WO1998004745A1 - Nucleic acid amplification method: hybridization signal amplification method (hsam) - Google Patents

Nucleic acid amplification method: hybridization signal amplification method (hsam) Download PDF

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Publication number
WO1998004745A1
WO1998004745A1 PCT/US1997/013390 US9713390W WO9804745A1 WO 1998004745 A1 WO1998004745 A1 WO 1998004745A1 US 9713390 W US9713390 W US 9713390W WO 9804745 A1 WO9804745 A1 WO 9804745A1
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WO
WIPO (PCT)
Prior art keywords
nucleic acid
probe
amplification
target nucleic
ligand
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.)
Ceased
Application number
PCT/US1997/013390
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English (en)
French (fr)
Inventor
David Y. Zhang
Margaret Brandwein
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Icahn School of Medicine at Mount Sinai
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Mount Sinai School of Medicine
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Publication date
Application filed by Mount Sinai School of Medicine filed Critical Mount Sinai School of Medicine
Priority to JP50912198A priority Critical patent/JP2001521373A/ja
Priority to EP97935207A priority patent/EP1007728A4/en
Publication of WO1998004745A1 publication Critical patent/WO1998004745A1/en
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING 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
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING 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
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING 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
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • C12Q1/682—Signal amplification
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING 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
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING 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
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/686—Polymerase chain reaction [PCR]
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING 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
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6862—Ligase chain reaction [LCR]
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING 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
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6865—Promoter-based amplification, e.g. nucleic acid sequence amplification [NASBA], self-sustained sequence replication [3SR] or transcription-based amplification system [TAS]

Definitions

  • the present invention is directed to the development of rapid, sensitive assays useful for the detection and monitoring of pathogenic organisms, as well as the detection of abnormal genes in an individual. Moreover, the methodology of the present invention can be readily standardized and automated for use in the clinical laboratory setting.
  • the amplification probes which in the method may be covalently joined end to end, form a contiguous ligated amplification sequence.
  • the assembly of the amplifiable DNA by ligation increases specificity, and makes possible the detection of a single mutation in a target.
  • This ligated amplification sequence rather than the target nucleic acid, is either directly detected or amplified, allowing for substantially the same amplification conditions to be used for a variety of different infectious agents and, thus, leading to more controlled and consistent results being obtained.
  • multiple infectious agents in a single sample may be detected using the multiplex amplification methodology disclosed.
  • the present methods may be used with routine clinical samples obtained for testing pu ⁇ oses by a clinical diagnostic laboratory.
  • Clinical samples that may be used in the present methods include, inter alia, whole blood, separated white blood cells, sputum, urine, tissue biopsies, throat swabbings and the like, Le., any patient sample normally sent to a clinical laboratory for analysis.
  • a series of tenfold dilutions (in TE Buffer) containing from 10 ng/ml to 1 fg/ml of the control template is made and stored at -70 °C until use.
  • Sample tissue e.g. liyer
  • Sample tissue that may be frozen, or formalin-fixed and embedded in paraffin
  • the sections may be washed with xylene and ethanol to remove the paraffin.
  • the sections may then be treated with a proteolytic enzyme, such as trypsin. to increase membrane permeability.
  • the sections may be further treated with RNAase-free DNAase to eliminate cellular DNA.
  • the DNA amplified by RAM is then detected by methods known in the art for detection of DNA. Because RAM results in exponential amplification, the resulting large quantities of DNA can be conveniently detected, for example by gel electrophoresis and visualization for example with ethidium bromide. Because the RAM extension products differ in size depending upon the number of units extended from the closed circular DNA, the RAM products appear as a smear or ladder when electrophoresed.
  • the circularizable probe is designed to contain a unique restriction site, and the RAM products are digested with the corresponding restriction endonuclease to provide a large amount of a single sized fragment of one unit length i.e., the length of the circularizable probe.
  • the fragment can be easily detected by gel electrophoresis as a single band.
  • a ligand such as biotin or digoxigenin can be inco ⁇ orated during primer extension and the ligand-labeled single stranded product can be detected as described hereinabove.
  • nucleotides at positions 71-92 comprise the 3' specific portion of this probe, complementary and hybridizable to a portion of the gag region of HIV- 1 RNA immediately adjacent to the portion of the gag region complementary to nucleotides 1-23 of Capture/Amp-probe-1 (HIV).
  • Nucleotides 1-70 comprise the generic 5' portion of Amp-probe-2 (HIV).
  • the second probe is Amp-probe-2 (MAV), an oligodeoxyribonucleotide of 90 nucleotides in length, with the following sequence (also listed below as SEQ ID NO. 11): 1 11 21 31
  • HCV A each contain a nucleotide sequence complementary to and hybridizable with the conserved 5'UTR of HCV RNA.
  • the amplification probes, Amp-probe-2 (HCV A) and Amp-probe-2A (HCV A), bound to target RNA were then covalently joined to create the ligated amplification sequence (HCV A) that was utilized as a template for PCR amplification.
  • the hybrid complex was resuspended in 20 ⁇ l ligase buffer with 5 units of T 4 DNA ligase (Boehringer) and incubated for 1 hour at 37° C for the ligation reaction.
  • the deparaffinized tissues were lysed by incubating at 100°C for 30 min in 250 ⁇ l of lysis buffer containing 5 M guanidinium thiocyanate
  • hybrids consisting of two DNA capture probes and two DNA hemiprobes bound to their HCV RNA target.
  • the first PCR reaction was combined with the reverse transcription step in the same tube containing 50 ⁇ l of reaction buffer prepared as follows: 20 units of Rnase inhibitor (Promega), 100 units of Moloney murine leukemia virus reverse transcriptase (Gibco BRL), 100 ng of each outer primer, 200 ⁇ M of each of the four deoxynucleotides, 1 unit of Taq DNA polymerae (Boehringer Mannheim) and IX Taq buffer containing 1.5 mM MgCl 2 .
  • reaction buffer prepared as follows: 20 units of Rnase inhibitor (Promega), 100 units of Moloney murine leukemia virus reverse transcriptase (Gibco BRL), 100 ng of each outer primer, 200 ⁇ M of each of the four deoxynucleotides, 1 unit of Taq DNA polymerae (Boehringer Mannheim) and IX Taq buffer containing 1.5 mM MgCl 2 .
  • a synthetic DNA target was detected by mixing 10 12 molecules of phosphorylated circularizable probe having SEQ ID NO.31 with 10 13 molecules of synthetic HCV DNA target in 10 ⁇ of IX ligation buffer, heating at 65°C for two minutes, and cooling to room temperature for ten minutes.
  • One ⁇ of ligase was added to the mix and incubated at 37°C for one hour, followed by addition of 10 13 molecules of 32 P-labeled Ext-primer having SEQ ID NO:27.
  • the mixture was heated to 100°C for five minutes and then cooled to room temperature for twenty minutes. Forty ⁇ l of Klenow mix and dNTPs were added to the reaction and incubated at 37°C. Ten ⁇ l aliquots were removed at 0.
  • Deparaffinized tissue was lysed by incubation at 100°C for 30 minutes, then 65 °C for 30 minutes in 250 ⁇ l of lysis buffer: 5M guanidium thiocyanate (GTC)(Fluka), 0.5% bovine serum albumin (Sigma), 80 mM EDTA, 400 mM Tris HCl (pH 7.5), and 0.5% sodium-N-lauroylsarcosine (Sigma).
  • GTC guanidium thiocyanate
  • bovine serum albumin Sigma
  • 80 mM EDTA 400 mM Tris HCl (pH 7.5)
  • sodium-N-lauroylsarcosine Sigma
  • TTCTCGATTAGGTTACTG antisense SEQ ID NO. 29
  • MOLECULE TYPE DNA (genomic)

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • General Engineering & Computer Science (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Analytical Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Genetics & Genomics (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • General Health & Medical Sciences (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
PCT/US1997/013390 1996-07-31 1997-07-30 Nucleic acid amplification method: hybridization signal amplification method (hsam) Ceased WO1998004745A1 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
JP50912198A JP2001521373A (ja) 1996-07-31 1997-07-30 核酸増幅法：ハイブリダイゼーションシグナル増幅法（ｈｓａｍ）
EP97935207A EP1007728A4 (en) 1996-07-31 1997-07-30 AMPLIFICATION METHOD OF NUCLEIC ACIDS: AMPLIFICATION METHOD WITH HYBRIDIZATION SIGNAL (HSAM)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US08/690,495 US5876924A (en) 1994-06-22 1996-07-31 Nucleic acid amplification method hybridization signal amplification method (HSAM)
US08/690,495 1996-07-31

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WO1998004745A1 true WO1998004745A1 (en) 1998-02-05

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EP (1) EP1007728A4 (enExample)
JP (1) JP2001521373A (enExample)
WO (1) WO1998004745A1 (enExample)

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