Real-space and real-time dynamics of CRISPR-Cas9 visualized by high-speed atomic force microscopy View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2017-12

AUTHORS

Mikihiro Shibata, Hiroshi Nishimasu, Noriyuki Kodera, Seiichi Hirano, Toshio Ando, Takayuki Uchihashi, Osamu Nureki

ABSTRACT

The CRISPR-associated endonuclease Cas9 binds to a guide RNA and cleaves double-stranded DNA with a sequence complementary to the RNA guide. The Cas9-RNA system has been harnessed for numerous applications, such as genome editing. Here we use high-speed atomic force microscopy (HS-AFM) to visualize the real-space and real-time dynamics of CRISPR-Cas9 in action. HS-AFM movies indicate that, whereas apo-Cas9 adopts unexpected flexible conformations, Cas9-RNA forms a stable bilobed structure and interrogates target sites on the DNA by three-dimensional diffusion. These movies also provide real-time visualization of the Cas9-mediated DNA cleavage process. Notably, the Cas9 HNH nuclease domain fluctuates upon DNA binding, and subsequently adopts an active conformation, where the HNH active site is docked at the cleavage site in the target DNA. Collectively, our HS-AFM data extend our understanding of the action mechanism of CRISPR-Cas9. More... »

PAGES

1430

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/s41467-017-01466-8

DOI

http://dx.doi.org/10.1038/s41467-017-01466-8

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1092558481

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/29127285


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"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "CRISPR-Cas Systems", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Catalytic Domain", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Computer Systems", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Enzyme Stability", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Microscopy, Atomic Force", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Microscopy, Video", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Models, Biological", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Models, Molecular", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "RNA", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Thermodynamics", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Kanazawa University", 
          "id": "https://www.grid.ac/institutes/grid.9707.9", 
          "name": [
            "High-speed AFM for Biological Application Unit, Institute for Frontier Science Initiative, Kanazawa University, 920-1192, Kakuma, Kanazawa, Japan", 
            "Bio-AFM Frontier Research Center, Kanazawa University, 920-1192, Kakuma, Kanazawa, Japan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Shibata", 
        "givenName": "Mikihiro", 
        "id": "sg:person.01231763237.05", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01231763237.05"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Japan Science and Technology Agency", 
          "id": "https://www.grid.ac/institutes/grid.419082.6", 
          "name": [
            "Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, 113-0032, Bunkyo-ku, Tokyo, Japan", 
            "JST, PRESTO, 4-1-8 Honcho, 332-0012, Kawaguchi, Saitama, Japan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Nishimasu", 
        "givenName": "Hiroshi", 
        "id": "sg:person.0617555127.19", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0617555127.19"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Japan Science and Technology Agency", 
          "id": "https://www.grid.ac/institutes/grid.419082.6", 
          "name": [
            "Bio-AFM Frontier Research Center, Kanazawa University, 920-1192, Kakuma, Kanazawa, Japan", 
            "JST, PRESTO, 4-1-8 Honcho, 332-0012, Kawaguchi, Saitama, Japan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Kodera", 
        "givenName": "Noriyuki", 
        "id": "sg:person.0622251437.22", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0622251437.22"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Tokyo", 
          "id": "https://www.grid.ac/institutes/grid.26999.3d", 
          "name": [
            "Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, 113-0032, Bunkyo-ku, Tokyo, Japan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Hirano", 
        "givenName": "Seiichi", 
        "id": "sg:person.01042054711.41", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01042054711.41"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Japan Science and Technology Agency", 
          "id": "https://www.grid.ac/institutes/grid.419082.6", 
          "name": [
            "Bio-AFM Frontier Research Center, Kanazawa University, 920-1192, Kakuma, Kanazawa, Japan", 
            "CREST/JST, 4-1-8 Honcho, 332-0012, Kawaguchi, Saitama, Japan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Ando", 
        "givenName": "Toshio", 
        "id": "sg:person.01277542337.19", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01277542337.19"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Nagoya University", 
          "id": "https://www.grid.ac/institutes/grid.27476.30", 
          "name": [
            "Bio-AFM Frontier Research Center, Kanazawa University, 920-1192, Kakuma, Kanazawa, Japan", 
            "CREST/JST, 4-1-8 Honcho, 332-0012, Kawaguchi, Saitama, Japan", 
            "Department of Physics, Kanazawa University, 920-1192, Kakuma, Kanazawa, Japan", 
            "Department of Physics, Nagoya University, 464-8602, Furo-cho, Chikusa-ku, Nagoya, Japan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Uchihashi", 
        "givenName": "Takayuki", 
        "id": "sg:person.01345655537.44", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01345655537.44"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Tokyo", 
          "id": "https://www.grid.ac/institutes/grid.26999.3d", 
          "name": [
            "Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, 113-0032, Bunkyo-ku, Tokyo, Japan"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Nureki", 
        "givenName": "Osamu", 
        "id": "sg:person.01043223704.15", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01043223704.15"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1016/j.cell.2014.02.001", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004290844"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nbt.3481", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004939292", 
          "https://doi.org/10.1038/nbt.3481"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2015.08.007", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004984500"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature09523", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009515358", 
          "https://doi.org/10.1038/nature09523"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature09523", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009515358", 
          "https://doi.org/10.1038/nature09523"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1247997", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010970903"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.1208507109", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011954581"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nprot.2012.047", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013400325", 
          "https://doi.org/10.1038/nprot.2012.047"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1231143", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019873131"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2015.10.017", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021221777"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.aac6572", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021899789"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1232033", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022072971"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1208386", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023394079"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.7554/elife.00471", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023633935"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature09886", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030591890", 
          "https://doi.org/10.1038/nature09886"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature09450", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030990737", 
          "https://doi.org/10.1038/nature09450"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature09450", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030990737", 
          "https://doi.org/10.1038/nature09450"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1021/cr4003837", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031289510"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ncomms12778", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032732755", 
          "https://doi.org/10.1038/ncomms12778"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature13579", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036390967", 
          "https://doi.org/10.1038/nature13579"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature13011", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037342101", 
          "https://doi.org/10.1038/nature13011"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nnano.2016.89", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037783982", 
          "https://doi.org/10.1038/nnano.2016.89"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2015.12.035", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038741332"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2014.05.010", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039182708"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1225829", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1041850060"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.aab1452", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042265317"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1205510", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046397104"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature15544", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047311922", 
          "https://doi.org/10.1038/nature15544"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature15386", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047471547", 
          "https://doi.org/10.1038/nature15386"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.aad8282", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049600810"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.aad5147", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052235744"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nnano.2010.7", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053623548", 
          "https://doi.org/10.1038/nnano.2010.7"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nnano.2010.7", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053623548", 
          "https://doi.org/10.1038/nnano.2010.7"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/sciadv.aao0027", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1091050435"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2017-12", 
    "datePublishedReg": "2017-12-01", 
    "description": "The CRISPR-associated endonuclease Cas9 binds to a guide RNA and cleaves double-stranded DNA with a sequence complementary to the RNA guide. The Cas9-RNA system has been harnessed for numerous applications, such as genome editing. Here we use high-speed atomic force microscopy (HS-AFM) to visualize the real-space and real-time dynamics of CRISPR-Cas9 in action. HS-AFM movies indicate that, whereas apo-Cas9 adopts unexpected flexible conformations, Cas9-RNA forms a stable bilobed structure and interrogates target sites on the DNA by three-dimensional diffusion. These movies also provide real-time visualization of the Cas9-mediated DNA cleavage process. Notably, the Cas9 HNH nuclease domain fluctuates upon DNA binding, and subsequently adopts an active conformation, where the HNH active site is docked at the cleavage site in the target DNA. Collectively, our HS-AFM data extend our understanding of the action mechanism of CRISPR-Cas9.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1038/s41467-017-01466-8", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.5846272", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.5861887", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.6142984", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.5923422", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.5900227", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.6081844", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.6134280", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.5846346", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.5897340", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1043282", 
        "issn": [
          "2041-1723"
        ], 
        "name": "Nature Communications", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "8"
      }
    ], 
    "name": "Real-space and real-time dynamics of CRISPR-Cas9 visualized by high-speed atomic force microscopy", 
    "pagination": "1430", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "143057f6ae3db042d2ea3e9310fda49181a1257f78bc22a8fcf785f80fb69891"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "29127285"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "101528555"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/s41467-017-01466-8"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1092558481"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/s41467-017-01466-8", 
      "https://app.dimensions.ai/details/publication/pub.1092558481"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T16:05", 
    "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_8664_00000608.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://www.nature.com/articles/s41467-017-01466-8"
  }
]
 

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.10.1038/s41467-017-01466-8'

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

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/s41467-017-01466-8'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/s41467-017-01466-8'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/s41467-017-01466-8'


 

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

293 TRIPLES      21 PREDICATES      71 URIs      32 LITERALS      20 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/s41467-017-01466-8 schema:about N11bc6d52c6db4d2a93f5cf38a387e11b
2 N1499a17d941c4819957b695ca790f119
3 N196d33a5ada94e2cb87a65c17345bbbe
4 N2412ce7b3f5a4e78983ad59fa7c99a24
5 N25355a678b864ecb9fcd35c8e6babb80
6 N8016336f5810426284e16970359b5ef2
7 N8104f41e49004414a390ab306cc08ed8
8 N917858602f13448a9fe060ebbb135451
9 Nc5986f1fd49d46f19333ebf0893c24dd
10 Nd4b1381fbe37479782704a08fdc7638a
11 Nf7829672cc82491aafbd80ca7e950022
12 anzsrc-for:06
13 anzsrc-for:0601
14 schema:author N372f8640de0848db994486c435c05767
15 schema:citation sg:pub.10.1038/nature09450
16 sg:pub.10.1038/nature09523
17 sg:pub.10.1038/nature09886
18 sg:pub.10.1038/nature13011
19 sg:pub.10.1038/nature13579
20 sg:pub.10.1038/nature15386
21 sg:pub.10.1038/nature15544
22 sg:pub.10.1038/nbt.3481
23 sg:pub.10.1038/ncomms12778
24 sg:pub.10.1038/nnano.2010.7
25 sg:pub.10.1038/nnano.2016.89
26 sg:pub.10.1038/nprot.2012.047
27 https://doi.org/10.1016/j.cell.2014.02.001
28 https://doi.org/10.1016/j.cell.2014.05.010
29 https://doi.org/10.1016/j.cell.2015.08.007
30 https://doi.org/10.1016/j.cell.2015.10.017
31 https://doi.org/10.1016/j.cell.2015.12.035
32 https://doi.org/10.1021/cr4003837
33 https://doi.org/10.1073/pnas.1208507109
34 https://doi.org/10.1126/sciadv.aao0027
35 https://doi.org/10.1126/science.1205510
36 https://doi.org/10.1126/science.1208386
37 https://doi.org/10.1126/science.1225829
38 https://doi.org/10.1126/science.1231143
39 https://doi.org/10.1126/science.1232033
40 https://doi.org/10.1126/science.1247997
41 https://doi.org/10.1126/science.aab1452
42 https://doi.org/10.1126/science.aac6572
43 https://doi.org/10.1126/science.aad5147
44 https://doi.org/10.1126/science.aad8282
45 https://doi.org/10.7554/elife.00471
46 schema:datePublished 2017-12
47 schema:datePublishedReg 2017-12-01
48 schema:description The CRISPR-associated endonuclease Cas9 binds to a guide RNA and cleaves double-stranded DNA with a sequence complementary to the RNA guide. The Cas9-RNA system has been harnessed for numerous applications, such as genome editing. Here we use high-speed atomic force microscopy (HS-AFM) to visualize the real-space and real-time dynamics of CRISPR-Cas9 in action. HS-AFM movies indicate that, whereas apo-Cas9 adopts unexpected flexible conformations, Cas9-RNA forms a stable bilobed structure and interrogates target sites on the DNA by three-dimensional diffusion. These movies also provide real-time visualization of the Cas9-mediated DNA cleavage process. Notably, the Cas9 HNH nuclease domain fluctuates upon DNA binding, and subsequently adopts an active conformation, where the HNH active site is docked at the cleavage site in the target DNA. Collectively, our HS-AFM data extend our understanding of the action mechanism of CRISPR-Cas9.
49 schema:genre research_article
50 schema:inLanguage en
51 schema:isAccessibleForFree true
52 schema:isPartOf N36f01264dbf8474ca1896482d633b994
53 N657dbbd10b2f42b49e21e5e4583d39f5
54 sg:journal.1043282
55 schema:name Real-space and real-time dynamics of CRISPR-Cas9 visualized by high-speed atomic force microscopy
56 schema:pagination 1430
57 schema:productId N3929feeeef2e4f569d8864b1228f9513
58 N9a333bd850e8481e8735c32249265312
59 N9e7dd67f9ff74ce793a03637ff51c327
60 Na1c753c062ed4c2c927ac6de15ba620b
61 Nb3f174c634a24d05bd015349d2919c19
62 schema:sameAs https://app.dimensions.ai/details/publication/pub.1092558481
63 https://doi.org/10.1038/s41467-017-01466-8
64 schema:sdDatePublished 2019-04-10T16:05
65 schema:sdLicense https://scigraph.springernature.com/explorer/license/
66 schema:sdPublisher N985c70128a3643ab99e8b58bb1dbbb1c
67 schema:url https://www.nature.com/articles/s41467-017-01466-8
68 sgo:license sg:explorer/license/
69 sgo:sdDataset articles
70 rdf:type schema:ScholarlyArticle
71 N11bc6d52c6db4d2a93f5cf38a387e11b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
72 schema:name Models, Biological
73 rdf:type schema:DefinedTerm
74 N1499a17d941c4819957b695ca790f119 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
75 schema:name Models, Molecular
76 rdf:type schema:DefinedTerm
77 N196d33a5ada94e2cb87a65c17345bbbe schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
78 schema:name RNA
79 rdf:type schema:DefinedTerm
80 N2412ce7b3f5a4e78983ad59fa7c99a24 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
81 schema:name Microscopy, Atomic Force
82 rdf:type schema:DefinedTerm
83 N25355a678b864ecb9fcd35c8e6babb80 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
84 schema:name Computer Systems
85 rdf:type schema:DefinedTerm
86 N36f01264dbf8474ca1896482d633b994 schema:volumeNumber 8
87 rdf:type schema:PublicationVolume
88 N372f8640de0848db994486c435c05767 rdf:first sg:person.01231763237.05
89 rdf:rest Na3bc136c5ff1450c8a5824d9084c953f
90 N3929feeeef2e4f569d8864b1228f9513 schema:name doi
91 schema:value 10.1038/s41467-017-01466-8
92 rdf:type schema:PropertyValue
93 N657dbbd10b2f42b49e21e5e4583d39f5 schema:issueNumber 1
94 rdf:type schema:PublicationIssue
95 N77ec73e997ea4d85bd7bb3fcf3ca9764 rdf:first sg:person.0622251437.22
96 rdf:rest N9ca6c220c7e949e6aa84abf2b1b66a0e
97 N8016336f5810426284e16970359b5ef2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
98 schema:name CRISPR-Cas Systems
99 rdf:type schema:DefinedTerm
100 N8104f41e49004414a390ab306cc08ed8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
101 schema:name Enzyme Stability
102 rdf:type schema:DefinedTerm
103 N8b31ad1b862144d4b567c9b93af1eee1 rdf:first sg:person.01277542337.19
104 rdf:rest Nbd32b402aafa4a4482f152848b2cca8e
105 N917858602f13448a9fe060ebbb135451 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
106 schema:name Catalytic Domain
107 rdf:type schema:DefinedTerm
108 N985c70128a3643ab99e8b58bb1dbbb1c schema:name Springer Nature - SN SciGraph project
109 rdf:type schema:Organization
110 N9a333bd850e8481e8735c32249265312 schema:name readcube_id
111 schema:value 143057f6ae3db042d2ea3e9310fda49181a1257f78bc22a8fcf785f80fb69891
112 rdf:type schema:PropertyValue
113 N9ca6c220c7e949e6aa84abf2b1b66a0e rdf:first sg:person.01042054711.41
114 rdf:rest N8b31ad1b862144d4b567c9b93af1eee1
115 N9e7dd67f9ff74ce793a03637ff51c327 schema:name dimensions_id
116 schema:value pub.1092558481
117 rdf:type schema:PropertyValue
118 Na1c753c062ed4c2c927ac6de15ba620b schema:name pubmed_id
119 schema:value 29127285
120 rdf:type schema:PropertyValue
121 Na3bc136c5ff1450c8a5824d9084c953f rdf:first sg:person.0617555127.19
122 rdf:rest N77ec73e997ea4d85bd7bb3fcf3ca9764
123 Nb3f174c634a24d05bd015349d2919c19 schema:name nlm_unique_id
124 schema:value 101528555
125 rdf:type schema:PropertyValue
126 Nbd32b402aafa4a4482f152848b2cca8e rdf:first sg:person.01345655537.44
127 rdf:rest Nd0ed1777b47949b4a213cc921bf611d8
128 Nc5986f1fd49d46f19333ebf0893c24dd schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
129 schema:name Thermodynamics
130 rdf:type schema:DefinedTerm
131 Nd0ed1777b47949b4a213cc921bf611d8 rdf:first sg:person.01043223704.15
132 rdf:rest rdf:nil
133 Nd4b1381fbe37479782704a08fdc7638a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
134 schema:name DNA
135 rdf:type schema:DefinedTerm
136 Nf7829672cc82491aafbd80ca7e950022 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
137 schema:name Microscopy, Video
138 rdf:type schema:DefinedTerm
139 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
140 schema:name Biological Sciences
141 rdf:type schema:DefinedTerm
142 anzsrc-for:0601 schema:inDefinedTermSet anzsrc-for:
143 schema:name Biochemistry and Cell Biology
144 rdf:type schema:DefinedTerm
145 sg:grant.5846272 http://pending.schema.org/fundedItem sg:pub.10.1038/s41467-017-01466-8
146 rdf:type schema:MonetaryGrant
147 sg:grant.5846346 http://pending.schema.org/fundedItem sg:pub.10.1038/s41467-017-01466-8
148 rdf:type schema:MonetaryGrant
149 sg:grant.5861887 http://pending.schema.org/fundedItem sg:pub.10.1038/s41467-017-01466-8
150 rdf:type schema:MonetaryGrant
151 sg:grant.5897340 http://pending.schema.org/fundedItem sg:pub.10.1038/s41467-017-01466-8
152 rdf:type schema:MonetaryGrant
153 sg:grant.5900227 http://pending.schema.org/fundedItem sg:pub.10.1038/s41467-017-01466-8
154 rdf:type schema:MonetaryGrant
155 sg:grant.5923422 http://pending.schema.org/fundedItem sg:pub.10.1038/s41467-017-01466-8
156 rdf:type schema:MonetaryGrant
157 sg:grant.6081844 http://pending.schema.org/fundedItem sg:pub.10.1038/s41467-017-01466-8
158 rdf:type schema:MonetaryGrant
159 sg:grant.6134280 http://pending.schema.org/fundedItem sg:pub.10.1038/s41467-017-01466-8
160 rdf:type schema:MonetaryGrant
161 sg:grant.6142984 http://pending.schema.org/fundedItem sg:pub.10.1038/s41467-017-01466-8
162 rdf:type schema:MonetaryGrant
163 sg:journal.1043282 schema:issn 2041-1723
164 schema:name Nature Communications
165 rdf:type schema:Periodical
166 sg:person.01042054711.41 schema:affiliation https://www.grid.ac/institutes/grid.26999.3d
167 schema:familyName Hirano
168 schema:givenName Seiichi
169 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01042054711.41
170 rdf:type schema:Person
171 sg:person.01043223704.15 schema:affiliation https://www.grid.ac/institutes/grid.26999.3d
172 schema:familyName Nureki
173 schema:givenName Osamu
174 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01043223704.15
175 rdf:type schema:Person
176 sg:person.01231763237.05 schema:affiliation https://www.grid.ac/institutes/grid.9707.9
177 schema:familyName Shibata
178 schema:givenName Mikihiro
179 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01231763237.05
180 rdf:type schema:Person
181 sg:person.01277542337.19 schema:affiliation https://www.grid.ac/institutes/grid.419082.6
182 schema:familyName Ando
183 schema:givenName Toshio
184 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01277542337.19
185 rdf:type schema:Person
186 sg:person.01345655537.44 schema:affiliation https://www.grid.ac/institutes/grid.27476.30
187 schema:familyName Uchihashi
188 schema:givenName Takayuki
189 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01345655537.44
190 rdf:type schema:Person
191 sg:person.0617555127.19 schema:affiliation https://www.grid.ac/institutes/grid.419082.6
192 schema:familyName Nishimasu
193 schema:givenName Hiroshi
194 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0617555127.19
195 rdf:type schema:Person
196 sg:person.0622251437.22 schema:affiliation https://www.grid.ac/institutes/grid.419082.6
197 schema:familyName Kodera
198 schema:givenName Noriyuki
199 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0622251437.22
200 rdf:type schema:Person
201 sg:pub.10.1038/nature09450 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030990737
202 https://doi.org/10.1038/nature09450
203 rdf:type schema:CreativeWork
204 sg:pub.10.1038/nature09523 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009515358
205 https://doi.org/10.1038/nature09523
206 rdf:type schema:CreativeWork
207 sg:pub.10.1038/nature09886 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030591890
208 https://doi.org/10.1038/nature09886
209 rdf:type schema:CreativeWork
210 sg:pub.10.1038/nature13011 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037342101
211 https://doi.org/10.1038/nature13011
212 rdf:type schema:CreativeWork
213 sg:pub.10.1038/nature13579 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036390967
214 https://doi.org/10.1038/nature13579
215 rdf:type schema:CreativeWork
216 sg:pub.10.1038/nature15386 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047471547
217 https://doi.org/10.1038/nature15386
218 rdf:type schema:CreativeWork
219 sg:pub.10.1038/nature15544 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047311922
220 https://doi.org/10.1038/nature15544
221 rdf:type schema:CreativeWork
222 sg:pub.10.1038/nbt.3481 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004939292
223 https://doi.org/10.1038/nbt.3481
224 rdf:type schema:CreativeWork
225 sg:pub.10.1038/ncomms12778 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032732755
226 https://doi.org/10.1038/ncomms12778
227 rdf:type schema:CreativeWork
228 sg:pub.10.1038/nnano.2010.7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053623548
229 https://doi.org/10.1038/nnano.2010.7
230 rdf:type schema:CreativeWork
231 sg:pub.10.1038/nnano.2016.89 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037783982
232 https://doi.org/10.1038/nnano.2016.89
233 rdf:type schema:CreativeWork
234 sg:pub.10.1038/nprot.2012.047 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013400325
235 https://doi.org/10.1038/nprot.2012.047
236 rdf:type schema:CreativeWork
237 https://doi.org/10.1016/j.cell.2014.02.001 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004290844
238 rdf:type schema:CreativeWork
239 https://doi.org/10.1016/j.cell.2014.05.010 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039182708
240 rdf:type schema:CreativeWork
241 https://doi.org/10.1016/j.cell.2015.08.007 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004984500
242 rdf:type schema:CreativeWork
243 https://doi.org/10.1016/j.cell.2015.10.017 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021221777
244 rdf:type schema:CreativeWork
245 https://doi.org/10.1016/j.cell.2015.12.035 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038741332
246 rdf:type schema:CreativeWork
247 https://doi.org/10.1021/cr4003837 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031289510
248 rdf:type schema:CreativeWork
249 https://doi.org/10.1073/pnas.1208507109 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011954581
250 rdf:type schema:CreativeWork
251 https://doi.org/10.1126/sciadv.aao0027 schema:sameAs https://app.dimensions.ai/details/publication/pub.1091050435
252 rdf:type schema:CreativeWork
253 https://doi.org/10.1126/science.1205510 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046397104
254 rdf:type schema:CreativeWork
255 https://doi.org/10.1126/science.1208386 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023394079
256 rdf:type schema:CreativeWork
257 https://doi.org/10.1126/science.1225829 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041850060
258 rdf:type schema:CreativeWork
259 https://doi.org/10.1126/science.1231143 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019873131
260 rdf:type schema:CreativeWork
261 https://doi.org/10.1126/science.1232033 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022072971
262 rdf:type schema:CreativeWork
263 https://doi.org/10.1126/science.1247997 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010970903
264 rdf:type schema:CreativeWork
265 https://doi.org/10.1126/science.aab1452 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042265317
266 rdf:type schema:CreativeWork
267 https://doi.org/10.1126/science.aac6572 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021899789
268 rdf:type schema:CreativeWork
269 https://doi.org/10.1126/science.aad5147 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052235744
270 rdf:type schema:CreativeWork
271 https://doi.org/10.1126/science.aad8282 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049600810
272 rdf:type schema:CreativeWork
273 https://doi.org/10.7554/elife.00471 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023633935
274 rdf:type schema:CreativeWork
275 https://www.grid.ac/institutes/grid.26999.3d schema:alternateName University of Tokyo
276 schema:name Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, 113-0032, Bunkyo-ku, Tokyo, Japan
277 rdf:type schema:Organization
278 https://www.grid.ac/institutes/grid.27476.30 schema:alternateName Nagoya University
279 schema:name Bio-AFM Frontier Research Center, Kanazawa University, 920-1192, Kakuma, Kanazawa, Japan
280 CREST/JST, 4-1-8 Honcho, 332-0012, Kawaguchi, Saitama, Japan
281 Department of Physics, Kanazawa University, 920-1192, Kakuma, Kanazawa, Japan
282 Department of Physics, Nagoya University, 464-8602, Furo-cho, Chikusa-ku, Nagoya, Japan
283 rdf:type schema:Organization
284 https://www.grid.ac/institutes/grid.419082.6 schema:alternateName Japan Science and Technology Agency
285 schema:name Bio-AFM Frontier Research Center, Kanazawa University, 920-1192, Kakuma, Kanazawa, Japan
286 CREST/JST, 4-1-8 Honcho, 332-0012, Kawaguchi, Saitama, Japan
287 Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, 113-0032, Bunkyo-ku, Tokyo, Japan
288 JST, PRESTO, 4-1-8 Honcho, 332-0012, Kawaguchi, Saitama, Japan
289 rdf:type schema:Organization
290 https://www.grid.ac/institutes/grid.9707.9 schema:alternateName Kanazawa University
291 schema:name Bio-AFM Frontier Research Center, Kanazawa University, 920-1192, Kakuma, Kanazawa, Japan
292 High-speed AFM for Biological Application Unit, Institute for Frontier Science Initiative, Kanazawa University, 920-1192, Kakuma, Kanazawa, Japan
293 rdf:type schema:Organization
 




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


...