Multiscale topological analysis of kinetoplast DNA <i>via</i> high-resolution AFM
Kinetoplast DNA is a complex nanoscale network, naturally assembled from thousands of interconnected DNA circles within the mitochondrion of certain parasites. Despite the relevance of this molecule to parasitology and the recent discovery of tuneable mechanics, its topology remains highly contested...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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Royal Society of Chemistry
2025
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| Online Access: | https://hdl.handle.net/1721.1/158255 |
| _version_ | 1826205183053398016 |
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| author | Diggines, Bradley Whittle, Sylvia Yadav, Indresh Holmes, Elizabeth P Rollins, Daniel E Catley, Thomas E Doyle, Patrick S Pyne, Alice LB |
| author2 | Massachusetts Institute of Technology. Department of Chemical Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Chemical Engineering Diggines, Bradley Whittle, Sylvia Yadav, Indresh Holmes, Elizabeth P Rollins, Daniel E Catley, Thomas E Doyle, Patrick S Pyne, Alice LB |
| author_sort | Diggines, Bradley |
| collection | MIT |
| description | Kinetoplast DNA is a complex nanoscale network, naturally assembled from thousands of interconnected DNA circles within the mitochondrion of certain parasites. Despite the relevance of this molecule to parasitology and the recent discovery of tuneable mechanics, its topology remains highly contested. Here we present a multiscale analysis into the structure of kDNA using a combination of high-resolution atomic force microscopy and custom-designed image analysis protocols. By capturing a notably large set of high-resolution images, we are able to look beyond individual kDNA variations and quantify population properties throughout several length scales. Within the sample, geometric fluctuations of area and mean curvature are observed, corresponding with previous in vitro measurements. These translate to localised variations in density, with a sample-wide decrease in DNA density from the outer rim of the molecule to the centre and an increase in pore size. Nodes were investigated in a single molecule study, and their estimated connectivity significantly exceeded mean valence, with a high dependence on their position in the network. While node separation was approximately half the minicircle circumference, it followed a strong bimodal distribution, suggesting more complex underlying behaviour. Finally, upon selective digestion of the network, breakdown of the fibril-cap heterogeneity was observed, with molecules expanding less upon immobilisation on the mica surface. Additionally, preferential digestion was seen in localised areas of the network, increasing pore size disproportionately. Overall, the combination of high-resolution AFM and single molecule image analysis provides a promising method to the continued investigation of complex nanoscale structures. These findings support the ongoing characterisation of kDNA topology to aid understanding of its biological and mechanical phenomena. |
| first_indexed | 2025-03-10T11:09:39Z |
| format | Article |
| id | mit-1721.1/158255 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2025-03-10T11:09:39Z |
| publishDate | 2025 |
| publisher | Royal Society of Chemistry |
| record_format | dspace |
| spelling | mit-1721.1/1582552025-02-24T20:13:15Z Multiscale topological analysis of kinetoplast DNA <i>via</i> high-resolution AFM Diggines, Bradley Whittle, Sylvia Yadav, Indresh Holmes, Elizabeth P Rollins, Daniel E Catley, Thomas E Doyle, Patrick S Pyne, Alice LB Massachusetts Institute of Technology. Department of Chemical Engineering Kinetoplast DNA is a complex nanoscale network, naturally assembled from thousands of interconnected DNA circles within the mitochondrion of certain parasites. Despite the relevance of this molecule to parasitology and the recent discovery of tuneable mechanics, its topology remains highly contested. Here we present a multiscale analysis into the structure of kDNA using a combination of high-resolution atomic force microscopy and custom-designed image analysis protocols. By capturing a notably large set of high-resolution images, we are able to look beyond individual kDNA variations and quantify population properties throughout several length scales. Within the sample, geometric fluctuations of area and mean curvature are observed, corresponding with previous in vitro measurements. These translate to localised variations in density, with a sample-wide decrease in DNA density from the outer rim of the molecule to the centre and an increase in pore size. Nodes were investigated in a single molecule study, and their estimated connectivity significantly exceeded mean valence, with a high dependence on their position in the network. While node separation was approximately half the minicircle circumference, it followed a strong bimodal distribution, suggesting more complex underlying behaviour. Finally, upon selective digestion of the network, breakdown of the fibril-cap heterogeneity was observed, with molecules expanding less upon immobilisation on the mica surface. Additionally, preferential digestion was seen in localised areas of the network, increasing pore size disproportionately. Overall, the combination of high-resolution AFM and single molecule image analysis provides a promising method to the continued investigation of complex nanoscale structures. These findings support the ongoing characterisation of kDNA topology to aid understanding of its biological and mechanical phenomena. 2025-02-24T20:13:14Z 2025-02-24T20:13:14Z 2024 2025-02-24T20:06:30Z Article http://purl.org/eprint/type/JournalArticle https://hdl.handle.net/1721.1/158255 Diggines, Bradley, Whittle, Sylvia, Yadav, Indresh, Holmes, Elizabeth P, Rollins, Daniel E et al. 2024. "Multiscale topological analysis of kinetoplast DNA <i>via</i> high-resolution AFM." Physical Chemistry Chemical Physics, 26 (40). en 10.1039/d4cp01795a Physical Chemistry Chemical Physics Creative Commons Attribution https://creativecommons.org/licenses/by/4.0/ application/pdf Royal Society of Chemistry Royal Society of Chemistry |
| spellingShingle | Diggines, Bradley Whittle, Sylvia Yadav, Indresh Holmes, Elizabeth P Rollins, Daniel E Catley, Thomas E Doyle, Patrick S Pyne, Alice LB Multiscale topological analysis of kinetoplast DNA <i>via</i> high-resolution AFM |
| title | Multiscale topological analysis of kinetoplast DNA <i>via</i> high-resolution AFM |
| title_full | Multiscale topological analysis of kinetoplast DNA <i>via</i> high-resolution AFM |
| title_fullStr | Multiscale topological analysis of kinetoplast DNA <i>via</i> high-resolution AFM |
| title_full_unstemmed | Multiscale topological analysis of kinetoplast DNA <i>via</i> high-resolution AFM |
| title_short | Multiscale topological analysis of kinetoplast DNA <i>via</i> high-resolution AFM |
| title_sort | multiscale topological analysis of kinetoplast dna i via i high resolution afm |
| url | https://hdl.handle.net/1721.1/158255 |
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