Spatiotemporal Control over Polynucleotide Brush Growth on DNA Origami Nanostructures

Yang, Yunqi; Lu, Qinyi; Chen, Yu; DeLuca, Marcello; Arya, Gaurav; Ke, Yonggang; Zauscher, Stefan

doi:10.1002/anie.202311727

Title: Spatiotemporal Control over Polynucleotide Brush Growth on DNA Origami Nanostructures

Journal Article · Wed Oct 25 00:00:00 EDT 2023 · Angewandte Chemie (International Edition)

DOI:https://doi.org/10.1002/anie.202311727· OSTI ID:2217562

Yang, Yunqi ^[1]; Lu, Qinyi ^[2]; Chen, Yu ^[3]; DeLuca, Marcello ^[4]; Arya, Gaurav ^[1]; Ke, Yonggang ^[5];

^[1]

Department of Mechanical Engineering and Materials Science Department of Biomedical Engineering Duke University Durham NC 27708 USA
Department of Chemistry Emory University Atlanta GA 30322 USA
University Program in Materials Science and Engineering Duke University Durham NC 27708 USA
Department of Mechanical Engineering and Materials Science Duke University Durham NC 27708 USA
Department of Biomedical Engineering Georgia Institute of Technology and Emory University Atlanta GA 30322 USA

Abstract DNA nanotechnology provides an approach to create precise, tunable, and biocompatible nanostructures for biomedical applications. However, the stability of these structures is severely compromised in biological milieu due to their fast degradation by nucleases. Recently, we showed how enzymatic polymerization could be harnessed to grow polynucleotide brushes of tunable length and location on the surface of DNA origami nanostructures, which greatly enhances their nuclease stability. Here, we report on strategies that allow for both spatial and temporal control over polymerization through activatable initiation, cleavage, and regeneration of polynucleotide brushes using restriction enzymes. The ability to site‐specifically decorate DNA origami nanostructures with polynucleotide brushes in a spatiotemporally controlled way provides access to “smart” functionalized DNA architectures with potential applications in drug delivery and supramolecular assembly.

View Accepted Manuscript (Publisher)

This content will become publicly available on Fri Oct 11 00:00:00 EDT 2024

Cite

Export

Save

Sponsoring Organization:: USDOE

OSTI ID:: 2217562

Journal Information:: Angewandte Chemie (International Edition), Journal Name: Angewandte Chemie (International Edition) Vol. 62 Journal Issue: 48; ISSN 1433-7851

Publisher:: Wiley Blackwell (John Wiley & Sons)Copyright Statement

Country of Publication:: Germany

Language:: English

References (27)

Systemic Delivery of Bc12‐Targeting siRNA by DNA Nanoparticles Suppresses Cancer Cell Growth Rahman, Mohammad Aminur; Wang, Pengfei; Zhao, Zhixiang Angewandte Chemie International Edition, Vol. 56, Issue 50 https://doi.org/10.1002/anie.201709485	journal	November 2017
Virus-Encapsulated DNA Origami Nanostructures for Cellular Delivery Mikkilä, Joona; Eskelinen, Antti-Pekka; Niemelä, Elina H. Nano Letters, Vol. 14, Issue 4 https://doi.org/10.1021/nl500677j	journal	March 2014
Polyhedra Self-Assembled from DNA Tripods and Characterized with 3D DNA-PAINT Iinuma, Ryosuke; Ke, Yonggang; Jungmann, Ralf Science, Vol. 344, Issue 6179 https://doi.org/10.1126/science.1250944	journal	March 2014
Enzymatic Fabrication of DNA Nanostructures: Extension of a Self-assembled Oligonucleotide Monolayer on Gold Arrays Chow, Dominic C.; Lee, Woo-Kyung; Zauscher, Stefan Journal of the American Chemical Society, Vol. 127, Issue 41 https://doi.org/10.1021/ja052491z	journal	October 2005
DNA origami protection and molecular interfacing through engineered sequence-defined peptoids Wang, Shih-Ting; Gray, Melissa A.; Xuan, Sunting Proceedings of the National Academy of Sciences, Vol. 117, Issue 12 https://doi.org/10.1073/pnas.1919749117	journal	March 2020
Introducing improved structural properties and salt dependence into a coarse-grained model of DNA Snodin, Benedict E. K.; Randisi, Ferdinando; Mosayebi, Majid The Journal of Chemical Physics, Vol. 142, Issue 23 https://doi.org/10.1063/1.4921957	journal	June 2015
Beyond the Fold: Emerging Biological Applications of DNA Origami Chandrasekaran, Arun Richard; Anderson, Nate; Kizer, Megan ChemBioChem, Vol. 17, Issue 12 https://doi.org/10.1002/cbic.201600038	journal	April 2016
Rapid prototyping of 3D DNA-origami shapes with caDNAno Douglas, Shawn M.; Marblestone, Adam H.; Teerapittayanon, Surat Nucleic Acids Research, Vol. 37, Issue 15 https://doi.org/10.1093/nar/gkp436	journal	June 2009
Scaling Behavior of Nanopatterned Polymer Brushes Lee, Woo-Kyung; Patra, Michael; Linse, Per Small, Vol. 3, Issue 1 https://doi.org/10.1002/smll.200600414	journal	January 2007
TacoxDNA: A user‐friendly web server for simulations of complex DNA structures, from single strands to origami Suma, Antonio; Poppleton, Erik; Matthies, Michael Journal of Computational Chemistry, Vol. 40, Issue 29 https://doi.org/10.1002/jcc.26029	journal	July 2019
Programmable Site‐Specific Functionalization of DNA Origami with Polynucleotide Brushes Yang, Yunqi; Lu, Qinyi; Huang, Chao‐Min Angewandte Chemie International Edition, Vol. 60, Issue 43 https://doi.org/10.1002/anie.202107829	journal	August 2021
Rücktitelbild: Fluorophores for Excited‐State Intramolecular Proton Transfer by an Yttrium Triflate Catalyzed Reaction of Isocyanides with Thiocarboxylic Acids (Angew. Chem. 23/2017) Tong, Shuo; Zhao, Shun; He, Qing Angewandte Chemie, Vol. 129, Issue 23 https://doi.org/10.1002/ange.201703995	journal	May 2017
Visualization of the Cellular Uptake and Trafficking of DNA Origami Nanostructures in Cancer Cells Wang, Pengfei; Rahman, Mohammad Aminur; Zhao, Zhixiang Journal of the American Chemical Society, Vol. 140, Issue 7 https://doi.org/10.1021/jacs.7b09024	journal	February 2018
Photocontrolled Dopamine Polymerization on DNA Origami with Nanometer Resolution Winterwerber, Pia; Harvey, Sean; Ng, David Y. W. Angewandte Chemie International Edition, Vol. 59, Issue 15 https://doi.org/10.1002/anie.201911249	journal	December 2019
Rationally Designed DNA‐Origami Nanomaterials for Drug Delivery In Vivo Jiang, Qiao; Liu, Shaoli; Liu, Jianbing Advanced Materials, Vol. 31, Issue 45 https://doi.org/10.1002/adma.201804785	journal	October 2018
Sequence-dependent thermodynamics of a coarse-grained DNA model Šulc, Petr; Romano, Flavio; Ouldridge, Thomas E. The Journal of Chemical Physics, Vol. 137, Issue 13 https://doi.org/10.1063/1.4754132	journal	October 2012
Oligolysine-based coating protects DNA nanostructures from low-salt denaturation and nuclease degradation Ponnuswamy, Nandhini; Bastings, Maartje M. C.; Nathwani, Bhavik Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/ncomms15654	journal	May 2017
Monitoring patterned enzymatic polymerization on DNA origami at single-molecule level Okholm, A. H.; Aslan, H.; Besenbacher, F. Nanoscale, Vol. 7, Issue 25 https://doi.org/10.1039/C5NR01945A	journal	January 2015
Block Copolymer Micellization as a Protection Strategy for DNA Origami Agarwal, Nayan P.; Matthies, Michael; Gür, Fatih N. Angewandte Chemie International Edition, Vol. 56, Issue 20 https://doi.org/10.1002/anie.201608873	journal	March 2017
UCSF ChimeraX : Structure visualization for researchers, educators, and developers Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C. Protein Science, Vol. 30, Issue 1 https://doi.org/10.1002/pro.3943	journal	October 2020
Virus-Inspired Membrane Encapsulation of DNA Nanostructures To Achieve In Vivo Stability Perrault, Steven D.; Shih, William M. ACS Nano, Vol. 8, Issue 5 https://doi.org/10.1021/nn5011914	journal	April 2014
A primer to scaffolded DNA origami Castro, Carlos Ernesto; Kilchherr, Fabian; Kim, Do-Nyun Nature Methods, Vol. 8, Issue 3 https://doi.org/10.1038/nmeth.1570	journal	February 2011
Coarse-graining DNA for simulations of DNA nanotechnology Doye, Jonathan P. K.; Ouldridge, Thomas E.; Louis, Ard A. Physical Chemistry Chemical Physics, Vol. 15, Issue 47 https://doi.org/10.1039/c3cp53545b	journal	January 2013
Amplified On-Chip Fluorescence Detection of DNA Hybridization by Surface-Initiated Enzymatic Polymerization Tjong, Vinalia; Yu, Hua; Hucknall, Angus Analytical Chemistry, Vol. 83, Issue 13 https://doi.org/10.1021/ac200946t	journal	June 2011
Enzymatic Polymerization of High Molecular Weight DNA Amphiphiles That Self-Assemble into Star-Like Micelles Tang, Lei; Tjong, Vinalia; Li, Nan Advanced Materials, Vol. 26, Issue 19 https://doi.org/10.1002/adma.201306049	journal	February 2014
Three-Dimensional Structures Self-Assembled from DNA Bricks Ke, Y.; Ong, L. L.; Shih, W. M. Science, Vol. 338, Issue 6111 https://doi.org/10.1126/science.1227268	journal	November 2012
Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model Ouldridge, Thomas E.; Louis, Ard A.; Doye, Jonathan P. K. The Journal of Chemical Physics, Vol. 134, Issue 8 https://doi.org/10.1063/1.3552946	journal	February 2011

Similar Records

Spatiotemporal Control over Polynucleotide Brush Growth on DNA Origami Nanostructures

Journal Article · Wed Oct 25 00:00:00 EDT 2023 · Angewandte Chemie · OSTI ID:2217562

Yang, Yunqi; Lu, Qinyi; Chen, Yu; +4 more

Programmable Site‐Specific Functionalization of DNA Origami with Polynucleotide Brushes

Journal Article · Mon Aug 16 00:00:00 EDT 2021 · Angewandte Chemie · OSTI ID:2217562

Yang, Yunqi; Lu, Qinyi; Huang, Chao‐Min; +6 more

Programmable Site-Specific Functionalization of DNA Origami with Polynucleotide Brushes

Journal Article · Fri Jul 23 00:00:00 EDT 2021 · Angewandte Chemie (International Edition) · OSTI ID:2217562

Yang, Yunqi; Lu, Qinyi; Huang, Chao‐Min; +6 more

Title: Spatiotemporal Control over Polynucleotide Brush Growth on DNA Origami Nanostructures

Citation Formats

References (27)

Similar Records

Related Subjects