Ontology type: schema:ScholarlyArticle Open Access: True
2019-12
AUTHORSFlorian Stehr, Johannes Stein, Florian Schueder, Petra Schwille, Ralf Jungmann
ABSTRACTSuper-resolution (SR) techniques have extended the optical resolution down to a few nanometers. However, quantitative treatment of SR data remains challenging due to its complex dependence on a manifold of experimental parameters. Among the different SR variants, DNA-PAINT is relatively straightforward to implement, since it achieves the necessary 'blinking' without the use of rather complex optical or chemical activation schemes. However, it still suffers from image and quantification artifacts caused by inhomogeneous optical excitation. Here we demonstrate that several experimental challenges can be alleviated by introducing a segment-wise analysis approach and ultimately overcome by implementing a flat-top illumination profile for TIRF microscopy using a commercially-available beam-shaping device. The improvements with regards to homogeneous spatial resolution and precise kinetic information over the whole field-of-view were quantitatively assayed using DNA origami and cell samples. Our findings open the door to high-throughput DNA-PAINT studies with thus far unprecedented accuracy for quantitative data interpretation. More... »
PAGES1268
http://scigraph.springernature.com/pub.10.1038/s41467-019-09064-6
DOIhttp://dx.doi.org/10.1038/s41467-019-09064-6
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1112879275
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/30894522
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/2008/0299",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Other Physical Sciences",
"type": "DefinedTerm"
},
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/02",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Physical Sciences",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Animals",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Artifacts",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "COS Cells",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Cercopithecus aethiops",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "DNA",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Humans",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Lighting",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Microscopy, Fluorescence",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Microscopy, Interference",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Oligonucleotides",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"alternateName": "Max Planck Institute of Biochemistry",
"id": "https://www.grid.ac/institutes/grid.418615.f",
"name": [
"Max Planck Institute of Biochemistry, 82152, Martinsried, Munich, Germany"
],
"type": "Organization"
},
"familyName": "Stehr",
"givenName": "Florian",
"type": "Person"
},
{
"affiliation": {
"alternateName": "Max Planck Institute of Biochemistry",
"id": "https://www.grid.ac/institutes/grid.418615.f",
"name": [
"Max Planck Institute of Biochemistry, 82152, Martinsried, Munich, Germany"
],
"type": "Organization"
},
"familyName": "Stein",
"givenName": "Johannes",
"type": "Person"
},
{
"affiliation": {
"alternateName": "Ludwig Maximilian University of Munich",
"id": "https://www.grid.ac/institutes/grid.5252.0",
"name": [
"Max Planck Institute of Biochemistry, 82152, Martinsried, Munich, Germany",
"Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, 80539, Munich, Germany"
],
"type": "Organization"
},
"familyName": "Schueder",
"givenName": "Florian",
"type": "Person"
},
{
"affiliation": {
"alternateName": "Max Planck Institute of Biochemistry",
"id": "https://www.grid.ac/institutes/grid.418615.f",
"name": [
"Max Planck Institute of Biochemistry, 82152, Martinsried, Munich, Germany"
],
"type": "Organization"
},
"familyName": "Schwille",
"givenName": "Petra",
"type": "Person"
},
{
"affiliation": {
"alternateName": "Ludwig Maximilian University of Munich",
"id": "https://www.grid.ac/institutes/grid.5252.0",
"name": [
"Max Planck Institute of Biochemistry, 82152, Martinsried, Munich, Germany",
"Faculty of Physics and Center for Nanoscience, Ludwig Maximilian University, 80539, Munich, Germany"
],
"type": "Organization"
},
"familyName": "Jungmann",
"givenName": "Ralf",
"type": "Person"
}
],
"citation": [
{
"id": "sg:pub.10.1038/nmeth.3804",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1004398235",
"https://doi.org/10.1038/nmeth.3804"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1364/boe.2.001377",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1013924879"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nmeth929",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1018882864",
"https://doi.org/10.1038/nmeth929"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nmeth929",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1018882864",
"https://doi.org/10.1038/nmeth929"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1126/science.1127344",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1022108219"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1083/jcb.89.1.141",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1022601525"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/s0091-679x(08)00607-9",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1032189820"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nmeth1171",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1032254220",
"https://doi.org/10.1038/nmeth1171"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1002/anie.201405991",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1035181323"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1073/pnas.0609643104",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1036737982"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nmeth0411-279",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1041596697",
"https://doi.org/10.1038/nmeth0411-279"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nmeth.2843",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1043364938",
"https://doi.org/10.1038/nmeth.2843"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nmeth.1768",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1043491552",
"https://doi.org/10.1038/nmeth.1768"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1073/pnas.1117430109",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1043508545"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nmeth.1978",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1043664538",
"https://doi.org/10.1038/nmeth.1978"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nphoton.2016.200",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1046291732",
"https://doi.org/10.1038/nphoton.2016.200"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1016/s0006-3495(02)75618-x",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1049070026"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/s00418-014-1192-3",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1050881172",
"https://doi.org/10.1007/s00418-014-1192-3"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nmeth.2835",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1051021562",
"https://doi.org/10.1038/nmeth.2835"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1109/tip.2011.2114359",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1061642766"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1364/ao.39.005488",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1065115513"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1364/ao.4.001400",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1065116024"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1364/oe.24.028080",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1065209426"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.14440/jbm.2014.36",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1067313372"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1039/c6sc05420j",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1074247091"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/acs.chemrev.6b00667",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1084121882"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nprot.2017.024",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1085434308",
"https://doi.org/10.1038/nprot.2017.024"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.3762/bjnano.8.229",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1092512789"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41467-017-02028-8",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1099597650",
"https://doi.org/10.1038/s41467-017-02028-8"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1146/annurev-biochem-060815-014801",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1099923780"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1146/annurev-biochem-060815-014801",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1099923780"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1146/annurev-biochem-060815-014801",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1099923780"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41598-018-24052-4",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1101862205",
"https://doi.org/10.1038/s41598-018-24052-4"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41598-018-24052-4",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1101862205",
"https://doi.org/10.1038/s41598-018-24052-4"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41598-018-24052-4",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1101862205",
"https://doi.org/10.1038/s41598-018-24052-4"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1021/acs.nanolett.8b00875",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1103268768"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41467-018-04031-z",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1103532601",
"https://doi.org/10.1038/s41467-018-04031-z"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1364/oe.26.015276",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1104359444"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41592-018-0072-5",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1105832126",
"https://doi.org/10.1038/s41592-018-0072-5"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41592-018-0072-5",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1105832126",
"https://doi.org/10.1038/s41592-018-0072-5"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.3390/molecules23123165",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1110286570"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.3390/molecules23123165",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1110286570"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.3390/molecules23123165",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1110286570"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.3390/molecules23123165",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1110286570"
],
"type": "CreativeWork"
}
],
"datePublished": "2019-12",
"datePublishedReg": "2019-12-01",
"description": "Super-resolution (SR) techniques have extended the optical resolution down to a few nanometers. However, quantitative treatment of SR data remains challenging due to its complex dependence on a manifold of experimental parameters. Among the different SR variants, DNA-PAINT is relatively straightforward to implement, since it achieves the necessary 'blinking' without the use of rather complex optical or chemical activation schemes. However, it still suffers from image and quantification artifacts caused by inhomogeneous optical excitation. Here we demonstrate that several experimental challenges can be alleviated by introducing a segment-wise analysis approach and ultimately overcome by implementing a flat-top illumination profile for TIRF microscopy using a commercially-available beam-shaping device. The improvements with regards to homogeneous spatial resolution and precise kinetic information over the whole field-of-view were quantitatively assayed using DNA origami and cell samples. Our findings open the door to high-throughput DNA-PAINT studies with thus far unprecedented accuracy for quantitative data interpretation.",
"genre": "research_article",
"id": "sg:pub.10.1038/s41467-019-09064-6",
"inLanguage": [
"en"
],
"isAccessibleForFree": true,
"isFundedItemOf": [
{
"id": "sg:grant.5494270",
"type": "MonetaryGrant"
}
],
"isPartOf": [
{
"id": "sg:journal.1043282",
"issn": [
"2041-1723"
],
"name": "Nature Communications",
"type": "Periodical"
},
{
"issueNumber": "1",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "10"
}
],
"name": "Flat-top TIRF illumination boosts DNA-PAINT imaging and quantification",
"pagination": "1268",
"productId": [
{
"name": "readcube_id",
"type": "PropertyValue",
"value": [
"bb0af47f674e826fa2840a18d153f0e2f7b71eab0ebf9028e6f27a21602db6fb"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"30894522"
]
},
{
"name": "nlm_unique_id",
"type": "PropertyValue",
"value": [
"101528555"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1038/s41467-019-09064-6"
]
},
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1112879275"
]
}
],
"sameAs": [
"https://doi.org/10.1038/s41467-019-09064-6",
"https://app.dimensions.ai/details/publication/pub.1112879275"
],
"sdDataset": "articles",
"sdDatePublished": "2019-04-11T14:01",
"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/v90/0000000371_0000000371/records_130829_00000006.jsonl",
"type": "ScholarlyArticle",
"url": "https://www.nature.com/articles/s41467-019-09064-6"
}
]Download the RDF metadata as: json-ld nt turtle xml License info
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/s41467-019-09064-6'
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/s41467-019-09064-6'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/s41467-019-09064-6'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/s41467-019-09064-6'
This table displays all metadata directly associated to this object as RDF triples.
257 TRIPLES
21 PREDICATES
74 URIs
31 LITERALS
19 BLANK NODES