Gibson Deletion: a novel application of isothermal in vitro recombination View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2018-12

AUTHORS

Swara Kalva, Jef D. Boeke, Paolo Mita

ABSTRACT

Background: Recombinant DNA technology is today a fundamental tool for virtually all biological research fields. Among the many techniques available for the construction of a "custom DNA" molecule, the isothermal in vitro assembly, or Gibson assembly, allows for an efficient, one-step, scarless recombination-based assembly. Results: Here, we apply and characterize the use of Gibson assembly for the deletion of DNA sequences around a DNA cut. This method, that we named "Gibson Deletion", can be used to easily substitute or delete one or more restriction sites within a DNA molecule. We show that Gibson Deletion is a viable method to delete up to 100 nucleotides from the DNA ends of a cleavage site. In addition, we found that Gibson Deletion can be performed using single strand DNA with the same efficiency as using double strand DNA molecules. Conclusions: Gibson Deletion is a novel, easy and convenient application of isothermal in vitro assembly, that performs with high efficiency and can be implemented for a broad range of applications. More... »

PAGES

2

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s12575-018-0068-7

DOI

http://dx.doi.org/10.1186/s12575-018-0068-7

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1100481200

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/29375275


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/2008/0601", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biochemistry and Cell Biology", 
        "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"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Bronx High School of Science", 
          "id": "https://www.grid.ac/institutes/grid.466525.6", 
          "name": [
            "The Bronx High School of Science, 75 West 205 Street, 10468, Bronx, NY, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Kalva", 
        "givenName": "Swara", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "New York University", 
          "id": "https://www.grid.ac/institutes/grid.137628.9", 
          "name": [
            "Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, Institute of Systems Genetics (ISG), 10016, New York, NY, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Boeke", 
        "givenName": "Jef D.", 
        "id": "sg:person.01022533774.72", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01022533774.72"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "New York University", 
          "id": "https://www.grid.ac/institutes/grid.137628.9", 
          "name": [
            "Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, Institute of Systems Genetics (ISG), 10016, New York, NY, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Mita", 
        "givenName": "Paolo", 
        "id": "sg:person.0601376506.53", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0601376506.53"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1146/annurev-biochem-072511-122603", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005783086"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1151721", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009412636"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/b978-0-12-385120-8.00015-2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018594279"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/18.20.6069", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025156014"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.2237126100", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028250908"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth.1318", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040405189", 
          "https://doi.org/10.1038/nmeth.1318"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth.1318", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040405189", 
          "https://doi.org/10.1038/nmeth.1318"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth.1515", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040432643", 
          "https://doi.org/10.1038/nmeth.1515"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0378-1119(95)00511-4", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047078949"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0003647", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047416429"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-1-4939-6472-7_24", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049517770", 
          "https://doi.org/10.1007/978-1-4939-6472-7_24"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/sb300131w", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1056295425"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.2144/000114261", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1069096747"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nprot.2017.016", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1084129553", 
          "https://doi.org/10.1038/nprot.2017.016"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2018-12", 
    "datePublishedReg": "2018-12-01", 
    "description": "Background: Recombinant DNA technology is today a fundamental tool for virtually all biological research fields. Among the many techniques available for the construction of a \"custom DNA\" molecule, the isothermal in vitro assembly, or Gibson assembly, allows for an efficient, one-step, scarless recombination-based assembly.\nResults: Here, we apply and characterize the use of Gibson assembly for the deletion of DNA sequences around a DNA cut. This method, that we named \"Gibson Deletion\", can be used to easily substitute or delete one or more restriction sites within a DNA molecule. We show that Gibson Deletion is a viable method to delete up to 100 nucleotides from the DNA ends of a cleavage site. In addition, we found that Gibson Deletion can be performed using single strand DNA with the same efficiency as using double strand DNA molecules.\nConclusions: Gibson Deletion is a novel, easy and convenient application of isothermal in vitro assembly, that performs with high efficiency and can be implemented for a broad range of applications.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1186/s12575-018-0068-7", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.2440551", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1023701", 
        "issn": [
          "1480-9222"
        ], 
        "name": "Biological Procedures Online", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "20"
      }
    ], 
    "name": "Gibson Deletion: a novel application of isothermal in vitro recombination", 
    "pagination": "2", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "847fe53929374e072ea77f66c7859c01107041bae1616163b605f6edb1e61dbd"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "29375275"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "100963717"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/s12575-018-0068-7"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1100481200"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/s12575-018-0068-7", 
      "https://app.dimensions.ai/details/publication/pub.1100481200"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T23:32", 
    "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/v90/0000000001_0000000264/records_8693_00000552.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://link.springer.com/10.1186/s12575-018-0068-7"
  }
]
 

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.10.1186/s12575-018-0068-7'

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

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/s12575-018-0068-7'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s12575-018-0068-7'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s12575-018-0068-7'


 

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

129 TRIPLES      21 PREDICATES      42 URIs      21 LITERALS      9 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/s12575-018-0068-7 schema:about anzsrc-for:06
2 anzsrc-for:0601
3 schema:author N379f6ef3355e4877bc24776f87ed6c4b
4 schema:citation sg:pub.10.1007/978-1-4939-6472-7_24
5 sg:pub.10.1038/nmeth.1318
6 sg:pub.10.1038/nmeth.1515
7 sg:pub.10.1038/nprot.2017.016
8 https://doi.org/10.1016/0378-1119(95)00511-4
9 https://doi.org/10.1016/b978-0-12-385120-8.00015-2
10 https://doi.org/10.1021/sb300131w
11 https://doi.org/10.1073/pnas.2237126100
12 https://doi.org/10.1093/nar/18.20.6069
13 https://doi.org/10.1126/science.1151721
14 https://doi.org/10.1146/annurev-biochem-072511-122603
15 https://doi.org/10.1371/journal.pone.0003647
16 https://doi.org/10.2144/000114261
17 schema:datePublished 2018-12
18 schema:datePublishedReg 2018-12-01
19 schema:description Background: Recombinant DNA technology is today a fundamental tool for virtually all biological research fields. Among the many techniques available for the construction of a "custom DNA" molecule, the isothermal in vitro assembly, or Gibson assembly, allows for an efficient, one-step, scarless recombination-based assembly. Results: Here, we apply and characterize the use of Gibson assembly for the deletion of DNA sequences around a DNA cut. This method, that we named "Gibson Deletion", can be used to easily substitute or delete one or more restriction sites within a DNA molecule. We show that Gibson Deletion is a viable method to delete up to 100 nucleotides from the DNA ends of a cleavage site. In addition, we found that Gibson Deletion can be performed using single strand DNA with the same efficiency as using double strand DNA molecules. Conclusions: Gibson Deletion is a novel, easy and convenient application of isothermal in vitro assembly, that performs with high efficiency and can be implemented for a broad range of applications.
20 schema:genre research_article
21 schema:inLanguage en
22 schema:isAccessibleForFree true
23 schema:isPartOf N64131dd47c734f919ea6b3a958a6f8ad
24 Na0c150b4612f40558682164552d85dc3
25 sg:journal.1023701
26 schema:name Gibson Deletion: a novel application of isothermal in vitro recombination
27 schema:pagination 2
28 schema:productId N505fce438b2244459c167aae14003aa7
29 N953dc9b3d9f04ae6a657f8ae85253fe5
30 Ne2b406bac3424d5392392c635239e7f7
31 Nee1ae90e6ccf4adcaa1e55d64c8fdf93
32 Nf1d61752729d487ba096c9b535183564
33 schema:sameAs https://app.dimensions.ai/details/publication/pub.1100481200
34 https://doi.org/10.1186/s12575-018-0068-7
35 schema:sdDatePublished 2019-04-10T23:32
36 schema:sdLicense https://scigraph.springernature.com/explorer/license/
37 schema:sdPublisher Naa9c6611affe428eb006397ea9a4bffe
38 schema:url http://link.springer.com/10.1186/s12575-018-0068-7
39 sgo:license sg:explorer/license/
40 sgo:sdDataset articles
41 rdf:type schema:ScholarlyArticle
42 N1b5e9f8c9a1d494e8cfa0574f21e536f rdf:first sg:person.0601376506.53
43 rdf:rest rdf:nil
44 N379f6ef3355e4877bc24776f87ed6c4b rdf:first N4d765255ddd049dcbc92ff4f87bc37af
45 rdf:rest Nf3638803bb824913bf2d17592ab15879
46 N4d765255ddd049dcbc92ff4f87bc37af schema:affiliation https://www.grid.ac/institutes/grid.466525.6
47 schema:familyName Kalva
48 schema:givenName Swara
49 rdf:type schema:Person
50 N505fce438b2244459c167aae14003aa7 schema:name pubmed_id
51 schema:value 29375275
52 rdf:type schema:PropertyValue
53 N64131dd47c734f919ea6b3a958a6f8ad schema:issueNumber 1
54 rdf:type schema:PublicationIssue
55 N953dc9b3d9f04ae6a657f8ae85253fe5 schema:name doi
56 schema:value 10.1186/s12575-018-0068-7
57 rdf:type schema:PropertyValue
58 Na0c150b4612f40558682164552d85dc3 schema:volumeNumber 20
59 rdf:type schema:PublicationVolume
60 Naa9c6611affe428eb006397ea9a4bffe schema:name Springer Nature - SN SciGraph project
61 rdf:type schema:Organization
62 Ne2b406bac3424d5392392c635239e7f7 schema:name nlm_unique_id
63 schema:value 100963717
64 rdf:type schema:PropertyValue
65 Nee1ae90e6ccf4adcaa1e55d64c8fdf93 schema:name readcube_id
66 schema:value 847fe53929374e072ea77f66c7859c01107041bae1616163b605f6edb1e61dbd
67 rdf:type schema:PropertyValue
68 Nf1d61752729d487ba096c9b535183564 schema:name dimensions_id
69 schema:value pub.1100481200
70 rdf:type schema:PropertyValue
71 Nf3638803bb824913bf2d17592ab15879 rdf:first sg:person.01022533774.72
72 rdf:rest N1b5e9f8c9a1d494e8cfa0574f21e536f
73 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
74 schema:name Biological Sciences
75 rdf:type schema:DefinedTerm
76 anzsrc-for:0601 schema:inDefinedTermSet anzsrc-for:
77 schema:name Biochemistry and Cell Biology
78 rdf:type schema:DefinedTerm
79 sg:grant.2440551 http://pending.schema.org/fundedItem sg:pub.10.1186/s12575-018-0068-7
80 rdf:type schema:MonetaryGrant
81 sg:journal.1023701 schema:issn 1480-9222
82 schema:name Biological Procedures Online
83 rdf:type schema:Periodical
84 sg:person.01022533774.72 schema:affiliation https://www.grid.ac/institutes/grid.137628.9
85 schema:familyName Boeke
86 schema:givenName Jef D.
87 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01022533774.72
88 rdf:type schema:Person
89 sg:person.0601376506.53 schema:affiliation https://www.grid.ac/institutes/grid.137628.9
90 schema:familyName Mita
91 schema:givenName Paolo
92 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0601376506.53
93 rdf:type schema:Person
94 sg:pub.10.1007/978-1-4939-6472-7_24 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049517770
95 https://doi.org/10.1007/978-1-4939-6472-7_24
96 rdf:type schema:CreativeWork
97 sg:pub.10.1038/nmeth.1318 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040405189
98 https://doi.org/10.1038/nmeth.1318
99 rdf:type schema:CreativeWork
100 sg:pub.10.1038/nmeth.1515 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040432643
101 https://doi.org/10.1038/nmeth.1515
102 rdf:type schema:CreativeWork
103 sg:pub.10.1038/nprot.2017.016 schema:sameAs https://app.dimensions.ai/details/publication/pub.1084129553
104 https://doi.org/10.1038/nprot.2017.016
105 rdf:type schema:CreativeWork
106 https://doi.org/10.1016/0378-1119(95)00511-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047078949
107 rdf:type schema:CreativeWork
108 https://doi.org/10.1016/b978-0-12-385120-8.00015-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018594279
109 rdf:type schema:CreativeWork
110 https://doi.org/10.1021/sb300131w schema:sameAs https://app.dimensions.ai/details/publication/pub.1056295425
111 rdf:type schema:CreativeWork
112 https://doi.org/10.1073/pnas.2237126100 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028250908
113 rdf:type schema:CreativeWork
114 https://doi.org/10.1093/nar/18.20.6069 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025156014
115 rdf:type schema:CreativeWork
116 https://doi.org/10.1126/science.1151721 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009412636
117 rdf:type schema:CreativeWork
118 https://doi.org/10.1146/annurev-biochem-072511-122603 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005783086
119 rdf:type schema:CreativeWork
120 https://doi.org/10.1371/journal.pone.0003647 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047416429
121 rdf:type schema:CreativeWork
122 https://doi.org/10.2144/000114261 schema:sameAs https://app.dimensions.ai/details/publication/pub.1069096747
123 rdf:type schema:CreativeWork
124 https://www.grid.ac/institutes/grid.137628.9 schema:alternateName New York University
125 schema:name Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, Institute of Systems Genetics (ISG), 10016, New York, NY, USA
126 rdf:type schema:Organization
127 https://www.grid.ac/institutes/grid.466525.6 schema:alternateName Bronx High School of Science
128 schema:name The Bronx High School of Science, 75 West 205 Street, 10468, Bronx, NY, USA
129 rdf:type schema:Organization
 




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


...