SG11201808514YA - Method for designing mutant primer - Google Patents

Method for designing mutant primer

Info

Publication number
SG11201808514YA
SG11201808514YA SG11201808514YA SG11201808514YA SG11201808514YA SG 11201808514Y A SG11201808514Y A SG 11201808514YA SG 11201808514Y A SG11201808514Y A SG 11201808514YA SG 11201808514Y A SG11201808514Y A SG 11201808514YA SG 11201808514Y A SG11201808514Y A SG 11201808514YA
Authority
SG
Singapore
Prior art keywords
primer
nucleotide residue
region
loop structure
designing
Prior art date
Application number
SG11201808514YA
Inventor
Makoto Takaishi
Original Assignee
Daiken Medical Co Ltd
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 Daiken Medical Co Ltd filed Critical Daiken Medical Co Ltd
Priority claimed from PCT/JP2017/004162 external-priority patent/WO2017169119A1/en
Publication of SG11201808514YA publication Critical patent/SG11201808514YA/en

Links

Classifications

    • 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
    • C12Q1/6853—Nucleic acid amplification reactions using modified primers or templates
    • 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
    • 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
    • C12Q1/6811—Selection methods for production or design of target specific oligonucleotides or binding molecules
    • 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]
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/20—Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Physics & Mathematics (AREA)
  • Biophysics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • General Health & Medical Sciences (AREA)
  • Molecular Biology (AREA)
  • Genetics & Genomics (AREA)
  • Analytical Chemistry (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • General Engineering & Computer Science (AREA)
  • Immunology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

METHOD FOR DESIGNING MUTANT PRIMER Provided is a novel method for designing a mutant primer in which a nonspecific amplification caused by a primer dimer or loop structure scarcely occurs. A method for designing a primer having a mutation introduced thereinto, said method comprising a mutation introduction site-selection step for selecting, as a mutation introduction site, one or more nucleotide residues, said nucleotide residue(s) being contained in a basic primer sequence and satisfying one or more requirements selected from the group consisting of the following requirements (1) to (4): (1) a nucleotide residue possibly contributing to the formation of a primer dimer; (2) a nucleotide residue possibly contributing to the formation of a loop structure in a single primer molecule; (3) when it is predicted that a primer comprising the aforesaid basic primer sequence forms a primer dimer, a nucleotide residue positioned in a region other than a region to which the primer is complementarily or non-complementarily hybridizable; and (4) when it is predicted that a primer comprising the aforesaid basic primer sequence forms a loop structure in a single primer molecule, a nucleotide residue positioned in a region other than a region which forms the loop structure. [Fig. 16]
SG11201808514YA 2016-03-30 2017-02-06 Method for designing mutant primer SG11201808514YA (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
JP2016067252 2016-03-30
JP2016154013A JP6681804B2 (en) 2016-03-30 2016-08-04 Mutation primer design method
PCT/JP2017/004162 WO2017169119A1 (en) 2016-03-30 2017-02-06 Method for designing mutant primer

Publications (1)

Publication Number Publication Date
SG11201808514YA true SG11201808514YA (en) 2018-10-30

Family

ID=60044331

Family Applications (1)

Application Number Title Priority Date Filing Date
SG11201808514YA SG11201808514YA (en) 2016-03-30 2017-02-06 Method for designing mutant primer

Country Status (8)

Country Link
US (1) US20190144933A1 (en)
EP (1) EP3438257A4 (en)
JP (1) JP6681804B2 (en)
KR (1) KR20180129806A (en)
CN (1) CN109072221A (en)
CA (1) CA3019468A1 (en)
SG (1) SG11201808514YA (en)
ZA (1) ZA201806890B (en)

Family Cites Families (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
ES2230631T3 (en) * 1997-03-20 2005-05-01 F. Hoffmann-La Roche Ag MODIFIED PRIMERS.
DE60115811T2 (en) * 2000-10-25 2006-08-03 Roche Diagnostics Gmbh Amplification using modified primers
JP2008535518A (en) * 2005-04-14 2008-09-04 アプレラ コーポレイション 3 'modified oligonucleotides containing pseudoisocytosine nucleobase derivatives and their application as primers or probes
EP2162551B1 (en) * 2007-07-03 2017-08-23 Genaphora LTD. Chimeric primers for improved nucleic acid amplification reactions
KR101110013B1 (en) * 2007-10-05 2012-02-29 (주)바이오니아 Primers for pcr amplification comprising abasic parts within the primer sequences
US9783844B2 (en) * 2012-04-27 2017-10-10 Kaneka Corporation Method for amplifying nucleic acid and method for detecting amplified nucleic acid
US9428802B2 (en) * 2012-07-03 2016-08-30 Mackay Memorial Hospital Selective-competitive primer and method of use
ES2874275T3 (en) * 2016-02-25 2021-11-04 Hoffmann La Roche Elimination of primer-primer interactions during primer extension

Also Published As

Publication number Publication date
JP6681804B2 (en) 2020-04-15
EP3438257A1 (en) 2019-02-06
CA3019468A1 (en) 2017-10-05
US20190144933A1 (en) 2019-05-16
EP3438257A4 (en) 2019-10-23
ZA201806890B (en) 2020-01-29
JP2017184710A (en) 2017-10-12
CN109072221A (en) 2018-12-21
KR20180129806A (en) 2018-12-05

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