Programming Structured DNA Assemblies to Probe Biophysical Processes
Structural DNA nanotechnology is beginning to emerge as a widely accessible research tool to mechanistically study diverse biophysical processes. Enabled by scaffolded DNA origami in which a long single strand of DNA is weaved throughout an entire target nucleic acid assembly to ensure its proper fo...
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| Format: | Article |
| Language: | English |
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Annual Reviews
2020
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| Online Access: | https://hdl.handle.net/1721.1/125280 |
| _version_ | 1826197057071742976 |
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| author | Wamhoff, Eike-Christian Banal, James L. Bricker, William P Shepherd, Tyson R Parsons, Molly F. Veneziano, Remi Stone, Matthew B. Jun, Hyungmin Wang, Xiao Bathe, Mark |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Wamhoff, Eike-Christian Banal, James L. Bricker, William P Shepherd, Tyson R Parsons, Molly F. Veneziano, Remi Stone, Matthew B. Jun, Hyungmin Wang, Xiao Bathe, Mark |
| author_sort | Wamhoff, Eike-Christian |
| collection | MIT |
| description | Structural DNA nanotechnology is beginning to emerge as a widely accessible research tool to mechanistically study diverse biophysical processes. Enabled by scaffolded DNA origami in which a long single strand of DNA is weaved throughout an entire target nucleic acid assembly to ensure its proper folding, assemblies of nearly any geometric shape can now be programmed in a fully automatic manner to interface with biology on the 1-100-nm scale. Here, we review the major design and synthesis principles that have enabled the fabrication of a specific subclass of scaffolded DNA origami objects called wireframe assemblies. These objects offer unprecedented control over the nanoscale organization of biomolecules, including biomolecular copy numbers, presentation on convex or concave geometries, and internal versus external functionalization, in addition to stability in physiological buffer. To highlight the power and versatility of this synthetic structural biology approach to probing molecular and cellular biophysics, we feature its application to three leading areas of investigation: light harvesting and nanoscale energy transport, RNA structural biology, and immune receptor signaling, with an outlook toward unique mechanistic insight that may be gained in these areas in the coming decade. |
| first_indexed | 2024-09-23T10:41:44Z |
| format | Article |
| id | mit-1721.1/125280 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T10:41:44Z |
| publishDate | 2020 |
| publisher | Annual Reviews |
| record_format | dspace |
| spelling | mit-1721.1/1252802022-09-30T22:21:24Z Programming Structured DNA Assemblies to Probe Biophysical Processes Wamhoff, Eike-Christian Banal, James L. Bricker, William P Shepherd, Tyson R Parsons, Molly F. Veneziano, Remi Stone, Matthew B. Jun, Hyungmin Wang, Xiao Bathe, Mark Massachusetts Institute of Technology. Department of Biology Massachusetts Institute of Technology. Department of Biological Engineering Massachusetts Institute of Technology. Department of Mechanical Engineering Structural DNA nanotechnology is beginning to emerge as a widely accessible research tool to mechanistically study diverse biophysical processes. Enabled by scaffolded DNA origami in which a long single strand of DNA is weaved throughout an entire target nucleic acid assembly to ensure its proper folding, assemblies of nearly any geometric shape can now be programmed in a fully automatic manner to interface with biology on the 1-100-nm scale. Here, we review the major design and synthesis principles that have enabled the fabrication of a specific subclass of scaffolded DNA origami objects called wireframe assemblies. These objects offer unprecedented control over the nanoscale organization of biomolecules, including biomolecular copy numbers, presentation on convex or concave geometries, and internal versus external functionalization, in addition to stability in physiological buffer. To highlight the power and versatility of this synthetic structural biology approach to probing molecular and cellular biophysics, we feature its application to three leading areas of investigation: light harvesting and nanoscale energy transport, RNA structural biology, and immune receptor signaling, with an outlook toward unique mechanistic insight that may be gained in these areas in the coming decade. United States. Office of Naval Research (Grant N00014-12-1-0621) United States. Office of Naval Research (Grant N00014-14-1-0609) United States. Office of Naval Research (Grant N00014-13-1-0664) United States. Office of Naval Research (Grant N00014-16-1-2506) United States. Office of Naval Research (Grant N00014-16-1-2181) United States. Office of Naval Research (Grant N00014-16-1-2953) United States. Office of Naval Research (Grant N00014-17-1-2609) United States. Office of Naval Research (Grant N00014-18-1-2290) National Science Foundation (U.S.) (Grant CCF-1547999) National Science Foundation (U.S.) (Grant CCF-1564025) National Science Foundation (U.S.) (Grant CMMI-1334109) National Science Foundation (U.S.) (Grant CBET-1729397) National Science Foundation (U.S.) (Grant CHE-1839155) National Science Foundation (U.S.) (Grant PHY-1305537) National Science Foundation (U.S.) (Grant PHY-1707999) United States. Army Research Office (Grant W911NF1210420) Human Frontier Science Program (Strasbourg, France) (Grant RGP0029/2014) United States. Department of Energy (Grant DE-SC0016353) United States. Department of Energy (Grant DE-SC0001088 National Institutes of Health (U.S.) (Grant U01-MH106011) National Institutes of Health (U.S.) (Grant R01-MH112694) National Institutes of Health (U.S.) (Grant R21-EB026008) National Institute of Environmental Health Sciences (Grant (P30-ES002109) 2020-05-18T12:59:28Z 2020-05-18T12:59:28Z 2019-05 2020-03-04T16:46:45Z Article http://purl.org/eprint/type/JournalArticle 1936-122X https://hdl.handle.net/1721.1/125280 Wamhoff, Eike-Christian et al. “Programming Structured DNA Assemblies to Probe Biophysical Processes.” Annual Review of Biophysics 48 (2019): 395-419 © 2019 The Author(s) en 10.1146/ANNUREV-BIOPHYS-052118-115259 Annual Review of Biophysics Creative Commons Attribution-Noncommercial-Share Alike http://creativecommons.org/licenses/by-nc-sa/4.0/ application/pdf Annual Reviews PMC |
| spellingShingle | Wamhoff, Eike-Christian Banal, James L. Bricker, William P Shepherd, Tyson R Parsons, Molly F. Veneziano, Remi Stone, Matthew B. Jun, Hyungmin Wang, Xiao Bathe, Mark Programming Structured DNA Assemblies to Probe Biophysical Processes |
| title | Programming Structured DNA Assemblies to Probe Biophysical Processes |
| title_full | Programming Structured DNA Assemblies to Probe Biophysical Processes |
| title_fullStr | Programming Structured DNA Assemblies to Probe Biophysical Processes |
| title_full_unstemmed | Programming Structured DNA Assemblies to Probe Biophysical Processes |
| title_short | Programming Structured DNA Assemblies to Probe Biophysical Processes |
| title_sort | programming structured dna assemblies to probe biophysical processes |
| url | https://hdl.handle.net/1721.1/125280 |
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