Super-Resolution Fingerprinting Detects Chemical Reactions and Idiosyncrasies of Single DNA Pegboards
We employ the single-particle fluorescence nanoscopy technique points accumulation for imaging in nanoscale topography (PAINT) using site-specific DNA probes to acquire two-dimensional density maps of specific features patterned on nanoscale DNA origami pegboards. We show that PAINT has a localizati...
| Main Authors: | , , , , , |
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| Other Authors: | |
| Format: | Article |
| Language: | en_US |
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American Chemical Society (ACS)
2014
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| Online Access: | http://hdl.handle.net/1721.1/92233 https://orcid.org/0000-0002-6199-6855 |
| _version_ | 1826188428250710016 |
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| author | Johnson-Buck, Alexander Nangreave, Jeanette Kim, Do-Nyun Bathe, Mark Yan, Hao Walter, Nils G. |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Johnson-Buck, Alexander Nangreave, Jeanette Kim, Do-Nyun Bathe, Mark Yan, Hao Walter, Nils G. |
| author_sort | Johnson-Buck, Alexander |
| collection | MIT |
| description | We employ the single-particle fluorescence nanoscopy technique points accumulation for imaging in nanoscale topography (PAINT) using site-specific DNA probes to acquire two-dimensional density maps of specific features patterned on nanoscale DNA origami pegboards. We show that PAINT has a localization accuracy of ∼10 nm that is sufficient to reliably distinguish dense (>10[superscript 4] features μm[superscript –2]) sub-100 nm patterns of oligonucleotide features. We employ two-color PAINT to follow enzyme-catalyzed modification of features on individual origami and to show that single nanopegboards exhibit stable, spatially heterogeneous probe-binding patterns, or “fingerprints.” Finally, we present experimental and modeling evidence suggesting that these fingerprints may arise from feature spacing variations that locally modulate the probe binding kinetics. Our study highlights the power of fluorescence nanoscopy to perform quality control on individual soft nanodevices that interact with and position reagents in solution. |
| first_indexed | 2024-09-23T07:59:11Z |
| format | Article |
| id | mit-1721.1/92233 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T07:59:11Z |
| publishDate | 2014 |
| publisher | American Chemical Society (ACS) |
| record_format | dspace |
| spelling | mit-1721.1/922332022-09-23T10:06:15Z Super-Resolution Fingerprinting Detects Chemical Reactions and Idiosyncrasies of Single DNA Pegboards Johnson-Buck, Alexander Nangreave, Jeanette Kim, Do-Nyun Bathe, Mark Yan, Hao Walter, Nils G. Massachusetts Institute of Technology. Department of Biological Engineering Bathe, Mark Bathe, Mark Kim, Do-Nyun We employ the single-particle fluorescence nanoscopy technique points accumulation for imaging in nanoscale topography (PAINT) using site-specific DNA probes to acquire two-dimensional density maps of specific features patterned on nanoscale DNA origami pegboards. We show that PAINT has a localization accuracy of ∼10 nm that is sufficient to reliably distinguish dense (>10[superscript 4] features μm[superscript –2]) sub-100 nm patterns of oligonucleotide features. We employ two-color PAINT to follow enzyme-catalyzed modification of features on individual origami and to show that single nanopegboards exhibit stable, spatially heterogeneous probe-binding patterns, or “fingerprints.” Finally, we present experimental and modeling evidence suggesting that these fingerprints may arise from feature spacing variations that locally modulate the probe binding kinetics. Our study highlights the power of fluorescence nanoscopy to perform quality control on individual soft nanodevices that interact with and position reagents in solution. National Science Foundation (U.S.) (Collaborative Research Award CCF-0829579) United States. Multidisciplinary University Research Initiative (W911NF-12-1-0420) 2014-12-08T19:53:40Z 2014-12-08T19:53:40Z 2013-01 2013-01 Article http://purl.org/eprint/type/JournalArticle 1530-6984 1530-6992 http://hdl.handle.net/1721.1/92233 Johnson-Buck, Alexander, Jeanette Nangreave, Do-Nyun Kim, Mark Bathe, Hao Yan, and Nils G. Walter. “Super-Resolution Fingerprinting Detects Chemical Reactions and Idiosyncrasies of Single DNA Pegboards.” Nano Lett. 13, no. 2 (February 13, 2013): 728–733. https://orcid.org/0000-0002-6199-6855 en_US http://dx.doi.org/10.1021/nl304415b Nano Letters Creative Commons Attribution-Noncommercial-Share Alike http://creativecommons.org/licenses/by-nc-sa/4.0/ application/pdf American Chemical Society (ACS) Prof. Bathe via Howard Silver |
| spellingShingle | Johnson-Buck, Alexander Nangreave, Jeanette Kim, Do-Nyun Bathe, Mark Yan, Hao Walter, Nils G. Super-Resolution Fingerprinting Detects Chemical Reactions and Idiosyncrasies of Single DNA Pegboards |
| title | Super-Resolution Fingerprinting Detects Chemical Reactions and Idiosyncrasies of Single DNA Pegboards |
| title_full | Super-Resolution Fingerprinting Detects Chemical Reactions and Idiosyncrasies of Single DNA Pegboards |
| title_fullStr | Super-Resolution Fingerprinting Detects Chemical Reactions and Idiosyncrasies of Single DNA Pegboards |
| title_full_unstemmed | Super-Resolution Fingerprinting Detects Chemical Reactions and Idiosyncrasies of Single DNA Pegboards |
| title_short | Super-Resolution Fingerprinting Detects Chemical Reactions and Idiosyncrasies of Single DNA Pegboards |
| title_sort | super resolution fingerprinting detects chemical reactions and idiosyncrasies of single dna pegboards |
| url | http://hdl.handle.net/1721.1/92233 https://orcid.org/0000-0002-6199-6855 |
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