DNA Canvas: Towards affordable and scalable enzymatic fabrication of DNA nanoarrays
In biological systems, DNA serves as a carrier of hereditary information, facilitated by predictable and programmable base-pairing rules. The field of DNA nanotechnology takes the DNA molecule out of its original context and using the same set of rules to construct complex structures and molecular m...
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| Format: | Thesis |
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Massachusetts Institute of Technology
2022
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| Online Access: | https://hdl.handle.net/1721.1/142837 https://orcid.org/0000-0003-3393-4996 |
| _version_ | 1811091561494085632 |
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| author | Perry, Eyal |
| author2 | Jacobson, Joseph M. |
| author_facet | Jacobson, Joseph M. Perry, Eyal |
| author_sort | Perry, Eyal |
| collection | MIT |
| description | In biological systems, DNA serves as a carrier of hereditary information, facilitated by predictable and programmable base-pairing rules. The field of DNA nanotechnology takes the DNA molecule out of its original context and using the same set of rules to construct complex structures and molecular machines at the nanoscale regime. At the nanoscale, precise organization of biological and non-biological materials in 2D or 3D space holds great promise for a vast range of applications in areas such as biophysics, point-of-care diagnostics, biomolecule structure determination, drug delivery, and more. Nucleic acid scaffolds, especially DNA origami, have emerged as a promising approach, by enabling <10nm assembly of nanomaterials such as gold particles, carbon nanotubes, and quantum dots. Two-dimensional DNA nanostructures with a plurality of uniquely-addressable linkage sites ("nanopixels") are known as DNA nanoarrays.
Expanding the size of DNA nanoarrays is desired for a variety of applications, from whole genomic sequencing at a fraction of the cost to sustainable digital information storage. Yet, due to the stochastic nature of self-assembly, DNA origami-based approaches suffer from an inherent scale limit. Top-down fabrication techniques enable nanometric precise patterning, yet single-molecule placement remains a daunting challenge. Currently, no method enables independent nanoscale manipulation of more than 10K diverse single-molecules.
In this thesis, we propose a new kind of DNA nanotechnology: DNA Canvas. We lay a theoretical and experimental foundation for the development of a low-cost DNA nanoarray. First, we present a computational model as feasibility proof, as well as statistical analysis of the experimental design space, aiming to minimize the cost per nanopixel. We demonstrate a novel fabrication process that fuses microfabrication by photolithography with enzymatic reactions to surpass the scale limit in previous approaches. Last, we chart a path towards full implementation of >1M DNA nanoarrays and enumerate potential applications to be disrupted by the introduction of such technology. |
| first_indexed | 2024-09-23T15:04:19Z |
| format | Thesis |
| id | mit-1721.1/142837 |
| institution | Massachusetts Institute of Technology |
| last_indexed | 2024-09-23T15:04:19Z |
| publishDate | 2022 |
| publisher | Massachusetts Institute of Technology |
| record_format | dspace |
| spelling | mit-1721.1/1428372022-06-01T03:08:35Z DNA Canvas: Towards affordable and scalable enzymatic fabrication of DNA nanoarrays Perry, Eyal Jacobson, Joseph M. Program in Media Arts and Sciences (Massachusetts Institute of Technology) In biological systems, DNA serves as a carrier of hereditary information, facilitated by predictable and programmable base-pairing rules. The field of DNA nanotechnology takes the DNA molecule out of its original context and using the same set of rules to construct complex structures and molecular machines at the nanoscale regime. At the nanoscale, precise organization of biological and non-biological materials in 2D or 3D space holds great promise for a vast range of applications in areas such as biophysics, point-of-care diagnostics, biomolecule structure determination, drug delivery, and more. Nucleic acid scaffolds, especially DNA origami, have emerged as a promising approach, by enabling <10nm assembly of nanomaterials such as gold particles, carbon nanotubes, and quantum dots. Two-dimensional DNA nanostructures with a plurality of uniquely-addressable linkage sites ("nanopixels") are known as DNA nanoarrays. Expanding the size of DNA nanoarrays is desired for a variety of applications, from whole genomic sequencing at a fraction of the cost to sustainable digital information storage. Yet, due to the stochastic nature of self-assembly, DNA origami-based approaches suffer from an inherent scale limit. Top-down fabrication techniques enable nanometric precise patterning, yet single-molecule placement remains a daunting challenge. Currently, no method enables independent nanoscale manipulation of more than 10K diverse single-molecules. In this thesis, we propose a new kind of DNA nanotechnology: DNA Canvas. We lay a theoretical and experimental foundation for the development of a low-cost DNA nanoarray. First, we present a computational model as feasibility proof, as well as statistical analysis of the experimental design space, aiming to minimize the cost per nanopixel. We demonstrate a novel fabrication process that fuses microfabrication by photolithography with enzymatic reactions to surpass the scale limit in previous approaches. Last, we chart a path towards full implementation of >1M DNA nanoarrays and enumerate potential applications to be disrupted by the introduction of such technology. S.M. 2022-05-31T13:31:49Z 2022-05-31T13:31:49Z 2021-09 2022-05-25T15:55:44.385Z Thesis https://hdl.handle.net/1721.1/142837 https://orcid.org/0000-0003-3393-4996 In Copyright - Educational Use Permitted Copyright MIT http://rightsstatements.org/page/InC-EDU/1.0/ application/pdf Massachusetts Institute of Technology |
| spellingShingle | Perry, Eyal DNA Canvas: Towards affordable and scalable enzymatic fabrication of DNA nanoarrays |
| title | DNA Canvas: Towards affordable and scalable enzymatic fabrication of DNA nanoarrays |
| title_full | DNA Canvas: Towards affordable and scalable enzymatic fabrication of DNA nanoarrays |
| title_fullStr | DNA Canvas: Towards affordable and scalable enzymatic fabrication of DNA nanoarrays |
| title_full_unstemmed | DNA Canvas: Towards affordable and scalable enzymatic fabrication of DNA nanoarrays |
| title_short | DNA Canvas: Towards affordable and scalable enzymatic fabrication of DNA nanoarrays |
| title_sort | dna canvas towards affordable and scalable enzymatic fabrication of dna nanoarrays |
| url | https://hdl.handle.net/1721.1/142837 https://orcid.org/0000-0003-3393-4996 |
| work_keys_str_mv | AT perryeyal dnacanvastowardsaffordableandscalableenzymaticfabricationofdnananoarrays |