Enhancing PCR amplification and sequencing using DNA-binding proteins View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

1994-12

AUTHORS

Ralph Rapley

ABSTRACT

The polymerase chain reaction (PCR) is a powerful core molecular biology technique, which when coupled to chain termination sequencing allows gene and DNA sequence information to be derived rapidly. A number of modifications to the basic PCR format have been developed in an attempt to increase amplification efficiency and the specificity of the reaction. We have applied the use of DNA-binding protein, gene 32 protein from bacteriophage T4 (T4gp32) to increase amplification efficiency with a number of diverse templates. In addition, we have found that using single-stranded DNA-binding protein (SSB) or recA protein in DNA sequencing reactions dramatically increases the resolution of sequencing runs. The use of DNA-binding proteins in amplification and sequencing may prove to be generally applicable in improving the yield and quality of a number of templates from various sources. More... »

PAGES

295-298

Journal

TITLE

Molecular Biotechnology

ISSUE

3

VOLUME

2

Author Affiliations

Related Patents

  • Methods For Generating Polynucleotides Having Desired Characteristics By Iterative Selection And Recombination
  • Method For Creating Polynucleotide And Polypeptide Sequences
  • Methods And Compositions For Cellular And Metabolic Engineering
  • Methods For Generating Polynucleotides Having Desired Characteristics By Iterative Selection And Recombination
  • Highly Simplified Lateral Flow-Based Nucleic Acid Sample Preparation And Passive Fluid Flow Control
  • Methods For Sequencing A Biomolecule By Detecting Relative Positions Of Hybridized Probes
  • Biopolymer Sequencing By Hybridization Of Probes To Form Ternary Complexes And Variable Range Alignment
  • Use Of Longitudinally Displaced Nanoscale Electrodes For Voltage Sensing Of Biomolecules And Other Analytes In Fluidic Channels
  • Hot Start Nucleic Acid Amplification
  • Methods For Sequencing A Biomolecule By Detecting Relative Positions Of Hybridized Probes
  • Tagged-Fragment Map Assembly
  • Methods For Generating Polynucleotides Having Desired Characteristics By Iterative Selection And Recombination
  • Methods For Generating Polynucleotides Having Desired Characteristics By Iterative Selection And Recombination
  • Methods For Recombining Nucleic Acids
  • Shuffling Polynucleotides By Incomplete Extension
  • Methods For Generating Polynucleotides Having Desired Characteristics By Iterative Selection And Recombination
  • Methods For Generating Polynucleotides Having Desired Characteristics By Iterative Selection And Recombination
  • Recombination Of Polynucleotide Sequences Using Random Or Defined Primers
  • Assay Methods Using Nicking Endonucleases
  • Methods For Generating Polynucleotides Having Desired Characteristics By Iterative Selection And Recombination
  • Use Of Longitudinally Displaced Nanoscale Electrodes For Voltage Sensing Of Biomolecules And Other Analytes In Fluidic Channels
  • Recombination Of Polynucleotide Sequences Using Random Or Defined Primers
  • Method For Creating Polynucleotide And Polypeptide Sequences
  • Methods For Generating Polynucleotides Having Desired Characteristics By Iterative Selection And Recombination
  • Methods For Generating Polynucleotides Having Desired Characteristics By Iterative Selection And Recombination
  • Methods For Generating Polynucleotides Having Desired Characteristics By Iterative Selection And Recombination
  • Methods For Producing Recombined Antibodies
  • Devices And Methods For Determining The Length Of Biopolymers And Distances Between Probes Bound Thereto
  • Devices And Methods For Determining The Length Of Biopolymers And Distances Between Probes Bound Thereto
  • Methods For Generating Polynucleotides Having Desired Characteristics By Iterative Selection And Recombination
  • Methods For Generating Polynucleotides Having Desired Characteristics By Iterative Selection And Recombination
  • Methods And Compositions For Polypeptide Engineering
  • Hot Start Nucleic Acid Amplification
  • Apparatus And Methods For Analysis Of Biomolecules Using High Frequency Alternating Current Excitation
  • Methods For Generating Polynucleotides Having Desired Characteristics By Iterative Selection And Recombination
  • Methods Of Evolving A Polynucleotides By Mutagenesis And Recombination
  • Methods For Generating Polynucleotides Having Desired Characteristics By Iterative Selection And Recombination
  • Heat-Stable Reca Mutant Protein And A Nucleic Acid Amplification Method Using The Heat-Stable Reca Mutant Protein
  • Oscillating Amplification Reaction For Nucleic Acids
  • Methods For Generating Polynucleotides Having Desired Characteristics By Iterative Selection And Recombination
  • Hot Start Nucleic Acid Amplification
  • Assay Methods Using Nicking Endonucleases
  • Methods For Generating Polynucleotides Having Desired Characteristics By Iterative Selection And Recombination
  • Methods And Compositions For Cellular And Metabolic Engineering
  • Methods For Generating Polynucleotides Having Desired Characteristics By Iterative Selection And Recombination
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/bf02745882

    DOI

    http://dx.doi.org/10.1007/bf02745882

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1040020772

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/7866882


    Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
    Incoming Citations Browse incoming citations for this publication using opencitations.net

    JSON-LD is the canonical representation for SciGraph data.

    TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

    [
      {
        "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
        "about": [
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Genetics", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biological Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "DNA-Binding Proteins", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "DNA-Directed DNA Polymerase", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Polymerase Chain Reaction", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Rec A Recombinases", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Sequence Analysis, DNA", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Templates, Genetic", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Viral Proteins", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Coventry University", 
              "id": "https://www.grid.ac/institutes/grid.8096.7", 
              "name": [
                "Div. of Biological Sciences, School of Natural and Environmental Sciences, Coventry University, Priory St., CV1 5FB, Coventry, UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Rapley", 
            "givenName": "Ralph", 
            "id": "sg:person.01353227122.94", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01353227122.94"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "https://doi.org/10.1101/gr.1.4.222", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015316550"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/18.4.1079", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1020067879"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1073/pnas.74.12.5463", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1025360556"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/17.3.1266", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1048444800"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.2047872", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1062519692"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1126/science.2999980", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1062580102"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://app.dimensions.ai/details/publication/pub.1082823604", 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "1994-12", 
        "datePublishedReg": "1994-12-01", 
        "description": "The polymerase chain reaction (PCR) is a powerful core molecular biology technique, which when coupled to chain termination sequencing allows gene and DNA sequence information to be derived rapidly. A number of modifications to the basic PCR format have been developed in an attempt to increase amplification efficiency and the specificity of the reaction. We have applied the use of DNA-binding protein, gene 32 protein from bacteriophage T4 (T4gp32) to increase amplification efficiency with a number of diverse templates. In addition, we have found that using single-stranded DNA-binding protein (SSB) or recA protein in DNA sequencing reactions dramatically increases the resolution of sequencing runs. The use of DNA-binding proteins in amplification and sequencing may prove to be generally applicable in improving the yield and quality of a number of templates from various sources.", 
        "genre": "research_article", 
        "id": "sg:pub.10.1007/bf02745882", 
        "inLanguage": [
          "en"
        ], 
        "isAccessibleForFree": false, 
        "isPartOf": [
          {
            "id": "sg:journal.1106201", 
            "issn": [
              "1073-6085", 
              "1559-0305"
            ], 
            "name": "Molecular Biotechnology", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "3", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "2"
          }
        ], 
        "name": "Enhancing PCR amplification and sequencing using DNA-binding proteins", 
        "pagination": "295-298", 
        "productId": [
          {
            "name": "readcube_id", 
            "type": "PropertyValue", 
            "value": [
              "bea4d7b2c67fa97bfa4e4f0d730f951736d64f1dea0a6b545d7eaa16380065d8"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "7866882"
            ]
          }, 
          {
            "name": "nlm_unique_id", 
            "type": "PropertyValue", 
            "value": [
              "9423533"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1007/bf02745882"
            ]
          }, 
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1040020772"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1007/bf02745882", 
          "https://app.dimensions.ai/details/publication/pub.1040020772"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2019-04-11T13:28", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000370_0000000370/records_46741_00000002.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "http://link.springer.com/10.1007%2FBF02745882"
      }
    ]
     

    Download the RDF metadata as:  json-ld nt turtle xml License info

    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/bf02745882'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/bf02745882'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/bf02745882'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/bf02745882'


     

    This table displays all metadata directly associated to this object as RDF triples.

    117 TRIPLES      21 PREDICATES      43 URIs      28 LITERALS      16 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1007/bf02745882 schema:about N1e24e81c867f4604bf438bc02c4a1d4f
    2 N433f8d1b73954a8a8325fd78a51bb96a
    3 N6be5b679a70b47c98889fbc99d436686
    4 N90acd31ac7124b31b323c82225baf2af
    5 N97faa1fc75b14b238b3d310381e6690b
    6 Nb3d8505476144bc4a0e188fbfeeaf71e
    7 Nfbafc54472624b9ba40998ef43de3df3
    8 anzsrc-for:06
    9 anzsrc-for:0604
    10 schema:author Nd0ae13e8ed3643b88af56ebe709b17e8
    11 schema:citation https://app.dimensions.ai/details/publication/pub.1082823604
    12 https://doi.org/10.1073/pnas.74.12.5463
    13 https://doi.org/10.1093/nar/17.3.1266
    14 https://doi.org/10.1093/nar/18.4.1079
    15 https://doi.org/10.1101/gr.1.4.222
    16 https://doi.org/10.1126/science.2047872
    17 https://doi.org/10.1126/science.2999980
    18 schema:datePublished 1994-12
    19 schema:datePublishedReg 1994-12-01
    20 schema:description The polymerase chain reaction (PCR) is a powerful core molecular biology technique, which when coupled to chain termination sequencing allows gene and DNA sequence information to be derived rapidly. A number of modifications to the basic PCR format have been developed in an attempt to increase amplification efficiency and the specificity of the reaction. We have applied the use of DNA-binding protein, gene 32 protein from bacteriophage T4 (T4gp32) to increase amplification efficiency with a number of diverse templates. In addition, we have found that using single-stranded DNA-binding protein (SSB) or recA protein in DNA sequencing reactions dramatically increases the resolution of sequencing runs. The use of DNA-binding proteins in amplification and sequencing may prove to be generally applicable in improving the yield and quality of a number of templates from various sources.
    21 schema:genre research_article
    22 schema:inLanguage en
    23 schema:isAccessibleForFree false
    24 schema:isPartOf N26c096a4bfde4a3ca0014ad0a1511302
    25 N619a7e20fd8441e7bbb0bb5ed31ec461
    26 sg:journal.1106201
    27 schema:name Enhancing PCR amplification and sequencing using DNA-binding proteins
    28 schema:pagination 295-298
    29 schema:productId N30ebfae23e864c678e539236e51c002f
    30 N493416fc94c4424ba9fda83fae416978
    31 N6eeb2bfb58c84d5297a9fd3f5d026655
    32 Nb8a9d3ee7c9c4678a931b42c0dc9a750
    33 Nec9a21ef3e8e478aaeb0163bd04a4542
    34 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040020772
    35 https://doi.org/10.1007/bf02745882
    36 schema:sdDatePublished 2019-04-11T13:28
    37 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    38 schema:sdPublisher N6455f594e9ca48dfab6b3488a50df21a
    39 schema:url http://link.springer.com/10.1007%2FBF02745882
    40 sgo:license sg:explorer/license/
    41 sgo:sdDataset articles
    42 rdf:type schema:ScholarlyArticle
    43 N1e24e81c867f4604bf438bc02c4a1d4f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    44 schema:name DNA-Binding Proteins
    45 rdf:type schema:DefinedTerm
    46 N26c096a4bfde4a3ca0014ad0a1511302 schema:volumeNumber 2
    47 rdf:type schema:PublicationVolume
    48 N30ebfae23e864c678e539236e51c002f schema:name readcube_id
    49 schema:value bea4d7b2c67fa97bfa4e4f0d730f951736d64f1dea0a6b545d7eaa16380065d8
    50 rdf:type schema:PropertyValue
    51 N433f8d1b73954a8a8325fd78a51bb96a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    52 schema:name Rec A Recombinases
    53 rdf:type schema:DefinedTerm
    54 N493416fc94c4424ba9fda83fae416978 schema:name nlm_unique_id
    55 schema:value 9423533
    56 rdf:type schema:PropertyValue
    57 N619a7e20fd8441e7bbb0bb5ed31ec461 schema:issueNumber 3
    58 rdf:type schema:PublicationIssue
    59 N6455f594e9ca48dfab6b3488a50df21a schema:name Springer Nature - SN SciGraph project
    60 rdf:type schema:Organization
    61 N6be5b679a70b47c98889fbc99d436686 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    62 schema:name DNA-Directed DNA Polymerase
    63 rdf:type schema:DefinedTerm
    64 N6eeb2bfb58c84d5297a9fd3f5d026655 schema:name dimensions_id
    65 schema:value pub.1040020772
    66 rdf:type schema:PropertyValue
    67 N90acd31ac7124b31b323c82225baf2af schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    68 schema:name Viral Proteins
    69 rdf:type schema:DefinedTerm
    70 N97faa1fc75b14b238b3d310381e6690b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    71 schema:name Polymerase Chain Reaction
    72 rdf:type schema:DefinedTerm
    73 Nb3d8505476144bc4a0e188fbfeeaf71e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    74 schema:name Sequence Analysis, DNA
    75 rdf:type schema:DefinedTerm
    76 Nb8a9d3ee7c9c4678a931b42c0dc9a750 schema:name doi
    77 schema:value 10.1007/bf02745882
    78 rdf:type schema:PropertyValue
    79 Nd0ae13e8ed3643b88af56ebe709b17e8 rdf:first sg:person.01353227122.94
    80 rdf:rest rdf:nil
    81 Nec9a21ef3e8e478aaeb0163bd04a4542 schema:name pubmed_id
    82 schema:value 7866882
    83 rdf:type schema:PropertyValue
    84 Nfbafc54472624b9ba40998ef43de3df3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    85 schema:name Templates, Genetic
    86 rdf:type schema:DefinedTerm
    87 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    88 schema:name Biological Sciences
    89 rdf:type schema:DefinedTerm
    90 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    91 schema:name Genetics
    92 rdf:type schema:DefinedTerm
    93 sg:journal.1106201 schema:issn 1073-6085
    94 1559-0305
    95 schema:name Molecular Biotechnology
    96 rdf:type schema:Periodical
    97 sg:person.01353227122.94 schema:affiliation https://www.grid.ac/institutes/grid.8096.7
    98 schema:familyName Rapley
    99 schema:givenName Ralph
    100 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01353227122.94
    101 rdf:type schema:Person
    102 https://app.dimensions.ai/details/publication/pub.1082823604 schema:CreativeWork
    103 https://doi.org/10.1073/pnas.74.12.5463 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025360556
    104 rdf:type schema:CreativeWork
    105 https://doi.org/10.1093/nar/17.3.1266 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048444800
    106 rdf:type schema:CreativeWork
    107 https://doi.org/10.1093/nar/18.4.1079 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020067879
    108 rdf:type schema:CreativeWork
    109 https://doi.org/10.1101/gr.1.4.222 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015316550
    110 rdf:type schema:CreativeWork
    111 https://doi.org/10.1126/science.2047872 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062519692
    112 rdf:type schema:CreativeWork
    113 https://doi.org/10.1126/science.2999980 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062580102
    114 rdf:type schema:CreativeWork
    115 https://www.grid.ac/institutes/grid.8096.7 schema:alternateName Coventry University
    116 schema:name Div. of Biological Sciences, School of Natural and Environmental Sciences, Coventry University, Priory St., CV1 5FB, Coventry, UK
    117 rdf:type schema:Organization
     




    Preview window. Press ESC to close (or click here)


    ...