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  1. Article ; Online: Solid Phase Synthesis of DNA Nanostructures in Heavy Liquid.

    Smyrlaki, Ioanna / Shaw, Alan / Yang, Yunshi / Shen, Boxuan / Högberg, Björn

    Small (Weinheim an der Bergstrasse, Germany)

    2022  Volume 19, Issue 4, Page(s) e2204513

    Abstract: Introduction of the solid phase method to synthesize biopolymers has revolutionized the field of biological research by enabling efficient production of peptides and oligonucleotides. One of the advantages of this method is the ease of removal of excess ... ...

    Abstract Introduction of the solid phase method to synthesize biopolymers has revolutionized the field of biological research by enabling efficient production of peptides and oligonucleotides. One of the advantages of this method is the ease of removal of excess production materials from the desired product, as it is immobilized on solid substrate. The DNA origami method utilizes the nature of nucleotide base-pairing to construct well-defined objects at the nanoscale, and has become a potent tool for manipulating matter in the fields of chemistry, physics, and biology. Here, the development of an approach to synthesize DNA nanostructures directly on magnetic beads, where the reaction is performed in heavy liquid to maintain the beads in suspension is reported. It is demonstrated that the method can achieve high folding yields of up to 90% for various DNA shapes, comparable to standard folding. At the same time, this establishes an easy, fast, and efficient way to further functionalize the DNA origami in one-pot, as well as providing a built-in purification method for easy removal of excess by-products such as non-integrated DNA strands and residual functionalization molecules.
    MeSH term(s) Nanotechnology/methods ; Solid-Phase Synthesis Techniques ; Nucleic Acid Conformation ; Nanostructures/chemistry ; DNA/chemistry
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2022-11-27
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2168935-0
    ISSN 1613-6829 ; 1613-6810
    ISSN (online) 1613-6829
    ISSN 1613-6810
    DOI 10.1002/smll.202204513
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Stochastic modeling of antibody binding predicts programmable migration on antigen patterns.

    Hoffecker, Ian T / Shaw, Alan / Sorokina, Viktoria / Smyrlaki, Ioanna / Högberg, Björn

    Nature computational science

    2022  Volume 2, Page(s) 179–192

    Abstract: Viruses and bacteria commonly exhibit spatial repetition of surface molecules that directly interface with the host immune system. However the complex interaction of patterned surfaces with immune molecules containing multiple binding domains is poorly ... ...

    Abstract Viruses and bacteria commonly exhibit spatial repetition of surface molecules that directly interface with the host immune system. However the complex interaction of patterned surfaces with immune molecules containing multiple binding domains is poorly understood. We developed a pipeline for constructing mechanistic models of antibody interactions with patterned antigen substrates. Our framework relies on immobilized DNA origami nanostructures decorated with precisely placed antigens. The results revealed that antigen spacing is a spatial control parameter that can be tuned to influence antibody residence time and migration speed. The model predicts that gradients in antigen spacing can drive persistent, directed antibody migration in the direction of more stable spacing. These results depict antibody-antigen interactions as a computational system wherein antigen geometry constrains and potentially directs antibody movement. We propose that this form of molecular programmability could be exploited during co-evolution of pathogens and immune systems or in the design of molecular machines.
    Language English
    Publishing date 2022-03-24
    Publishing country United States
    Document type Journal Article
    ISSN 2662-8457
    ISSN (online) 2662-8457
    DOI 10.1038/s43588-022-00218-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Soluble and multivalent Jag1 DNA origami nanopatterns activate Notch without pulling force.

    Smyrlaki, Ioanna / Fördős, Ferenc / Rocamonde-Lago, Iris / Wang, Yang / Shen, Boxuan / Lentini, Antonio / Luca, Vincent C / Reinius, Björn / Teixeira, Ana I / Högberg, Björn

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 465

    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 ... ...

    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.
    MeSH term(s) Receptors, Notch/metabolism ; Jagged-1 Protein/genetics ; Jagged-1 Protein/metabolism ; Signal Transduction/physiology ; Calcium-Binding Proteins/metabolism
    Chemical Substances Receptors, Notch ; Jagged-1 Protein ; Calcium-Binding Proteins
    Language English
    Publishing date 2024-01-18
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-44059-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Publisher Correction: Binding to nanopatterned antigens is dominated by the spatial tolerance of antibodies.

    Shaw, Alan / Hoffecker, Ian T / Smyrlaki, Ioanna / Rosa, Joao / Grevys, Algirdas / Bratlie, Diane / Sandlie, Inger / Michaelsen, Terje Einar / Andersen, Jan Terje / Högberg, Björn

    Nature nanotechnology

    2019  Volume 14, Issue 4, Page(s) 398

    Abstract: In the Supplementary Information file originally published with this Article, the Supplementary references 48-62 were missing; the amended file has now been uploaded. ...

    Abstract In the Supplementary Information file originally published with this Article, the Supplementary references 48-62 were missing; the amended file has now been uploaded.
    Language English
    Publishing date 2019-02-19
    Publishing country England
    Document type Published Erratum
    ZDB-ID 2254964-X
    ISSN 1748-3395 ; 1748-3387
    ISSN (online) 1748-3395
    ISSN 1748-3387
    DOI 10.1038/s41565-019-0404-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-PCR.

    Smyrlaki, Ioanna / Ekman, Martin / Lentini, Antonio / Rufino de Sousa, Nuno / Papanicolaou, Natali / Vondracek, Martin / Aarum, Johan / Safari, Hamzah / Muradrasoli, Shaman / Rothfuchs, Antonio Gigliotti / Albert, Jan / Högberg, Björn / Reinius, Björn

    Nature communications

    2020  Volume 11, Issue 1, Page(s) 4812

    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 ... ...

    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.
    MeSH term(s) Benchmarking ; Betacoronavirus/genetics ; Betacoronavirus/isolation & purification ; COVID-19 ; COVID-19 Testing ; Clinical Laboratory Techniques/methods ; Clinical Laboratory Techniques/standards ; Clinical Laboratory Techniques/statistics & numerical data ; Coronavirus Infections/diagnosis ; Coronavirus Infections/epidemiology ; Coronavirus Infections/virology ; DNA Primers/genetics ; Hot Temperature ; Humans ; Pandemics ; Pneumonia, Viral/diagnosis ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/virology ; RNA, Viral/genetics ; RNA, Viral/isolation & purification ; Reverse Transcriptase Polymerase Chain Reaction/methods ; Reverse Transcriptase Polymerase Chain Reaction/standards ; Reverse Transcriptase Polymerase Chain Reaction/statistics & numerical data ; SARS-CoV-2 ; Sensitivity and Specificity ; Sweden/epidemiology ; Viral Plaque Assay/methods
    Chemical Substances DNA Primers ; RNA, Viral
    Keywords covid19
    Language English
    Publishing date 2020-09-23
    Publishing country England
    Document type Comparative Study ; Evaluation Study ; Journal Article ; Research Support, Non-U.S. Gov't ; Validation Study
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-020-18611-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-qPCR

    Smyrlaki, Ioanna / Ekman, Martin / Vondracek, Martin / Papanicoloau, Natali / Lentini, Antonio / Aarum, Johan / Muradrasoli, Shaman / Albert, Jan / Högberg, Björn / Reinius, Björn

    Abstract: Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The most widely used method of COVID-19 diagnostics is a reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay, ... ...

    Abstract Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The most widely used method of COVID-19 diagnostics is a reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay, detecting the presence of SARS-CoV-2 RNA in patient samples, typically from nasopharyngeal swabs. The RNA extraction is a major bottleneck in current COVID-19 testing, in terms of turn-around, logistics, component availability and cost, which delays or completely precludes COVID-19 diagnostics in many settings. Efforts to simplify the current methods are important, as increased diagnostic availability and efficiency is expected to benefit patient care and infection control. Here, we describe methods to circumvent RNA extraction in COVID-19 testing by performing RT-qPCR directly on heat-inactivated subject samples as well as samples lysed with readily available detergents. Our data, including cross-comparisons with clinically diagnosed patient samples, suggest that direct RT-qPCR is a viable option to extraction-based COVID-19 diagnostics. We argue that significant savings in terms of time and cost can be achieved by embracing RNA-extraction-free protocols, that feeds directly into the established PCR-based testing pipeline. This could aid the expansion of COVID-19 testing.
    Keywords covid19
    Publisher MedRxiv; WHO
    Document type Article ; Online
    DOI 10.1101/2020.04.17.20067348
    Database COVID19

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  7. Article ; Online: Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-qPCR

    Smyrlaki, Ioanna / Ekman, Martin / Vondracek, Martin / Papanicoloau, Natali / Lentini, Antonio / Aarum, Johan / Muradrasoli, Shaman / Albert, Jan / Högberg, Björn / Reinius, Björn

    medRxiv

    Abstract: Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The most widely used method of COVID-19 diagnostics is a reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay, ... ...

    Abstract Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The most widely used method of COVID-19 diagnostics is a reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay, detecting the presence of SARS-CoV-2 RNA in patient samples, typically from nasopharyngeal swabs. The RNA extraction is a major bottleneck in current COVID-19 testing, in terms of turn-around, logistics, component availability and cost, which delays or completely precludes COVID-19 diagnostics in many settings. Efforts to simplify the current methods are important, as increased diagnostic availability and efficiency is expected to benefit patient care and infection control. Here, we describe methods to circumvent RNA extraction in COVID-19 testing by performing RT-qPCR directly on heat-inactivated subject samples as well as samples lysed with readily available detergents. Our data, including cross-comparisons with clinically diagnosed patient samples, suggest that direct RT-qPCR is a viable option to extraction-based COVID-19 diagnostics. We argue that significant savings in terms of time and cost can be achieved by embracing RNA-extraction-free protocols, that feeds directly into the established PCR-based testing pipeline. This could aid the expansion of COVID-19 testing.
    Keywords covid19
    Language English
    Publishing date 2020-04-18
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2020.04.17.20067348
    Database COVID19

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  8. Article ; Online: Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-PCR

    Ioanna Smyrlaki / Martin Ekman / Antonio Lentini / Nuno Rufino de Sousa / Natali Papanicolaou / Martin Vondracek / Johan Aarum / Hamzah Safari / Shaman Muradrasoli / Antonio Gigliotti Rothfuchs / Jan Albert / Björn Högberg / Björn Reinius

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 12

    Abstract: SARS-CoV-2 infection is widely diagnosed by RT-PCR, but RNA extraction is a bottleneck for fast and cheap diagnosis. Here, the authors develop protocols to perform RT-PCR directly on heat-inactivated subject samples or samples lysed with readily ... ...

    Abstract SARS-CoV-2 infection is widely diagnosed by RT-PCR, but RNA extraction is a bottleneck for fast and cheap diagnosis. Here, the authors develop protocols to perform RT-PCR directly on heat-inactivated subject samples or samples lysed with readily available detergents and benchmark performance against 597 clinically diagnosed patient samples.
    Keywords Science ; Q
    Language English
    Publishing date 2020-09-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-PCR

    Ioanna Smyrlaki / Martin Ekman / Antonio Lentini / Nuno Rufino de Sousa / Natali Papanicolaou / Martin Vondracek / Johan Aarum / Hamzah Safari / Shaman Muradrasoli / Antonio Gigliotti Rothfuchs / Jan Albert / Björn Högberg / Björn Reinius

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 12

    Abstract: SARS-CoV-2 infection is widely diagnosed by RT-PCR, but RNA extraction is a bottleneck for fast and cheap diagnosis. Here, the authors develop protocols to perform RT-PCR directly on heat-inactivated subject samples or samples lysed with readily ... ...

    Abstract SARS-CoV-2 infection is widely diagnosed by RT-PCR, but RNA extraction is a bottleneck for fast and cheap diagnosis. Here, the authors develop protocols to perform RT-PCR directly on heat-inactivated subject samples or samples lysed with readily available detergents and benchmark performance against 597 clinically diagnosed patient samples.
    Keywords Science ; Q ; covid19
    Language English
    Publishing date 2020-09-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Binding to nanopatterned antigens is dominated by the spatial tolerance of antibodies.

    Shaw, Alan / Hoffecker, Ian T / Smyrlaki, Ioanna / Rosa, Joao / Grevys, Algirdas / Bratlie, Diane / Sandlie, Inger / Michaelsen, Terje Einar / Andersen, Jan Terje / Högberg, Björn

    Nature nanotechnology

    2019  Volume 14, Issue 2, Page(s) 184–190

    Abstract: Although repetitive patterns of antigens are crucial for certain immune responses, an understanding of how antibodies bind and dynamically interact with various spatial arrangements of molecules is lacking. Hence, we introduced a new method in which ... ...

    Abstract Although repetitive patterns of antigens are crucial for certain immune responses, an understanding of how antibodies bind and dynamically interact with various spatial arrangements of molecules is lacking. Hence, we introduced a new method in which molecularly precise nanoscale patterns of antigens are displayed using DNA origami and immobilized in a surface plasmon resonance set-up. Using antibodies with identical antigen-binding domains, we found that all the subclasses and isotypes studied bind bivalently to two antigens separated at distances that range from 3 to 17 nm. The binding affinities of these antibodies change with the antigen distances, with a distinct preference for antigens separated by approximately 16 nm, and considerable differences in spatial tolerance exist between IgM and IgG and between low- and high-affinity antibodies.
    MeSH term(s) Antibodies/metabolism ; Antigens/metabolism ; Cell Line ; Humans ; Immune Tolerance ; Immunoglobulin G/chemistry ; Nanoparticles/chemistry ; Protein Binding ; Surface Plasmon Resonance
    Chemical Substances Antibodies ; Antigens ; Immunoglobulin G
    Language English
    Publishing date 2019-01-14
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2254964-X
    ISSN 1748-3395 ; 1748-3387
    ISSN (online) 1748-3395
    ISSN 1748-3387
    DOI 10.1038/s41565-018-0336-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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