåret svagt ved presning af en sprøjte gennem en fin injektionsnål. En prøve på 250 μΐ af homogenisatet blev udtaget, svarende til ca. 5x10^ celler. Homogenisatet blev derefter sat til 10 sandwich-hybridiseringstesten uden denaturering. Sandwich-hybridisering fandt sted som beskrevet i eksemplerne 2c og Ib, dog med den forskel at der kun sattes DHFR-sonder til hybridiseringsopløsningen. I en parallel prøve med 250 μΐ homogenisat bestemtes celleantallet ved hjælp af 15 MT-sonden som beskrevet i eksempel 2c.The cells were analyzed by sodium dodecyl sulfate and their DNA was weakly cut by pressing a syringe through a fine injection needle. A sample of 250 μΐ of the homogenate was taken, corresponding to approx. 5x10 5 cells. The homogenate was then added to the 10 sandwich hybridization test without denaturation. Sandwich hybridization took place as described in Examples 2c and 1b, with the exception that only DHFR probes were added to the hybridization solution. In a 250 µΐ parallel homogenize sample, the cell number was determined using the 15 MT probe as described in Example 2c.
Resultaterne fremgår af tabel 6.The results are shown in Table 6.
Tabel 6 20 Celle MT Celleantal _DHFR_ cpm* i prøven cpm* antal mole- .antal pr..Table 6 20 Cell MT Cell count _DHFR_ cpm * in sample cpm * number of mole number.
kyler i prøven cellecools in the sample cell
Linie I 380 3,5 x 106 1465 3,45 x 108 100Line I 380 3.5 x 106 1465 3.45 x 108 100
Linie II 430 4,2 x 106 4800 2 x 109 500 25 ---- * cmp: Den aflæsning der opnås med blindfilteret er fratrukket.Line II 430 4.2 x 106 4800 2 x 109 500 25 ---- * cmp: The reading obtained with the blank filter is deducted.
Resultaterne viste at cellelinie I pr. celle pro-30 ducerede ca. 100 messenger-RNA molekyler ud fra DHFR- generne og cellelinie II producerede ca. 500 messenger-RNA molekyler fra DHFR-generne.The results showed that cell line I per cell produced approx. 100 messenger RNA molecules from the DHFR genes and cell line II produced approx. 500 messenger RNA molecules from the DHFR genes.
35 16 DK 174784 B135 16 DK 174784 B1
Eksempel 4Example 4
Kvantificering af opformeret gen ved opløsnings-hybri- disering_ a ) Nukleinsyrereagenser_og_fremstillingderafQuantification of Amplified Gene by Solution Hybridization_ (a) Nucleic Acid Reagents_and_ Preparation of
5 STANDARD-SONDER5 STANDARD WITHOUT
Cellestandard-nukleinsyren, standarddetektoren og standardf angersonden var som beskrevet i eksempel 2.The cell standard nucleic acid, standard detector and standard capture probe were as described in Example 2.
Det 1,2 kb EcoRI-Kpnl-(Hindlll) fragment i pATl53 blev 125 mærket ved indskærings-translatering med I-mærket 10 deoxycytidin. De 0,8 kb Kpnl-Bglll-fragmenter i M13 mp18 og M13 mpl9 blev modificeret med biotin under anvendelse af "Photoprobe" reagenset (Vector Laboratories, CA, USA, produkt nr. SP-1000).The 1.2 kb Eco RI-KpnI (HindIII) fragment in pAT153 was 125 labeled by cut-in translation with I-labeled 10 deoxycytidine. The 0.8 kb Kpnl-Bglll fragments in M13 mp18 and M13 mpl9 were modified with biotin using the Photoprobe reagent (Vector Laboratories, CA, USA, product no. SP-1000).
15 TESTSONDER15 TESTS WITHOUT
Test-nukleinsyren, test-detektoren og test-fan-gersonden var som beskrevet i eksempel 2. Det 0,75 kb Hindlll-Bglll fragment i pAT153 blev mærket med I-mærket deoxycytidin. De 1,4 kb Hindlll-fragmenter i M13 20 mp18 og Ml 3 mp19 blev biotinyleret ved hjælp af "Photo-probe" som ovenfor.The test nucleic acid, test detector and test capture probe were as described in Example 2. The 0.75 kb HindIII-BglII fragment in pAT153 was labeled with I-labeled deoxycytidine. The 1.4 kb HindIII fragments in M13 20 mp18 and M1 3 mp19 were biotinylated by "Photo-probe" as above.
b) §§§temmelse_af_standardkurverneb) §§§ mood_of_standard curves
Der fremstilledes en cellestandardkurve ved hjælp 25 af en kendt mængde celler, ud fra hvilken hybridiserings-signalet måltes under anvendelse af standardsonderne som genkender MT-genet. Der fremstilledes en test-nuklein-syre-standardkurve ved pMTVdhfr-plasmidet og de testsonder som genkender dette plasmid. Der udførtes hybridise-ringer i 200 μΐ af en opløsning bestående af 0,6 M NaCl, 20 mM fosfatpuffer, pH 7,5, 1 mM EDTA, 4% polyætylengly-kol (PEG 6000) i 1,5 time ved 70°C. Efter reaktionen tilsattes der 50 μΐ streptavidin-agarose (Betheseda Research Laboratories, Maryland, USA, produkt nr. 5942SA), og 1 M NaCl, 10 mM natriumfosfat, pH 7,5, 1 mM EDTA til et slutrumfang på 500 μΐ. Hybriderne opsamledes på strep- 17 DK 174784 B1 tavidin-agarosen ved 37°C i 15 minutter. Agarosen vaskedes én gang i 5 minutter med den pufrede 1 M NaCl-opløs-ning ved 37°C og to gange i 2 minuter med 15 mM NaCl, 1,5 niM natriumcitrat ved 55°C. Mængden af bundne hydrider 5 bestemtes ved måling af agarosen i en gammatæller (Sy-vånen et al., Nucleic Acids Res. J_4, 5037-5048, 1986). Resultaterne fremgår af tabellerne 7 og 8.A cell standard curve was prepared using a known amount of cells from which the hybridization signal was measured using the standard probes recognizing the MT gene. A test nucleic acid standard curve was prepared by the pMTVdhfr plasmid and the test probes recognizing this plasmid. Hybridizations were performed in 200 µl of a solution consisting of 0.6 M NaCl, 20 mM phosphate buffer, pH 7.5, 1 mM EDTA, 4% polyethylene glycol (PEG 6000) for 1.5 hours at 70 ° C. . After the reaction, 50 μΐ of streptavidin agarose (Betheseda Research Laboratories, Maryland, USA, product no. 5942SA) and 1 M NaCl, 10 mM sodium phosphate, pH 7.5, 1 mM EDTA were added to a final volume of 500 μΐ. The hybrids were collected on the strep-tavidine agarose at 37 ° C for 15 minutes. The agarose was washed once for 5 minutes with the buffered 1 M NaCl solution at 37 ° C and twice for 2 minutes with 15 mM NaCl, 1.5 µM sodium citrate at 55 ° C. The amount of bound hydrides 5 was determined by measuring the agarose in a gamma counter (Syvånen et al., Nucleic Acids Res. J_4, 5037-5048, 1986). The results are shown in Tables 7 and 8.
Tabel 7 10 _Table 7
Prøve_ cpm_ celler/test MT-sonder 0,8 x 106 162 1,6 x 106 216 15 3 x 106 298Sample_ cpm_ cells / test MT probes 0.8 x 106 162 1.6 x 106 216 15 3 x 106 298
Tabel 8 20 Prøve_ cpm_ molekyler/test DHFR-sonder 106 148 5 x 106 394 5 x 107 2240 25 c) Bestemmelse_af_antal_generTable 8 20 Sample_ cpm_ molecules / test DHFR probes 106 148 5 x 106 394 5 x 107 2240 25 c) Determination_of_number of genes
Prøver af de i eksempel 2 beskrevne cellelinier blev behandlet på lignende måde, dog således at rumfan-30 get pr. prøve svarende til 2 x 10^ celler var 125 μΐ.Samples of the cell lines described in Example 2 were treated in a similar manner, however, so that the sample corresponding to 2 x 10 6 cells was 125 μΐ.
Bestemmelserne af antal celler og antal test-nukleinsyre-molekyler udførtes i særskilte ampuller ved tilsætning af celleprøven, vedkommende detektor og fangersonder, og komponenterne af hybridiseringsblandingen til et slut-35 rumfang på 200 μΐ. Der indgik også kontrolbestemmelser uden cellestandard eller test-DNA. Hybridisering, opsamling af hybrider, vask og måling udførtes som beskre- 18 DK 174784 B1 vet i eksempel 4b. Resultaterne aflæstes fra standardkurver fremstillet i parallel som beskrevet i eksempel 4b. Resultaterne fremgår af tabel 9.The determinations of the number of cells and the number of test nucleic acid molecules were carried out in separate ampoules by the addition of the cell sample, the detector and capture probes, and the components of the hybridization mixture to a final volume of 200 μΐ. Control determinations were also included without cell standard or test DNA. Hybridization, collection of hybrids, washing and measurement were performed as described in Example 4b. The results are read from standard curves prepared in parallel as described in Example 4b. The results are shown in Table 9.
5 Tabel 9Table 9
Celle _J4T_ DHFR______ cpm* antal cel- cpm* antal mole- antal ler i prøven kyler i prøven kopier 10--Cell _J4T_ DHFR______ cpm * number of cell cpm * number of mole number of clays in sample cool in sample copies 10--
Kontrolcelle 253 2,3 x 106 73 < 105Control cell 253 2.3 x 106 73 <105
Linie I 210 1,5 x 106 233 3,8 x 106 3Line I 210 1.5 x 106 233 3.8 x 106 3
Linie II 237 2,1 x 106 3059 8,8 x 107 42 15 * cpm: Værdier fra kontrolbestemmelser uden cellestan dard eller test-nukleinsyre er fratrukket.Line II 237 2.1 x 106 3059 8.8 x 107 42 15 * cpm: Values from control assays without cellular or test nucleic acid are deducted.
20 25 30 3520 25 30 35
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US5714380A (en) | 1986-10-23 | 1998-02-03 | Amoco Corporation | Closed vessel for isolating target molecules and for performing amplification |
IL86724A (en) | 1987-06-19 | 1995-01-24 | Siska Diagnostics Inc | Method and kits for the amplification and detection of nucleic acid sequences |
EP0304845A3 (en) * | 1987-08-28 | 1991-03-06 | Profile Diagnostic Sciences Inc. | Method and kit for assaying gene expressions |
DE68921918T2 (en) * | 1988-05-09 | 1995-09-07 | Univ Temple | Procedure for predicting the effectiveness of antineoplastic treatment in individual patients. |
AU629845B2 (en) * | 1988-08-30 | 1992-10-15 | Abbott Laboratories | Detection and amplification of target nucleic acid sequences |
WO1990014440A1 (en) * | 1989-05-18 | 1990-11-29 | The United States Of America, Represented By The Secretary, United States Department Of Commerce | RNA PROBE FOR DETECTING c-fes mRNA |
US5232829A (en) * | 1989-09-29 | 1993-08-03 | Hoffmann-La Roche Inc. | Detection of chlamydia trachomatis by polymerase chain reaction using biotin labelled lina primers and capture probes |
DK138090D0 (en) * | 1990-06-06 | 1990-06-06 | Novo Nordisk As | DIAGNOSTIC METHOD OF ANALYSIS |
EP0534640B1 (en) * | 1991-09-23 | 1996-10-02 | Pfizer Inc. | Process for detecting specific mRNA and DNA in cells |
US6300058B1 (en) | 1992-01-29 | 2001-10-09 | Hitachi Chemical Research Center, Inc. | Method for measuring messenger RNA |
GB9210916D0 (en) * | 1992-05-21 | 1992-07-08 | Isis Innovation | Nucleic acid quantification |
US5580971A (en) * | 1992-07-28 | 1996-12-03 | Hitachi Chemical Company, Ltd. | Fungal detection system based on rRNA probes |
CA2140763A1 (en) * | 1992-07-28 | 1994-02-03 | Masato Mitsuhashi | Gene detection system |
ES2055661B1 (en) * | 1993-01-20 | 1995-03-01 | Univ Malaga | DETERMINATION OF THE GENE EXPRESSION BY SPECIFIC CAPTURE OF RNA AND ITS DIRECT QUANTIFICATION BY CAPILLARY ELECTROPHORESIS IN A FREE ZONE. |
GB9309966D0 (en) * | 1993-05-14 | 1993-06-30 | Nordion Int Inc | Detection of prostrate-specific antigen in breast tumors |
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AT401062B (en) * | 1994-09-26 | 1996-06-25 | Immuno Ag | Method for quantifying nucleic acids |
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