DNA Origami. Группа авторов
Чтение книги онлайн.
Читать онлайн книгу DNA Origami - Группа авторов страница 25
Название: DNA Origami
Автор: Группа авторов
Издательство: John Wiley & Sons Limited
Жанр: Отраслевые издания
isbn: 9781119682585
isbn:
100 100 Gerling, T., Wagenbauer, K.F., Neuner, A.M., and Dietz, H. (2015). Dynamic DNA devices and assemblies formed by shape‐complementary, non‐base pairing 3D components. Science 347: 1446–1452.
101 101 Kuzyk, A., Yang, Y., Duan, X. et al. (2016). A light‐driven three‐dimensional plasmonic nanosystem that translates molecular motion into reversible chiroptical function. Nature Communications 7: 10591.
102 102 Kuzyk, A., Schreiber, R., Zhang, H. et al. (2014). Reconfigurable 3D plasmonic metamolecules. Nature Materials 13: 862–866.
103 103 Langecker, M., Arnaut, V., Martin, T.G. et al. (2012). Synthetic lipid membrane channels formed by designed DNA nanostructures. Science 338: 932–936.
104 104 Yang, Y., Wang, J., Shigematsu, H. et al. (2016). Self‐assembly of size‐controlled liposomes on DNA nanotemplates. Nature Chemistry 8: 476–483.
105 105 Zhang, Z., Yang, Y., Pincet, F. et al. (2017). Placing and shaping liposomes with reconfigurable DNA nanocages. Nature Chemistry 9: 653–659.
106 106 Castro, C.E., Kilchherr, F., Kim, D.N. et al. (2011). A primer to scaffolded DNA origami. Nature Methods 8: 221–229.
107 107 Mei, Q., Wei, X., Su, F. et al. (2011). Stability of DNA origami nanoarrays in cell lysate. Nano Letters 11: 1477–1482.
108 108 Jiang, Q., Song, C., Nangreave, J. et al. (2012). DNA origami as a carrier for circumvention of drug resistance. Journal of the American Chemical Society 134: 13396–13403.
109 109 Zhao, Y.X., Shaw, A., Zeng, X. et al. (2012). DNA origami delivery system for cancer therapy with tunable release properties. ACS Nano 6: 8684–8691.
110 110 Perrault, S.D. and Shih, W.M. (2014). Virus‐inspired membrane encapsulation of DNA nanostructures to achieve in vivo stability. ACS Nano 8: 5132–5140.
111 111 Ponnuswamy, N., Bastings, M.M.C., Nathwani, B. et al. (2017). Oligolysine‐based coating protects DNA nanostructures from low‐salt denaturation and nuclease degradation. Nature Communications 8: 15654.
112 112 Zhang, Q., Jiang, Q., Li, N. et al. (2014). DNA origami as an in vivo drug delivery vehicle for cancer therapy. ACS Nano 8: 6633–6643.
113 113 Rahman, M.A., Wang, P., Zhao, Z. et al. (2017). Systemic delivery of Bc12‐targeting siRNA by DNA nanoparticles suppresses cancer cell growth. Angewandte Chemie 56: 16023–16027.
114 114 Takenaka, T., Endo, M., Suzuki, Y. et al. (2014). Photoresponsive DNA nanocapsule having an open/close system for capture and release of nanomaterials. Chemistry—A European Journal 20: 14951–14954.
115 115 Douglas, S.M., Bachelet, I., and Church, G.M. (2012). A logic‐gated nanorobot for targeted transport of molecular payloads. Science 335: 831–834.
116 116 Hu, Q., Li, H., Wang, L. et al. (2018). DNA nanotechnology‐enabled drug delivery systems. Chemical Reviews.
117 117 Li, S., Jiang, Q., Liu, S. et al. (2018). A DNA nanorobot functions as a cancer therapeutic in response to a molecular trigger in vivo. Nature Biotechnology 36: 258–264.
2 Wireframe DNA Origami and Its Application as Tools for Molecular Force Generation
Marco Lolaico and Björn Högberg
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
2.1 Introduction
In recent years, DNA origami has proved to be a valid and powerful technique for construction of structures on the nanoscale, ranging from small 2D sheets to large 3D structures [1–3]. The most common design paradigm is based on tightly packed helices and the use of the design software caDNAno [4]. Using this software, the target shape is “sculpted” from lattices (usually honeycomb or square) of densely packed helices, abstracted as cylinders [5, 6]. Twisted and curved structures have also been designed by introducing asymmetric insertions or deletions of base pairs in the helices [7, 8]. These structures have found application in a substantial number of fields: examples can be found in super‐resolution microscopy [9], biomedical research [10, 11], photonics [12, 13], and nanofabrication [14–16]. These applications have been helped by the presence of the GUI caDNAno and the existence of diverse computational framework to simulate the final design, such as the finite‐element‐based CanDo [17], the coarse‐grained simulation software oxDNA [18–20] or the more recent multi‐resolution simulation framework mrDNA [21].
Nonetheless, this DNA origami design has some limitations and drawbacks. The first limitation is the constraint to lattices of closely packed helices only, which makes it difficult (although not impossible) to create open, material‐efficient or porous nanoscale structures, especially for nonexperts. Another drawback is the low stability of these lattice‐based structures in low‐salt buffers: because of the repulsion between the helices, high concentrations of cations are required to keep the structures from unfolding. Although new methods have largely addressed this issue [22–24], the low stability can be a serious issue for the use of DNA origami in the biomedical field.
An alternative to these block‐like structures are polygonal wireframe designs, commonly used in 3D computer graphics design and modern architecture (where they are also called space frames). These structures are usually based on a mesh, i.e. a set of shape‐defining vertices, edges, and faces. In architecture, these designs are usually made rigid through tessellation, which provides a high strength‐to‐weight ratio. In addition, they are more space‐efficient, meaning that a bigger area can be covered with less material [25].
Because of these advantages, the attempts on constructing wireframe DNA origami have increased rapidly. Here, we review how the wireframe principles have been applied in DNA origami and subsequently introduce new in silico data showing how these kinds of structures can be valuable tools for molecular force generation.
Mechanobiology examines how biological systems respond to mechanical stresses [26–29]. Mechanical forces are ubiquitous in vivo, and it has been demonstrated how they regulate a wide variety of biological processes [26], such as changes in focal adhesion dynamics [30, 31], activation of mechanosensitive channel at the membrane [32], or nuclear localization of mechanosensitive transcriptional regulators [33]. DNA origami nanostructures have been used with success in different studies to measure the force produced or required by different biological processes [34–37]. In addition, DNA origami has also been used to guide the cellular behavior, interfacing with cellular receptors [11, 38]. We think that DNA origami nanostructures can be a valuable tool to study mechanobiology, and in the last section, we propose a DNA origami nanostructure design that could be used to apply mechanical force on cellular receptors.
2.2 Pre‐Origami Wireframe DNA Nanostructures
In this section, we will present some example of strategies adopted for the creation of polygonal DNA nanostructures. Although the examples in this section precedes what we today call DNA origami, we think it is important to show them both from a historical perspective and for the impact they had on subsequent DNA nanostructure design strategies.
The first example of successful experimental application of structural DNA nanotechnology was the construction СКАЧАТЬ