{"entity": "researcher", "timestamp": "2026-09-12T08:02:34.486Z", "family": "H\u00f6gberg", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0003-2715-7887", "affiliations": [], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc6147217ff7477db7d6c14847da3d58.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc6147217ff7477db7d6c14847da3d58"}}, "publications": [{"entity": "publication", "iuid": "5fa60f0f466444c08a2e0578827a4e57", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/5fa60f0f466444c08a2e0578827a4e57.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/5fa60f0f466444c08a2e0578827a4e57"}}, "title": "Soluble and multivalent Jag1 DNA origami nanopatterns activate Notch without pulling force.", "authors": [{"family": "Smyrlaki", "given": "Ioanna", "initials": "I"}, {"family": "F\u00f6rd\u0151s", "given": "Ferenc", "initials": "F", "orcid": "0000-0002-2274-5594", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/92e5d6f6ed814c69a85b1c09021afb28.json"}}, {"family": "Rocamonde-Lago", "given": "Iris", "initials": "I"}, {"family": "Wang", "given": "Yang", "initials": "Y", "orcid": "0000-0002-7911-9551", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b6a9aa7f9d8749b3843f4e7730e12840.json"}}, {"family": "Shen", "given": "Boxuan", "initials": "B", "orcid": "0000-0002-1107-828X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13923ea488c649d79e28dcbb9dbeabcf.json"}}, {"family": "Lentini", "given": "Antonio", "initials": "A", "orcid": "0000-0003-1239-5495", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5042d3005814ad0a2d1eaeee5d2de3b.json"}}, {"family": "Luca", "given": "Vincent C", "initials": "VC", "orcid": "0000-0001-9427-5520", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/45fe34fbca3245549e4df5f43df718f7.json"}}, {"family": "Reinius", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-7021-5248", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7c1abacc8d446bf8855254246b8d899.json"}}, {"family": "Teixeira", "given": "Ana I", "initials": "AI", "orcid": "0000-0001-8169-8815", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e1e6497a9de14f5b901fbca4a223ddad.json"}}, {"family": "H\u00f6gberg", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0003-2715-7887", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc6147217ff7477db7d6c14847da3d58.json"}}], "type": "journal article", "published": "2024-01-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "465", "issn-l": "2041-1723"}, "abstract": "The Notch signaling pathway has fundamental roles in embryonic development and in the nervous system. The current model of receptor activation involves initiation via a force-induced conformational change. Here, we define conditions that reveal pulling force-independent Notch activation using soluble multivalent constructs. We treat neuroepithelial stem-like cells with molecularly precise ligand nanopatterns displayed from solution using DNA origami. Notch signaling follows with clusters of Jag1, and with chimeric structures where most Jag1 proteins are replaced by other binders not targeting Notch. Our data rule out several confounding factors and suggest a model where Jag1 activates Notch upon prolonged binding without appearing to need a pulling force. These findings reveal a distinct mode of activation of Notch and lay the foundation for the development of soluble agonists.", "doi": "10.1038/s41467-023-44059-4", "pmid": "38238313", "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10796381"}, {"db": "pii", "key": "10.1038/s41467-023-44059-4"}], "notes": [], "created": "2025-03-28T07:03:08.537Z", "modified": "2025-03-28T07:03:08.704Z"}, {"entity": "publication", "iuid": "7a0120e1ffd2468991bd9de55ea66308", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7a0120e1ffd2468991bd9de55ea66308.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7a0120e1ffd2468991bd9de55ea66308"}}, "title": "Myeloid cell-specific topoisomerase 1 inhibition using DNA origami mitigates neuroinflammation.", "authors": [{"family": "Zhu", "given": "Keying", "initials": "K", "orcid": "0000-0001-7500-1532", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a3555d961bb34bedae569a2b05ffc474.json"}}, {"family": "Wang", "given": "Yang", "initials": "Y", "orcid": "0000-0002-7911-9551", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b6a9aa7f9d8749b3843f4e7730e12840.json"}}, {"family": "Sarlus", "given": "Heela", "initials": "H", "orcid": "0000-0001-7880-9828", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2458d82ce194489a9ef5719882dfba0c.json"}}, {"family": "Geng", "given": "Keyi", "initials": "K", "orcid": "0000-0003-0892-7460", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a56ac387ab324409b2c0dc24b9be5d73.json"}}, {"family": "Nutma", "given": "Erik", "initials": "E"}, {"family": "Sun", "given": "Jingxian", "initials": "J"}, {"family": "Kung", "given": "Shin-Yu", "initials": "SY", "orcid": "0000-0003-4002-2848", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ffccfc627579496ea4baf20afa00116e.json"}}, {"family": "Bay", "given": "Cindy", "initials": "C", "orcid": "0000-0003-3898-3148", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/337c271c08004081903d2308c5bf3c8d.json"}}, {"family": "Han", "given": "Jinming", "initials": "J", "orcid": "0000-0002-6084-3275", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a33af0dcff9543d8aaf6c599814ca52c.json"}}, {"family": "Min", "given": "Jin-Hong", "initials": "JH"}, {"family": "Benito-Cuesta", "given": "Irene", "initials": "I"}, {"family": "Lund", "given": "Harald", "initials": "H", "orcid": "0000-0001-8046-0805", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/447fceec6f074e869ffb736d5dab13c1.json"}}, {"family": "Amor", "given": "Sandra", "initials": "S", "orcid": "0000-0001-6169-9845", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8523f177f5d4b2ca288b1deda7d5beb.json"}}, {"family": "Wang", "given": "Jun", "initials": "J", "orcid": "0000-0002-4530-0758", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d877a3366dca4550831e463f83d9ad02.json"}}, {"family": "Zhang", "given": "Xing-Mei", "initials": "XM", "orcid": "0000-0002-8728-8849", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/65a68d96961247bb8bb9890b20fa2305.json"}}, {"family": "Kutter", "given": "Claudia", "initials": "C", "orcid": "0000-0002-8047-0058", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a4c9dcde56304ab2a99bb1032e4ce834.json"}}, {"family": "Guerreiro-Cacais", "given": "Andr\u00e9 Ortlieb", "initials": "AO", "orcid": "0000-0002-4561-2823", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8c2ecf483cb7442b9de5c99dcc11c1a5.json"}}, {"family": "H\u00f6gberg", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0003-2715-7887", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc6147217ff7477db7d6c14847da3d58.json"}}, {"family": "Harris", "given": "Robert A", "initials": "RA", "orcid": "0000-0003-4990-509X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7558fb5ceba54b689244b4e771714b76.json"}}], "type": "journal article", "published": "2022-07-05", "journal": {"title": "EMBO Rep.", "issn": "1469-3178", "volume": "23", "issue": "7", "pages": "e54499", "issn-l": "1469-221X"}, "abstract": "Targeting myeloid cells, especially microglia, for the treatment of neuroinflammatory diseases such as multiple sclerosis (MS), is underappreciated. Our in silico drug screening reveals topoisomerase 1 (TOP1) inhibitors as promising drug candidates for microglial modulation. We show that TOP1 is highly expressed in neuroinflammatory conditions, and TOP1 inhibition using camptothecin (CPT) and its FDA-approved analog topotecan (TPT) reduces inflammatory responses in microglia/macrophages and ameliorates neuroinflammation in vivo. Transcriptomic analyses of sorted microglia from LPS-challenged mice reveal an altered transcriptional phenotype following TPT treatment. To target myeloid cells, we design a nanosystem using \u03b2-glucan-coated DNA origami (MyloGami) loaded with TPT (TopoGami). MyloGami shows enhanced specificity to myeloid cells while preventing the degradation of the DNA origami scaffold. Myeloid-specific TOP1 inhibition using TopoGami significantly suppresses the inflammatory response in microglia and mitigates MS-like disease progression. Our findings suggest that TOP1 inhibition in myeloid cells represents a therapeutic strategy for neuroinflammatory diseases and that the myeloid-specific nanosystems we designed may also benefit the treatment of other diseases with dysfunctional myeloid cells.", "doi": "10.15252/embr.202154499", "pmid": "35593064", "labels": {"SciLifeLab Fellow": null, "Claudia Kutter": null}, "xrefs": [{"db": "pmc", "key": "PMC9253741"}], "notes": [], "created": "2022-11-28T11:21:24.134Z", "modified": "2022-11-28T11:21:24.513Z"}, {"entity": "publication", "iuid": "10c986a2ba014858989987a38ceeb1be", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/10c986a2ba014858989987a38ceeb1be.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/10c986a2ba014858989987a38ceeb1be"}}, "title": "Nanoengineered DNA origami with repurposed TOP1 inhibitors targeting myeloid cells for the mitigation of neuroinflammation", "authors": [{"family": "Zhu", "given": "Keying", "initials": "K", "orcid": "0000-0001-7500-1532", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a3555d961bb34bedae569a2b05ffc474.json"}}, {"family": "Wang", "given": "Yang", "initials": "Y", "orcid": "0000-0002-7911-9551", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b6a9aa7f9d8749b3843f4e7730e12840.json"}}, {"family": "Sarlus", "given": "Heela", "initials": "H", "orcid": "0000-0001-7880-9828", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2458d82ce194489a9ef5719882dfba0c.json"}}, {"family": "Geng", "given": "Keyi", "initials": "K"}, {"family": "Nutma", "given": "Erik", "initials": "E"}, {"family": "Sun", "given": "Jingxian", "initials": "J"}, {"family": "Kung", "given": "Shin Yu", "initials": "SY"}, {"family": "Bay", "given": "Cindy", "initials": "C"}, {"family": "Han", "given": "Jinming", "initials": "J", "orcid": "0000-0002-6084-3275", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a33af0dcff9543d8aaf6c599814ca52c.json"}}, {"family": "Lund", "given": "Harald", "initials": "H", "orcid": "0000-0001-8046-0805", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/447fceec6f074e869ffb736d5dab13c1.json"}}, {"family": "Amor", "given": "Sandra", "initials": "S"}, {"family": "Wang", "given": "Jun", "initials": "J"}, {"family": "Zhang", "given": "Xingmei", "initials": "X", "orcid": "0000-0002-8728-8849", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/65a68d96961247bb8bb9890b20fa2305.json"}}, {"family": "Kutter", "given": "Claudia", "initials": "C", "orcid": "0000-0002-8047-0058", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a4c9dcde56304ab2a99bb1032e4ce834.json"}}, {"family": "Guerreiro Cacais", "given": "Andr\u00e9 Ortlieb", "initials": "AO"}, {"family": "H\u00f6gberg", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0003-2715-7887", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc6147217ff7477db7d6c14847da3d58.json"}}, {"family": "Harris", "given": "Robert A", "initials": "RA", "orcid": "0000-0003-4990-509X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7558fb5ceba54b689244b4e771714b76.json"}}], "type": "posted-content", "published": "2021-10-04", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.10.04.462880", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:06:58.642Z", "modified": "2026-08-20T10:06:58.757Z"}, {"entity": "publication", "iuid": "6fcaeba11cb74b619ae008a35aeaa01e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6fcaeba11cb74b619ae008a35aeaa01e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6fcaeba11cb74b619ae008a35aeaa01e"}}, "title": "DNA Origami Penetration in Cell Spheroid Tissue Models is Enhanced by Wireframe Design.", "authors": [{"family": "Wang", "given": "Yang", "initials": "Y", "orcid": "0000-0002-7911-9551", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b6a9aa7f9d8749b3843f4e7730e12840.json"}}, {"family": "Benson", "given": "Erik", "initials": "E"}, {"family": "F\u00f6rd\u0151s", "given": "Ferenc", "initials": "F"}, {"family": "Lolaico", "given": "Marco", "initials": "M"}, {"family": "Baars", "given": "Igor", "initials": "I"}, {"family": "Fang", "given": "Trixy", "initials": "T"}, {"family": "Teixeira", "given": "Ana I", "initials": "AI"}, {"family": "H\u00f6gberg", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0003-2715-7887", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc6147217ff7477db7d6c14847da3d58.json"}}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Adv. Mater. Weinheim", "issn": "1521-4095", "issn-l": "0935-9648", "volume": "33", "issue": "29", "pages": "e2008457"}, "abstract": "As DNA origami applications in biomedicine are expanding, more knowledge is needed to assess these structures' interaction with biological systems. Here, uptake and penetration in cell and cell spheroid tissue models (CSTMs) are studied to elucidate whether differences in internal structure can be a factor in the efficacy of DNA-origami-based delivery. Two structures bearing largely similar features in terms of both geometry and molecular weight, but with different internal designs-being either compact, lattice-based origami or following an open, wireframe design-are designed. In CSTMs, wireframe rods are able to penetrate deeper than close-packed rods. Moreover, doxorubicin-loaded wireframe rods show a higher cytotoxicity in CSTMs. These results can be explained by differences in structural mechanics, local deformability, local material density, and accessibility to cell receptors between these two DNA origami design paradigms. In particular, it is suggested that the main reason for the difference in penetration dynamic arises from differences in interaction with scavenger receptors where lattice-based structures appear to be internalized to a higher degree than polygonal structures of the same size and shape. It is thus argued that the choice of structural design method constitutes a crucial parameter for the application of DNA origami in drug delivery.", "doi": "10.1002/adma.202008457", "pmid": "34096116", "labels": {"Erik Benson": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "mid", "key": "EMS155931"}, {"db": "pmc", "key": "PMC7613750"}], "notes": [], "created": "2023-05-23T09:20:02.888Z", "modified": "2023-05-23T12:32:00.607Z"}, {"entity": "publication", "iuid": "f61f862ae78c4d09a7589be5b13e9e09", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/f61f862ae78c4d09a7589be5b13e9e09.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/f61f862ae78c4d09a7589be5b13e9e09"}}, "title": "Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-PCR.", "authors": [{"family": "Smyrlaki", "given": "Ioanna", "initials": "I"}, {"family": "Ekman", "given": "Martin", "initials": "M"}, {"family": "Lentini", "given": "Antonio", "initials": "A", "orcid": "0000-0003-1239-5495", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5042d3005814ad0a2d1eaeee5d2de3b.json"}}, {"family": "Rufino de Sousa", "given": "Nuno", "initials": "N", "orcid": "0000-0002-0670-9788", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/366a797e8288463ea7f0c15847fb377b.json"}}, {"family": "Papanicolaou", "given": "Natali", "initials": "N"}, {"family": "Vondracek", "given": "Martin", "initials": "M"}, {"family": "Aarum", "given": "Johan", "initials": "J"}, {"family": "Safari", "given": "Hamzah", "initials": "H"}, {"family": "Muradrasoli", "given": "Shaman", "initials": "S"}, {"family": "Rothfuchs", "given": "Antonio Gigliotti", "initials": "AG", "orcid": "0000-0001-6001-7240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d455e35b8fa4c40baade7ec4c9ece3a.json"}}, {"family": "Albert", "given": "Jan", "initials": "J", "orcid": "0000-0001-9020-0521", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5945a41c8836474a8decf9c8b8db52ab.json"}}, {"family": "H\u00f6gberg", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0003-2715-7887", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc6147217ff7477db7d6c14847da3d58.json"}}, {"family": "Reinius", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0002-7021-5248", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a7c1abacc8d446bf8855254246b8d899.json"}}], "type": "comparative study", "published": "2020-09-23", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "4812", "issn-l": "2041-1723"}, "abstract": "Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is commonly diagnosed by reverse transcription polymerase chain reaction (RT-PCR) to detect viral RNA in patient samples, but RNA extraction constitutes a major bottleneck in current testing. Methodological simplification could increase diagnostic availability and efficiency, benefitting patient care and infection control. Here, we describe methods circumventing RNA extraction in COVID-19 testing by performing RT-PCR directly on heat-inactivated or lysed samples. Our data, including benchmarking using 597 clinical patient samples and a standardised diagnostic system, demonstrate that direct RT-PCR is viable option to extraction-based tests. Using controlled amounts of active SARS-CoV-2, we confirm effectiveness of heat inactivation by plaque assay and evaluate various generic buffers as transport medium for direct RT-PCR. Significant savings in time and cost are achieved through RNA-extraction-free protocols that are directly compatible with established PCR-based testing pipelines. This could aid expansion of COVID-19 testing.", "doi": "10.1038/s41467-020-18611-5", "pmid": "32968075", "labels": {"Antonio Lentini": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC7511968"}, {"db": "pii", "key": "10.1038/s41467-020-18611-5"}], "notes": [], "created": "2025-03-28T07:11:57.060Z", "modified": "2025-03-28T07:11:57.197Z"}, {"entity": "publication", "iuid": "0748b822e01843dbadec8cc694bbc2ca", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0748b822e01843dbadec8cc694bbc2ca.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0748b822e01843dbadec8cc694bbc2ca"}}, "title": "Evolutionary Refinement of DNA Nanostructures Using Coarse-Grained Molecular Dynamics Simulations.", "authors": [{"family": "Benson", "given": "Erik", "initials": "E"}, {"family": "Lolaico", "given": "Marco", "initials": "M"}, {"family": "Tarasov", "given": "Yevgen", "initials": "Y"}, {"family": "G\u00e5din", "given": "Andreas", "initials": "A"}, {"family": "H\u00f6gberg", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0003-2715-7887", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc6147217ff7477db7d6c14847da3d58.json"}}], "type": "journal article", "published": "2019-11-26", "journal": {"title": "ACS Nano", "issn": "1936-086X", "issn-l": "1936-0851", "volume": "13", "issue": "11", "pages": "12591-12598"}, "abstract": "In the past decade, DNA nanostructures have made the leap from small assemblies of a handful of oligonucleotides to megadalton objects assembled from hundreds or thousands of component DNA strands. Most DNA designs today are either lattice based with simple and reliable design tools or lattice free with a larger shape space but more challenging design and lower rigidity. In parallel with the development of DNA nanostructures, software packages for the simulation of nucleic acids have seen rapid development allowing for the simulation of the dynamics of full DNA nanostructure assemblies. Here, we implement an unsupervised software based on the coarse-grained molecular dynamics package oxDNA to simulate DNA origami structures and evaluate their rigidity. From this, the software autonomously produces mutant structures by adding or removing base pairs or modifying the positions of internal supports. These mutant structures are iteratively generated and evaluated by simulation to create an in silico evolution toward more rigid DNA nanostructures.", "doi": "10.1021/acsnano.9b03473", "pmid": "31613092", "labels": {"Erik Benson": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "mid", "key": "EMS155929"}, {"db": "pmc", "key": "PMC7613751"}], "notes": [], "created": "2023-05-23T09:20:04.239Z", "modified": "2023-05-23T12:32:25.643Z"}, {"entity": "publication", "iuid": "9dc8012360394c1a802c7d4528dd7625", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9dc8012360394c1a802c7d4528dd7625.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9dc8012360394c1a802c7d4528dd7625"}}, "title": "Effects of Design Choices on the Stiffness of Wireframe DNA Origami Structures.", "authors": [{"family": "Benson", "given": "Erik", "initials": "E"}, {"family": "Mohammed", "given": "Abdulmelik", "initials": "A"}, {"family": "Rayneau-Kirkhope", "given": "Daniel", "initials": "D"}, {"family": "G\u00e5din", "given": "Andreas", "initials": "A"}, {"family": "Orponen", "given": "Pekka", "initials": "P"}, {"family": "H\u00f6gberg", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0003-2715-7887", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc6147217ff7477db7d6c14847da3d58.json"}}], "type": "journal article", "published": "2018-09-25", "journal": {"title": "ACS Nano", "issn": "1936-086X", "issn-l": "1936-0851", "volume": "12", "issue": "9", "pages": "9291-9299"}, "abstract": "DNA origami is a powerful method for the creation of 3D nanoscale objects, and in the past few years, interest in wireframe origami designs has increased due to their potential for biomedical applications. In DNA wireframe designs, the construction material is double-stranded DNA, which has a persistence length of around 50 nm. In this work, we study the effect of various design choices on the stiffness versus final size of nanoscale wireframe rods, given the constraints on origami designs set by the DNA origami scaffold size. An initial theoretical analysis predicts two competing mechanisms limiting rod stiffness, whose balancing results in an optimal edge length. For small edge lengths, the bending of the rod's overall frame geometry is the dominant factor, while the flexibility of individual DNA edges has a greater contribution at larger edge lengths. We evaluate our design choices through simulations and experiments and find that the stiffness of the structures increases with the number of sides in the cross-section polygon and that there are indications of an optimal member edge length. We also ascertain the effect of nicked DNA edges on the stiffness of the wireframe rods and demonstrate that ligation of the staple breakpoint nicks reduces the observed flexibility. Our simulations also indicate that the persistence length of wireframe DNA structures significantly decreases with increasing monovalent salt concentration.", "doi": "10.1021/acsnano.8b04148", "pmid": "30188123", "labels": {"Erik Benson": null, "SciLifeLab Fellow": null}, "xrefs": [], "notes": [], "created": "2023-05-23T09:20:05.485Z", "modified": "2023-05-23T12:32:40.077Z"}, {"entity": "publication", "iuid": "dce9360770024bbd967d92b119b83801", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/dce9360770024bbd967d92b119b83801.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/dce9360770024bbd967d92b119b83801"}}, "title": "Measuring true localization accuracy in super resolution microscopy with DNA-origami nanostructures", "authors": [{"family": "Reuss", "given": "Matthias", "initials": "M", "orcid": "0000-0001-8914-3830", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/340f4d00ef094def97b55cd32ac50d7e.json"}}, {"family": "F\u00f6rd\u0151s", "given": "Ferenc", "initials": "F"}, {"family": "Blom", "given": "Hans", "initials": "H"}, {"family": "\u00d6ktem", "given": "Ozan", "initials": "O", "orcid": "0000-0002-1118-6483", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ed0d6330708d454ea8d61f721527c5a7.json"}}, {"family": "H\u00f6gberg", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0003-2715-7887", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc6147217ff7477db7d6c14847da3d58.json"}}, {"family": "Brismar", "given": "Hjalmar", "initials": "H", "orcid": "0000-0003-0578-4003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/04321d9fb805493db538489927a42c8f.json"}}], "type": "journal-article", "published": "2017-02-27", "journal": {"title": "New J. Phys.", "issn": "1367-2630", "volume": "19", "issue": "2", "pages": "025013", "issn-l": "1367-2630"}, "abstract": null, "doi": "10.1088/1367-2630/aa5f74", "pmid": null, "labels": {"Affiliated researcher": null}, "xrefs": [], "notes": [], "created": "2018-12-05T13:11:25.048Z", "modified": "2021-07-09T09:32:54.014Z"}, {"entity": "publication", "iuid": "7b83600b3b1c45aabee489af8d5c953e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7b83600b3b1c45aabee489af8d5c953e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7b83600b3b1c45aabee489af8d5c953e"}}, "title": "Computer-Aided Production of Scaffolded DNA Nanostructures from Flat Sheet Meshes.", "authors": [{"family": "Benson", "given": "Erik", "initials": "E"}, {"family": "Mohammed", "given": "Abdulmelik", "initials": "A"}, {"family": "Bosco", "given": "Alessandro", "initials": "A"}, {"family": "Teixeira", "given": "Ana I", "initials": "AI"}, {"family": "Orponen", "given": "Pekka", "initials": "P"}, {"family": "H\u00f6gberg", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0003-2715-7887", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc6147217ff7477db7d6c14847da3d58.json"}}], "type": "journal article", "published": "2016-07-25", "journal": {"title": "Angew. Chem. Int. Ed. Engl.", "issn": "1521-3773", "issn-l": "1433-7851", "volume": "55", "issue": "31", "pages": "8869-8872"}, "abstract": "The use of DNA as a nanoscale construction material has been a rapidly developing field since the 1980s, in particular since the introduction of scaffolded DNA origami in 2006. Although software is available for DNA origami design, the user is generally limited to architectures where finding the scaffold path through the object is trivial. Herein, we demonstrate the automated conversion of arbitrary two-dimensional sheets in the form of digital meshes into scaffolded DNA nanostructures. We investigate the properties of DNA meshes based on three different internal frameworks in standard folding buffer and physiological salt buffers. We then employ the triangulated internal framework and produce four 2D structures with complex outlines and internal features. We demonstrate that this highly automated technique is capable of producing complex DNA nanostructures that fold with high yield to their programmed configurations, covering around 70 % more surface area than classic origami flat sheets.", "doi": "10.1002/anie.201602446", "pmid": "27304204", "labels": {"Erik Benson": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC6680348"}], "notes": [], "created": "2023-05-23T09:20:06.838Z", "modified": "2023-05-23T12:32:51.705Z"}]}