Journal: Cancer Science

Article Title: DNA origami applications in cancer therapy

doi: 10.1111/cas.13290

Figure Lengend Snippet: DNA origami technique and nanostructures. (a) Principles of DNA origami technique. Hundreds of staples (red) fix the scaffold (gray) to create a desired shape. Reproduced from Sandersen (2010), with permission from [Nature Publishing Group]. (b) First examples of DNA origami nanostructures from Rothemund. Top panels are the designed shapes and bottom panels are atomic force microscope ( AFM ) images. Reproduced from Rothemund (2006), with permission from [Nature Publishing Group]. (c) Multilayered DNA origami nanostructures. Top panels, designed shapes; bottom panels, AFM images. Reproduced from Douglas et al . (2009), with permission from [Nature Publishing Group]. (d) Wireframe DNA origami nanostructures. Top panels, designed shapes; bottom panels, AFM images. Reproduced from Benson et al . (2015), with permission from [Nature Publishing Group]. (e) Movable DNA origami nanostructures. Reproduced from Marras et al . (2015), with permission from [US National Academy of Sciences].

Article Snippet: This work has inspired the idea of using DNA nanostructures as a nanocarrier in a drug delivery system.

Techniques: Microscopy

Journal: Cancer Science

Article Title: DNA origami applications in cancer therapy

doi: 10.1111/cas.13290

Figure Lengend Snippet: Functionalized DNA origami nanostructures. (a) Anti‐ Pf LDH aptamer‐modified DNA origami rectangles as a diagnostic tool for malaria. Reproduced from Godonoga et al . (2012), with permission from [Nature Publishing Group]. (b) DNA origami monoliths modified with cholesterols (yellow) and fluorescent molecules (green). Reproduced from Czogalla et al ., with permission from [John Wiley and Sons]. (c) Transferrin‐modified DNA origami rectangles for enhanced cellular internalization. Reproduced from Schaffert et al . (2016), with permission from [John Wiley and Sons]. (d) Silver nanoparticles (Ag NP ) (yellow) and gold nanoparticles (Au NP ) (red) precisely organized onto DNA origami triangles. Reproduced from Pal et al . (2010), with permission from [John Wiley and Sons]. (e) Azo‐benzene modified DNA origami nanocapsules which their conformational changes could be controlled by light. Reproduced from Takenaka et al . (2014), with permission from [John Wiley and Sons].

Article Snippet: This work has inspired the idea of using DNA nanostructures as a nanocarrier in a drug delivery system.

Techniques: Modification, Diagnostic Assay

Journal: Cancer Science

Article Title: DNA origami applications in cancer therapy

doi: 10.1111/cas.13290

Figure Lengend Snippet: DNA origami nanostructures as drug carriers. (a) DNA octahedron (blue) encapsulated inside lipid bilayer. Top panels, transmission electron microscopy images of free octahedrons; bottom panels, transmission electron microscopy images of lipid encapsulated octahedrons. Reproduced from Perrault and Shih (2014), with permission from [American Chemical Society]. DOPC , 1,2‐dioleoyl‐sn‐glycero‐3‐ phosphocholine; PEG ‐ PE , polyethylene glycol‐ phosphatidylethanolamine. (b) Fluorescently labeled DNA origami tubes for cellular tracking. Reproduced from Shen et al . (2012), with permission from [American Chemical Society]. (c) Virus capsid protein ( CP ; blue) covered DNA origami rectangles (orange). Reproduced from Mikkila et al . (2014), with permission from [Royal Society of Chemistry]. (d) Doxorubicin ( DOX )‐containing DNA origami triangles showing enhanced permeability and retention ( EPR ) effects. Reproduced from Zhang et al . (2014), with permission from [American Chemical Society].

Article Snippet: This work has inspired the idea of using DNA nanostructures as a nanocarrier in a drug delivery system.

Techniques: Transmission Assay, Electron Microscopy, Labeling, Virus, Permeability

Journal: Topics in Current Chemistry (Cham)

Article Title: DNA-Programmed Chemical Synthesis of Polymers and Inorganic Nanomaterials

doi: 10.1007/s41061-020-0292-x

Figure Lengend Snippet: Biopolymers interacting with DNA nanostructures. a Liposome membrane encapsulation of DNA nanostructures. Reproduced with permission from Ref. . Copyright 2014 American Chemical Society. b Positively charged cowpea chlorotic mottle virus capsid protein encapsulated square DNA origami. Reproduced with permission from Ref. . Copyright 2014 American Chemical Society. c Electrostatic adsorption between synthetic polymer and DNA nanostructure template. Reproduced with permission from Ref. . Copyright 2017 Nature Publishing Group. d Reversible assembly of synthetic and natural cationic polymers with DNA nanostructures. Reproduced with permission from Ref. Copyright 2018 Royal Society of Chemistry

Article Snippet: Inspired by these studies, Fan and Yan and their coworkers recently also presented a general method for creating biomimetic complex silica composite nanomaterials based on 1D, 2D, and 3D DNA nanostructures ranging in size from 10 to 1000 nm (Fig. b) [ ].

Techniques: Membrane, Encapsulation, Virus, Adsorption, Polymer

Journal: Topics in Current Chemistry (Cham)

Article Title: DNA-Programmed Chemical Synthesis of Polymers and Inorganic Nanomaterials

doi: 10.1007/s41061-020-0292-x

Figure Lengend Snippet: In situ synthesis of DNA nanostructure templated polymers. a Bottom-up fabrication of polymers on DNA origami template by in situ atom transfer radical polymerization (ATRP). Reproduced with permission from Ref. . Copyright 2016 Wiley-VCH. b Polymeric shell on DNA origami template for enhancing the stability of DNA materials. Reproduced with permission from Ref. . Copyright 2018 Royal Society of Chemistry. c Shape-controlled conductive polyaniline on DNA templates. Reproduced with permission from Ref. . Copyright 2014 American Chemical Society. d Shape-controlled nanofabrication of polydopamine on DNA templates Reproduced with permission from Ref. [ , ]. Copyright 2018 Wiley–VCH

Article Snippet: Inspired by these studies, Fan and Yan and their coworkers recently also presented a general method for creating biomimetic complex silica composite nanomaterials based on 1D, 2D, and 3D DNA nanostructures ranging in size from 10 to 1000 nm (Fig. b) [ ].

Techniques: In Situ

Journal: Topics in Current Chemistry (Cham)

Article Title: DNA-Programmed Chemical Synthesis of Polymers and Inorganic Nanomaterials

doi: 10.1007/s41061-020-0292-x

Figure Lengend Snippet: Morphology control of polymersomes on DNA nanostructures as scaffolds. a DNA origami mediated “frame guided assembly”. Reproduced with permission from Ref. [ , ]. Copyright 2017 and 2016 Wiley-VCH. b Formation of hydrophobic polymer nanoparticle in DNA templates. Reproduced with permission from Ref. . Copyright 2017 Nature Publishing Group

Article Snippet: Inspired by these studies, Fan and Yan and their coworkers recently also presented a general method for creating biomimetic complex silica composite nanomaterials based on 1D, 2D, and 3D DNA nanostructures ranging in size from 10 to 1000 nm (Fig. b) [ ].

Techniques: Control, Polymer

Journal: Topics in Current Chemistry (Cham)

Article Title: DNA-Programmed Chemical Synthesis of Polymers and Inorganic Nanomaterials

doi: 10.1007/s41061-020-0292-x

Figure Lengend Snippet: DNA-nanostructure-templated synthesis of single synthetic polymers. a Single polymer screening process based on DNA origami templates. Reproduced with permission from Ref. . Copyright 2015 Nature Publishing Group. b Programmed switching of single polymer conformation on DNA origami template. Reproduced with permission from Ref. . Copyright 2016 American Chemical Society. c Single polymer manipulation and energy transfer investigation of poly(F-DNA) conjugated polymer. Reproduced with permission from Ref. . Copyright 2016 Wiley-VCH

Article Snippet: Inspired by these studies, Fan and Yan and their coworkers recently also presented a general method for creating biomimetic complex silica composite nanomaterials based on 1D, 2D, and 3D DNA nanostructures ranging in size from 10 to 1000 nm (Fig. b) [ ].

Techniques: Polymer

Journal: Topics in Current Chemistry (Cham)

Article Title: DNA-Programmed Chemical Synthesis of Polymers and Inorganic Nanomaterials

doi: 10.1007/s41061-020-0292-x

Figure Lengend Snippet: DNA-nanostructure-templated casting growth of metal nanoparticles with controllable dimensionality. a Casting metal nanoparticles with predesigned 3D shapes based on DNA nanostructure templates. Reproduced with permission from Ref. . Copyright 2014 American Association for the Advancement of Science. b Complex silica composite nanomaterials templated by DNA origami. Reproduced with permission from Ref. . Copyright 2018 Nature Publishing Group

Article Snippet: Inspired by these studies, Fan and Yan and their coworkers recently also presented a general method for creating biomimetic complex silica composite nanomaterials based on 1D, 2D, and 3D DNA nanostructures ranging in size from 10 to 1000 nm (Fig. b) [ ].

Techniques:

Journal: Topics in Current Chemistry (Cham)

Article Title: DNA-Programmed Chemical Synthesis of Polymers and Inorganic Nanomaterials

doi: 10.1007/s41061-020-0292-x

Figure Lengend Snippet: DNA-nanostructure-templated arrangement of nanoparticles with chiral plasmonic properties. a Left- and right-handed arrangement and circular dichroism (CD) spectra of gold nanoparticles (AuNPs) on rod-like DNA origami template. Reproduced with permission from Ref. . Copyright 2012 Nature Publishing Group. b Anisotropic gold nanorod (AuNR) helical superstructures based on DNA origami sheets. Reproduced with permission from Ref. . Copyright 2015 American Chemical Society. c Plasmonic toroidal metamolecules assembled by a DNA origami template. Reproduced with permission from Ref. . Copyright 2016 American Chemical Society. d Light-responsive and e pH-responsive dynamic plasmonic switching between a relaxed state or left-/right- handed version based on two DNA origami bundles templates. Reproduced with permission from refs. and . Copyright 2016 American Chemical Society and 2015 Nature Publishing Group. f Two and g three AuNRs plasmonic walking on DNA origami template. Reproduced with permission from Refs. and . Copyright 2017 Wiley-VCH and 2018 American Chemical Society

Article Snippet: Inspired by these studies, Fan and Yan and their coworkers recently also presented a general method for creating biomimetic complex silica composite nanomaterials based on 1D, 2D, and 3D DNA nanostructures ranging in size from 10 to 1000 nm (Fig. b) [ ].

Techniques: Circular Dichroism

Journal: Science Advances

Article Title: Piggybacking functionalized DNA nanostructures into live-cell nuclei

doi: 10.1126/sciadv.adn9423

Figure Lengend Snippet: DO nanostructures functionalized with RNA Pol II–targeting antibodies and eight Cy5 fluorophores are electroporated into cells, bound to Pol II, and then are imported, or piggybacked, into the nucleus.

Article Snippet: DNA nanostructure designs are available at nanobase.org ( https://nanobase.org/structure/237 ).

Techniques:

Journal: Nucleic acids research

Article Title: CRISPR-Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells.

doi: 10.1093/nar/gkac049

Figure Lengend Snippet: Figure 2. Nuclear localization and genome integration of nanostructured DNA. (A) Schematic of experimental approach: 0.5 pmol of each template either was transfected with 500 ng Cas9 nuclease expression plasmid along with 150 ng of sgRNA expressing plasmid or electroporated with 57.2 nmol of Cas9 RNPs. Genomic integration was assessed via flow cytometry after 7 days. (B) (i) Flow cytometry data measuring mNeonGreen+ cells (GFP+) show that looped templates are more efficiently incorporated into the genome compared to unstructured and 18-helix nanostructures. (ii) Flow cytometry of electroporated cells shows similar values across unstructured, looped and 18-helix nanostructures. (C) Aggregated flow cytometry data show that looped templates perform best for both transfection and electroporation. Error bars represent standard deviations (SDs) from three experiments, **P < 0.01, one-way ANOVA. (D) PCR using primers flanking the insertion site confirms mNeonGreen insertion at the target site (right triangle). (E) AFM images of the 18-helix nanostructure before and after electroporation. Scale bar: 100 nm.

Article Snippet: Nanostructured DNA comprising a human gene enhances human primary cell HDR compared to unstructured dsDNA. (A) Schematic of knock-in strategy of a 3.5-kb HDR template encoding IL2RA–GFP fusion and mCherry driven by an EF1a promoter. (B) oxDNA simulations and AFM images of four distinct versions of 18-helix DNA nanostructured HDR templates, including 50% Staples, Only Top, Open and Complex.

Techniques: Transfection, Expressing, Plasmid Preparation, Flow Cytometry, Electroporation

Journal: Nucleic acids research

Article Title: CRISPR-Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells.

doi: 10.1093/nar/gkac049

Figure Lengend Snippet: Figure 4. Nanostructured DNA comprising a human gene enhances human primary cell HDR compared to unstructured dsDNA. (A) Schematic of knock-in strategy of a 3.5-kb HDR template encoding IL2RA–GFP fusion and mCherry driven by an EF1a promoter. (B) oxDNA simulations and AFM images of four distinct versions of 18-helix DNA nanostructured HDR templates, including 50% Staples, Only Top, Open and Complex. Scale bar: 100 nm. (C) Unstructured ssDNA and 18-helix nanostructure templates show increased knock-in efficiency compared to dsDNA. Error bars represent SDs from duplicate experiments. (D) Live cell count shows that unstructured ssDNA and 18-helix nanostructured templates display lower toxicity compared to dsDNA. Error bars represent SDs from duplicate experiments.

Article Snippet: Nanostructured DNA comprising a human gene enhances human primary cell HDR compared to unstructured dsDNA. (A) Schematic of knock-in strategy of a 3.5-kb HDR template encoding IL2RA–GFP fusion and mCherry driven by an EF1a promoter. (B) oxDNA simulations and AFM images of four distinct versions of 18-helix DNA nanostructured HDR templates, including 50% Staples, Only Top, Open and Complex.

Techniques: Knock-In, Cell Counting

Journal: Nucleic acids research

Article Title: CRISPR-Cas9-mediated nuclear transport and genomic integration of nanostructured genes in human primary cells.

doi: 10.1093/nar/gkac049

Figure Lengend Snippet: Figure 5. VLPs enable intracellular delivery of nanostructured DNA. (A) Schematic of experimental setup where successful incorporation of HDR tem- plates results in mNeonGreen+ cells. (B) Knock-in efficiencies of unstructured, looped and 18-helix nanostructures show comparable values for delivery using electroporation. Error bars represent SDs from duplicate experiments. (C) Cas9-VLP delivery shows that 18-helix nanostructured templates display a 2.5-fold higher knock-in efficiency compared to unstructured and looped templates. Error bars represent SDs from duplicate experiments, **P < 0.01, one-way ANOVA.

Article Snippet: Nanostructured DNA comprising a human gene enhances human primary cell HDR compared to unstructured dsDNA. (A) Schematic of knock-in strategy of a 3.5-kb HDR template encoding IL2RA–GFP fusion and mCherry driven by an EF1a promoter. (B) oxDNA simulations and AFM images of four distinct versions of 18-helix DNA nanostructured HDR templates, including 50% Staples, Only Top, Open and Complex.

Techniques: Knock-In, Electroporation