1
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Babbe H, Sundberg TB, Tichenor M, Seierstad M, Bacani G, Berstler J, Chai W, Chang L, Chung DM, Coe K, Collins B, Finley M, Guletsky A, Lemke CT, Mak PA, Mathur A, Mercado-Marin EV, Metkar S, Raymond DD, Rives ML, Rizzolio M, Shaffer PL, Smith R, Smith J, Steele R, Steffens H, Suarez J, Tian G, Majewski N, Volak LP, Wei J, Desai PT, Ong LL, Koudriakova T, Goldberg SD, Hirst G, Kaushik VK, Ort T, Seth N, Graham DB, Plevy S, Venable JD, Xavier RJ, Towne JE. Identification of highly selective SIK1/2 inhibitors that modulate innate immune activation and suppress intestinal inflammation. Proc Natl Acad Sci U S A 2024; 121:e2307086120. [PMID: 38147543 PMCID: PMC10769863 DOI: 10.1073/pnas.2307086120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 11/07/2023] [Indexed: 12/28/2023] Open
Abstract
The salt-inducible kinases (SIK) 1-3 are key regulators of pro- versus anti-inflammatory cytokine responses during innate immune activation. The lack of highly SIK-family or SIK isoform-selective inhibitors suitable for repeat, oral dosing has limited the study of the optimal SIK isoform selectivity profile for suppressing inflammation in vivo. To overcome this challenge, we devised a structure-based design strategy for developing potent SIK inhibitors that are highly selective against other kinases by engaging two differentiating features of the SIK catalytic site. This effort resulted in SIK1/2-selective probes that inhibit key intracellular proximal signaling events including reducing phosphorylation of the SIK substrate cAMP response element binding protein (CREB) regulated transcription coactivator 3 (CRTC3) as detected with an internally generated phospho-Ser329-CRTC3-specific antibody. These inhibitors also suppress production of pro-inflammatory cytokines while inducing anti-inflammatory interleukin-10 in activated human and murine myeloid cells and in mice following a lipopolysaccharide challenge. Oral dosing of these compounds ameliorates disease in a murine colitis model. These findings define an approach to generate highly selective SIK1/2 inhibitors and establish that targeting these isoforms may be a useful strategy to suppress pathological inflammation.
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Affiliation(s)
- Holger Babbe
- Janssen Research and Development, LLC., Spring House, PA19477
| | - Thomas B. Sundberg
- Broad Institute of MIT and Harvard, Center for the Development of Therapeutics, Cambridge, MA02142
| | - Mark Tichenor
- Janssen Research and Development, LLC., San Diego, CA92121
| | - Mark Seierstad
- Janssen Research and Development, LLC., San Diego, CA92121
| | - Genesis Bacani
- Janssen Research and Development, LLC., San Diego, CA92121
| | - James Berstler
- Broad Institute of MIT and Harvard, Center for the Development of Therapeutics, Cambridge, MA02142
| | - Wenying Chai
- Janssen Research and Development, LLC., San Diego, CA92121
| | - Leon Chang
- Janssen Research and Development, LLC., San Diego, CA92121
| | | | - Kevin Coe
- Janssen Research and Development, LLC., San Diego, CA92121
| | | | - Michael Finley
- Janssen Research and Development, LLC., Spring House, PA19477
| | - Alexander Guletsky
- Broad Institute of MIT and Harvard, Center for the Development of Therapeutics, Cambridge, MA02142
| | - Christopher T. Lemke
- Broad Institute of MIT and Harvard, Center for the Development of Therapeutics, Cambridge, MA02142
| | - Puiying A. Mak
- Janssen Research and Development, LLC., San Diego, CA92121
| | - Ashok Mathur
- Janssen Research and Development, LLC., Spring House, PA19477
| | | | - Shailesh Metkar
- Broad Institute of MIT and Harvard, Center for the Development of Therapeutics, Cambridge, MA02142
| | - Donald D. Raymond
- Broad Institute of MIT and Harvard, Center for the Development of Therapeutics, Cambridge, MA02142
| | | | | | - Paul L. Shaffer
- Janssen Research and Development, LLC., Spring House, PA19477
| | - Russell Smith
- Janssen Research and Development, LLC., San Diego, CA92121
| | | | - Ruth Steele
- Janssen Research and Development, LLC., Spring House, PA19477
| | | | - Javier Suarez
- Janssen Research and Development, LLC., Spring House, PA19477
| | - Gaochao Tian
- Janssen Research and Development, LLC., Spring House, PA19477
| | - Nathan Majewski
- Janssen Research and Development, LLC., Spring House, PA19477
| | | | - Jianmei Wei
- Janssen Research and Development, LLC., San Diego, CA92121
| | - Prerak T. Desai
- Janssen Research and Development, LLC., Spring House, PA19477
| | - Luvena L. Ong
- Janssen Research and Development, LLC., Spring House, PA19477
| | | | | | - Gavin Hirst
- Janssen Research and Development, LLC., San Diego, CA92121
| | - Virendar K. Kaushik
- Broad Institute of MIT and Harvard, Center for the Development of Therapeutics, Cambridge, MA02142
| | - Tatiana Ort
- Janssen Research and Development, LLC., Spring House, PA19477
| | - Nilufer Seth
- Janssen Research and Development, LLC., Spring House, PA19477
| | - Daniel B. Graham
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA02114
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA02114
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA02142
| | - Scott Plevy
- Janssen Research and Development, LLC., Spring House, PA19477
| | | | - Ramnik J. Xavier
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA02114
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA02114
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA02142
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2
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Boelders SM, De Baene W, Rutten GJM, Gehring K, Ong LL. P18.08.B Fully automatic meningioma segmentation using T1-weighted contrast-enhanced MR images only. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac174.335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Manual segmentation of brain tumors requires expertise, is time-consuming, and is subject to inter-rater variability. Fully automatic brain tumor segmentation is possible for glioma and meningioma when volumetric T1, T1 contrast-enhanced (T1c), T2, and Fluid-attenuated inversion recovery (FLAIR) MRIs are available. In clinical care of meningiomas, however, often only volumetric T1c scans are available. In this work, we trained a deep learning network to segment meningiomas using only T1c scans for use in clinical research.
Material and Methods
NnU-Net, a deep learning model that is optimized for medical image segmentation, was trained to segment meningiomas from T1c images. This was performed on a large clinically collected meningioma dataset (n=374) of T1c scans with semi-automatically generated enhancing tumor masks and additional data from the BraTS2020 glioma dataset. Model performance was compared against inter-rater reliability, between different models, between anatomical tumor locations, and against models using multiple MRI modalities.
Results
The best performing model obtained a Dice score of 0.90. This performance was 0.03 points lower when compared to inter-rater reliability (Dice=0.93) and almost equal to models using multiple MRI modalities. Model performance split over anatomical tumor locations was between 0.90 and 0.97 (Dice).
Conclusion
Fully automatic meningioma segmentation using only T1c images is possible with an accuracy that is similar to inter-rater reliability and models using multiple imaging modalities.
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Affiliation(s)
- S M Boelders
- Elisabeth-Tweesteden Hospital , Tilburg , Netherlands
- Tilburg University , Tilburg , Netherlands
| | - W De Baene
- Tilburg University , Tilburg , Netherlands
| | - G J M Rutten
- Elisabeth-Tweesteden Hospital , Tilburg , Netherlands
| | - K Gehring
- Elisabeth-Tweesteden Hospital , Tilburg , Netherlands
- Tilburg University , Tilburg , Netherlands
| | - L L Ong
- Tilburg University , Tilburg , Netherlands
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3
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Mathur D, Samanta A, Ancona MG, Díaz SA, Kim Y, Melinger JS, Goldman ER, Sadowski JP, Ong LL, Yin P, Medintz IL. Understanding Förster Resonance Energy Transfer in the Sheet Regime with DNA Brick-Based Dye Networks. ACS Nano 2021; 15:16452-16468. [PMID: 34609842 PMCID: PMC8823280 DOI: 10.1021/acsnano.1c05871] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Controlling excitonic energy transfer at the molecular level is a key requirement for transitioning nanophotonics research to viable devices with the main inspiration coming from biological light-harvesting antennas that collect and direct light energy with near-unity efficiency using Förster resonance energy transfer (FRET). Among putative FRET processes, point-to-plane FRET between donors and acceptors arrayed in two-dimensional sheets is predicted to be particularly efficient with a theoretical 1/r4 energy transfer distance (r) dependency versus the 1/r6 dependency seen for a single donor-acceptor interaction. However, quantitative validation has been confounded by a lack of robust experimental approaches that can rigidly place dyes in the required nanoscale arrangements. To create such assemblies, we utilize a DNA brick scaffold, referred to as a DNA block, which incorporates up to five two-dimensional planes with each displaying from 1 to 12 copies of five different donor, acceptor, or intermediary relay dyes. Nanostructure characterization along with steady-state and time-resolved spectroscopic data were combined with molecular dynamics modeling and detailed numerical simulations to compare the energy transfer efficiencies observed in the experimental DNA block assemblies to theoretical expectations. Overall, we demonstrate clear signatures of sheet regime FRET, and from this we provide a better understanding of what is needed to realize the benefits of such energy transfer in artificial dye networks along with FRET-based sensing and imaging.
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Affiliation(s)
| | | | | | - Sebastián A. Díaz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Youngchan Kim
- Center for Materials Physics and Technology Code 6390, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Joseph S. Melinger
- Electronic Science and Technology Division Code 6800, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Ellen R. Goldman
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - John Paul Sadowski
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States; American Society for Engineering Education, Washington, D.C. 20001, United States
| | - Luvena L. Ong
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
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Ong LL, Vasta JD, Monereau L, Locke G, Ribeiro H, Pattoli MA, Skala S, Burke JR, Watterson SH, Tino JA, Meisenheimer PL, Arey B, Lippy J, Zhang L, Robers MB, Tebben A, Chaudhry C. A High-Throughput BRET Cellular Target Engagement Assay Links Biochemical to Cellular Activity for Bruton's Tyrosine Kinase. SLAS Discov 2019; 25:176-185. [PMID: 31709883 DOI: 10.1177/2472555219884881] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein kinases are intensely studied mediators of cellular signaling. While traditional biochemical screens are capable of identifying compounds that modulate kinase activity, these assays are limited in their capability of predicting compound behavior in a cellular environment. Here, we aim to bridge target engagement and compound-cellular phenotypic behavior by utilizing a bioluminescence resonance energy transfer (BRET) assay to characterize target occupancy within living cells for Bruton's tyrosine kinase (BTK). Using a diverse chemical set of BTK inhibitors, we determine intracellular engagement affinity profiles and successfully correlate these measurements with BTK cellular functional readouts. In addition, we leveraged the kinetic capability of this technology to gain insight into in-cell target residence time and the duration of target engagement, and to explore a structural hypothesis.
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Affiliation(s)
- L L Ong
- Leads Discovery and Optimization, Bristol Myers Squibb, Princeton, NJ, USA
| | - J D Vasta
- Promega Corporation, Madison, WI, USA
| | - L Monereau
- Leads Discovery and Optimization, Bristol Myers Squibb, Princeton, NJ, USA
| | - G Locke
- Leads Discovery and Optimization, Bristol Myers Squibb, Princeton, NJ, USA
| | - H Ribeiro
- Leads Discovery and Optimization, Bristol Myers Squibb, Princeton, NJ, USA
| | - M A Pattoli
- Immunoscience Discovery Biology, Bristol Myers Squibb, Princeton, NJ, USA
| | - S Skala
- Immunoscience Discovery Biology, Bristol Myers Squibb, Princeton, NJ, USA
| | - J R Burke
- Immunoscience Discovery Biology, Bristol Myers Squibb, Princeton, NJ, USA
| | - S H Watterson
- Immunosciences Discovery Chemistry, Bristol Myers Squibb, Princeton, NJ, USA
| | - J A Tino
- Immunosciences Discovery Chemistry, Bristol Myers Squibb, Princeton, NJ, USA
| | | | - B Arey
- Leads Discovery and Optimization, Bristol Myers Squibb, Princeton, NJ, USA
| | - J Lippy
- Leads Discovery and Optimization, Bristol Myers Squibb, Princeton, NJ, USA
| | - L Zhang
- Leads Discovery and Optimization, Bristol Myers Squibb, Princeton, NJ, USA
| | | | - A Tebben
- Molecular Structure and Design, Molecular Discovery Technologies, Bristol Myers Squibb, Princeton, NJ, USA
| | - C Chaudhry
- Leads Discovery and Optimization, Bristol Myers Squibb, Princeton, NJ, USA
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5
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Lin T, Yan J, Ong LL, Robaszewski J, Lu HD, Mi Y, Yin P, Wei B. Hierarchical Assembly of DNA Nanostructures Based on Four-Way Toehold-Mediated Strand Displacement. Nano Lett 2018; 18:4791-4795. [PMID: 29989824 DOI: 10.1021/acs.nanolett.8b01355] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Because of its attractive cost and yield, hierarchical assembly, in which constituent structures of lower hierarchy share a majority of components, is an appealing approach to scale up DNA self-assembly. A few strategies have already been investigated to combine preformed DNA nanostructures. In this study, we present a new hierarchical assembly method based on four-way toehold-mediated strand displacement to facilitate the combination of preformed DNA structural units. Employing such a method, we have constructed a series of higher-order structures composed of 5, 7, 9, 11, 13, and 15 preformed units respectively.
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Affiliation(s)
- Tong Lin
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology , Tsinghua University , Beijing 100084 , China
- Department of Chemical and Biological Engineering , The Hong Kong University of Science and Technology , Kowloon , Hong Kong SAR
| | - Jun Yan
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology , Tsinghua University , Beijing 100084 , China
| | - Luvena L Ong
- Wyss Institute for Biologically Inspired Engineering , Harvard University , Boston , Massachusetts 02115 , United States
- Harvard-Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology , MIT , Cambridge , Massachusetts 02139 , United States
| | - Joanna Robaszewski
- Wyss Institute for Biologically Inspired Engineering , Harvard University , Boston , Massachusetts 02115 , United States
| | - Hoang D Lu
- Wyss Institute for Biologically Inspired Engineering , Harvard University , Boston , Massachusetts 02115 , United States
| | - Yongli Mi
- Department of Chemical and Biological Engineering , The Hong Kong University of Science and Technology , Kowloon , Hong Kong SAR
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering , Harvard University , Boston , Massachusetts 02115 , United States
- Department of Systems Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Bryan Wei
- School of Life Sciences, Tsinghua University-Peking University Center for Life Sciences, Center for Synthetic and Systems Biology , Tsinghua University , Beijing 100084 , China
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6
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Woehrstein JB, Strauss MT, Ong LL, Wei B, Zhang DY, Jungmann R, Yin P. Sub-100-nm metafluorophores with digitally tunable optical properties self-assembled from DNA. Sci Adv 2017; 3:e1602128. [PMID: 28691083 PMCID: PMC5479647 DOI: 10.1126/sciadv.1602128] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 04/28/2017] [Indexed: 05/21/2023]
Abstract
Fluorescence microscopy allows specific target detection down to the level of single molecules and has become an enabling tool in biological research. To transduce the biological information to an imageable signal, we have developed a variety of fluorescent probes, such as organic dyes or fluorescent proteins with different colors. Despite their success, a limitation on constructing small fluorescent probes is the lack of a general framework to achieve precise and programmable control of critical optical properties, such as color and brightness. To address this challenge, we introduce metafluorophores, which are constructed as DNA nanostructure-based fluorescent probes with digitally tunable optical properties. Each metafluorophore is composed of multiple organic fluorophores, organized in a spatially controlled fashion in a compact sub-100-nm architecture using a DNA nanostructure scaffold. Using DNA origami with a size of 90 × 60 nm2, substantially smaller than the optical diffraction limit, we constructed small fluorescent probes with digitally tunable brightness, color, and photostability and demonstrated a palette of 124 virtual colors. Using these probes as fluorescent barcodes, we implemented an assay for multiplexed quantification of nucleic acids. Additionally, we demonstrated the triggered in situ self-assembly of fluorescent DNA nanostructures with prescribed brightness upon initial hybridization to a nucleic acid target.
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Affiliation(s)
- Johannes B. Woehrstein
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Physics and Center for NanoScience, Ludwig Maximilian University, 80539 Munich, Germany
- Max Planck Institute of Biochemistry, 82152 Martinsried near Munich, Germany
| | - Maximilian T. Strauss
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Physics and Center for NanoScience, Ludwig Maximilian University, 80539 Munich, Germany
- Max Planck Institute of Biochemistry, 82152 Martinsried near Munich, Germany
| | - Luvena L. Ong
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Bryan Wei
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - David Y. Zhang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Ralf Jungmann
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Physics and Center for NanoScience, Ludwig Maximilian University, 80539 Munich, Germany
- Max Planck Institute of Biochemistry, 82152 Martinsried near Munich, Germany
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Corresponding author. (P.Y.); (R.J.)
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
- Corresponding author. (P.Y.); (R.J.)
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7
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Myhrvold C, Baym M, Hanikel N, Ong LL, Gootenberg JS, Yin P. Barcode extension for analysis and reconstruction of structures. Nat Commun 2017; 8:14698. [PMID: 28287117 PMCID: PMC5355802 DOI: 10.1038/ncomms14698] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 01/24/2017] [Indexed: 12/17/2022] Open
Abstract
Collections of DNA sequences can be rationally designed to self-assemble into predictable three-dimensional structures. The geometric and functional diversity of DNA nanostructures created to date has been enhanced by improvements in DNA synthesis and computational design. However, existing methods for structure characterization typically image the final product or laboriously determine the presence of individual, labelled strands using gel electrophoresis. Here we introduce a new method of structure characterization that uses barcode extension and next-generation DNA sequencing to quantitatively measure the incorporation of every strand into a DNA nanostructure. By quantifying the relative abundances of distinct DNA species in product and monomer bands, we can study the influence of geometry and sequence on assembly. We have tested our method using 2D and 3D DNA brick and DNA origami structures. Our method is general and should be extensible to a wide variety of DNA nanostructures. Techniques for structural characterization and quantification of DNA origami are still poorly developed, despite advances in other aspects of DNA nanotechnology. Here, the authors combine barcoding and next generation sequencing to simultaneously image and quantify self-assembled DNA nanostructures.
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Affiliation(s)
- Cameron Myhrvold
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Michael Baym
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nikita Hanikel
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
| | - Luvena L Ong
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
| | - Jonathan S Gootenberg
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
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8
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Abstract
DNA nanostructures are a useful technology for precisely organizing and manipulating nanomaterials. The DNA bricks method is a modular and versatile platform for applications requiring discrete or periodic structures with complex three-dimensional features. Here, we describe how structures are designed from the fundamental strand architecture through assembly and characterization of the formed structures.
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Affiliation(s)
- Luvena L Ong
- Wyss Institute for Biologically Inspired Engineering, Harvard University, CLSB 5th Floor, Blackfan Circle, Boston, MA, 02115, USA.
- The Harvard-MIT Health Sciences and Technology Program, MIT, Cambridge, MA, 02139, USA.
| | - Yonggang Ke
- The Wallace H. Coulter Department of Biomedical Engineering at Georgia Institute of Technology and Emory University, Atlanta, GA, 30322, USA
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9
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Scheible MB, Ong LL, Woehrstein JB, Jungmann R, Yin P, Simmel FC. A Compact DNA Cube with Side Length 10 nm. Small 2015; 11:5200-5. [PMID: 26294348 PMCID: PMC4707664 DOI: 10.1002/smll.201501370] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/09/2015] [Indexed: 05/09/2023]
Abstract
A small and compact DNA cube with zeptoliter volume is constructed by means of a generalized DNA brick concept using short synthetic oligonucleotides with varying lengths. By mimicking design principles from the DNA origami technique, the DNA cube offers higher stability and assembly yields compared to other approaches. Its potential application as nanoscale fluorescent probe is demonstrated using super-resolution imaging.
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Affiliation(s)
- Max B. Scheible
- Physics Department and ZNN/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
- Nanosystems Initiative Munich, Schellingstr. 4, 80799 München, Germany
| | - Luvena L. Ong
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Cir, Boston, MA 02115, USA
| | - Johannes B. Woehrstein
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Cir, Boston, MA 02115, USA
- Max Planck Institute of Biochemistry and LMU, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry and LMU, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Cir, Boston, MA 02115, USA
| | - Friedrich C. Simmel
- Physics Department and ZNN/WSI, Technische Universität München, Am Coulombwall 4a, 85748 Garching, Germany
- Nanosystems Initiative Munich, Schellingstr. 4, 80799 München, Germany
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10
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11
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Abstract
Nucleic acids have been used to create diverse synthetic structural and dynamic systems. Toehold-mediated strand displacement has enabled the construction of sophisticated circuits, motors, and molecular computers. Yet it remains challenging to demonstrate complex structural reconfiguration in which a structure changes from a starting shape to another arbitrarily prescribed shape. To address this challenge, we have developed a general structural-reconfiguration method that utilizes the modularly interconnected architecture of single-stranded DNA tile and brick structures. The removal of one component strand reveals a newly exposed toehold on a neighboring strand, thus enabling us to remove regions of connected component strands without the need to modify the strands with predesigned external toeholds. By using this method, we reconfigured a two-dimensional rectangular DNA canvas into diverse prescribed shapes. We also used this method to reconfigure a three-dimensional DNA cuboid.
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Affiliation(s)
- Bryan Wei
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115 (USA) http://molecular-systems.net http://yin.hms.harvard.edu; Department of Systems Biology, Harvard Medical School, Boston, MA 02115 (USA).
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12
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Abstract
We describe a simple and robust method to construct complex three-dimensional (3D) structures by using short synthetic DNA strands that we call "DNA bricks." In one-step annealing reactions, bricks with hundreds of distinct sequences self-assemble into prescribed 3D shapes. Each 32-nucleotide brick is a modular component; it binds to four local neighbors and can be removed or added independently. Each 8-base pair interaction between bricks defines a voxel with dimensions of 2.5 by 2.5 by 2.7 nanometers, and a master brick collection defines a "molecular canvas" with dimensions of 10 by 10 by 10 voxels. By selecting subsets of bricks from this canvas, we constructed a panel of 102 distinct shapes exhibiting sophisticated surface features, as well as intricate interior cavities and tunnels.
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Affiliation(s)
- Yonggang Ke
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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13
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Park JH, von Maltzahn G, Ong LL, Centrone A, Hatton TA, Ruoslahti E, Bhatia SN, Sailor MJ. Cooperative nanoparticles for tumor detection and photothermally triggered drug delivery. Adv Mater 2010; 22:880-5. [PMID: 20217810 PMCID: PMC3057607 DOI: 10.1002/adma.200902895] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Affiliation(s)
- Ji-Ho Park
- Materials Science and Engineering Program, Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman, La Jolla, CA 92093 (USA)
| | - Geoffrey von Maltzahn
- Howard Hughes Medical Institute and Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 (USA)
| | - Luvena L. Ong
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 (USA)
| | - Andrea Centrone
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 (USA)
| | - T. Alan Hatton
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 (USA)
| | - Erkki Ruoslahti
- Burnham Institute for Medical Research at UCSB, University of California, Santa Barbara, 1105 Life Sciences Technology Bldg, Santa Barbara, CA 93106 (USA)
| | - Sangeeta N. Bhatia
- Howard Hughes Medical Institute and Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 (USA)
| | - Michael J. Sailor
- Materials Science and Engineering Program, Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman, La Jolla, CA 92093 (USA)
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14
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Klopsch C, Gäbel R, Furlani D, Ong LL, Li W, Piechaczek C, Liebold A, Stamm C, Ma N, Steinhoff G. Intramyocardium application of mesenchymal stem cells combined with erythropoetin improves left ventricle function in a rat myocardial infarction model. Thorac Cardiovasc Surg 2007. [DOI: 10.1055/s-2007-967442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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15
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Li W, Gäbel R, Furlani D, Klopsch C, Piechaczek C, Kaminski A, Ong LL, Liebold A, Stamm C, Ma N, Steinhoff G. High-mobility group protein box 1 (HMGB1) gene delivery induces angiogenesis in rat myocardial infarction model. Thorac Cardiovasc Surg 2007. [DOI: 10.1055/s-2007-967552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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16
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Ma N, Ladilov Y, Moebius J, Choi YH, David A, Kaminski A, Li W, Ong LL, Stamm C, Skrabal C, Piechaczek C, Liebold A, Steinhoff G. A comparison study of AC133+ cell transplantation of myocardial infarction model. Thorac Cardiovasc Surg 2006. [DOI: 10.1055/s-2006-925667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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17
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Ma N, Li W, Nesselmann C, Ong LL, Tang G, Öri F, Lorenz P, Kaminski A, Stamm C, Choi YH, Skrabal C, Liebold A, Steinhoff G. Novel gene carrier enhances therapeutic gene VEGF165 expression in myocardial infarction model. Thorac Cardiovasc Surg 2006. [DOI: 10.1055/s-2006-925755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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18
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Ma N, Li W, Ong LL, Nesselmann C, Pützer B, Choi YH, Kaminski A, Skrabal C, Liebold A, Stamm C, Steinhoff G. Anti-apoptotic Bcl-2 gene modified rat MSCs improves heart function after myocardial infarction. Thorac Cardiovasc Surg 2006. [DOI: 10.1055/s-2006-925640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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19
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Abstract
Intracellular organelle motility involves motor proteins that move along microtubules or actin filaments. One of these motor proteins, kinesin, was proposed to bind to kinectin on membrane organelles during movement. Whether kinectin is the kinesin receptor on organelles with a role in organelle motility has been controversial. We have characterized the sites of interaction between human kinectin and conventional kinesin using in vivo and in vitro assays. The kinectin-binding domain on the kinesin tail partially overlaps its head-binding domain and the myosin-Va binding domain. The kinesin-binding domain on kinectin resides near the COOH terminus and enhances the microtubule-stimulated kinesin-ATPase activity, and the overexpression of the kinectin-kinesin binding domains inhibited kinesin-dependent organelle motility in vivo. These data, when combined with other studies, suggest a role for kinectin in organelle motility.
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Affiliation(s)
- L L Ong
- National University Medical Institutes, Faculty of Medicine, National University of Singapore, Singapore 117597
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Abstract
The myocardial wall of the vertebrate heart changes from a simple epithelium to a trabeculated structure during embryogenesis. This process occurs when epithelioid cardiomyocytes migrate toward the endocardium, which we show is coincident with up-regulation of the cell adhesion molecule, N-cadherin. To study the role of N-cadherin expressed at the trabeculation stage, a replication-defective retrovirus expressing a dominant negative mutant of N-cadherin (delta N-cadherin) was engineered. Control viruses were designed to express beta-galactosidase or a full-length N-cadherin. Viruses were introduced into epithelioid presumptive myocytes at the time they initiate the epithelial-mesenchymal transformation. Individual cells infected with control viruses generated daughter myocytes which migrated toward endocardium as a tight cluster, thereby generating a clone that forms a single or at most two trabeculae. In contrast, myocytes expressing delta N-cadherin were sparsely distributed within the myocardium and failed to form the ridge-shaped clone. Thus, in addition to its known roles in myocyte epithelialization and intercalated disc formation, N-cadherin appears to play a role in homotypic interactions between nonepithelial migratory myocytes during trabecular formation of the embryonic heart.
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Affiliation(s)
- L L Ong
- Department of Cell Biology and Anatomy, Cornell University Medical College, New York, New York 10021, USA
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21
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Rodrigo MR, Ong LL, Waheed AA. Dorsal nerve block of penis in Chinese children. Br J Anaesth 1984; 56:934-5. [PMID: 6743463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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22
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Ong LL, Schardein JL, Petrere JA, Sakowski R, Jordan H, Humphrey RR, Fitzgerald JE, de la Iglesia FA. Teratogenesis of calcium valproate in rats. Fundam Appl Toxicol 1983; 3:121-6. [PMID: 6409702 DOI: 10.1016/s0272-0590(83)80067-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Studies were conducted to determine the teratogenic potential of the calcium salt of valproic acid in rats when given orally at doses of 600, 150, and 50 mg/kg on days 6--15 of gestation. The sodium salt of valproic acid was used as a reference agent at a dose level of 600 mg/kg. The administration of 600 mg/kg/day of either calcium or sodium valproate resulted in transient, severe sedation in the dams. Four dams receiving 600 mg/kg of either salt died during the experiment, with deaths occurring between day 7 and 11 of gestation. Food consumption and body weight gain were significantly reduced during the dosing period with both salts at dose levels of 600 mg/kg. Embryotoxicity at the high doses (600 mg/kg) with either salt was manifested by increases in fetal resorption, reduced body weights, and significantly increased incidence of supernumerary ribs and bifid vertebral centra among the surviving fetuses. A teratogenic effect was evident at 600 mg/kg with either salt of valproic acid. Seven of 16 fetuses from dams given the calcium salt were abnormal. Findings included one with omphalocele and six others with skeletal malformations. Eleven of 24 fetuses from dams given the sodium salt were abnormal: three littermates had bilateral ectrodactyly of the rear feet and malformed vertebral centra and eight others had skeletal malformations. No teratogenic effect was evident among the fetuses from dams given 150 mg/kg calcium salt. Embryotoxicity was demonstrated by a significant increase in the incidence of supernumerary ribs. No adverse effect was observed among the fetuses from dams given 50 mg/kg of the calcium salt.
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