Ion beam processing of DNA origami nanostructures

• Leo Sala,
• Agnes Zerolová,
• Violaine Vizcaino,
• Alain Mery,
• Alicja Domaracka,
• Hermann Rothard,
• Philippe Boduch,
• Dominik Pinkas and
• Jaroslav Kocišek

Beilstein J. Nanotechnol. 2024, 15, 207–214, doi:10.3762/bjnano.15.20

• , ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, Boulevard Henri Becquerel, BP 5133, 14070, Caen cedex 5, France Electron Microscopy Center, Institute of Molecular Genetics of the CAS, Vídenská 1083, 142 20, Prague, Czech Republic 10.3762/bjnano.15.20 Abstract DNA origami nanostructures are emerging as a bottom-up

• nanopatterning approach. Direct combination of this approach with top-down nanotechnology, such as ion beams, has not been considered because of the soft nature of the DNA material. Here we demonstrate that the shape of 2D DNA origami nanostructures deposited on Si substrates is well preserved upon irradiation

• by ion beams, modeling ion implantation, lithography, and sputtering conditions. Structural changes in 2D DNA origami nanostructures deposited on Si are analyzed using AFM imaging. The observed effects on DNA origami include structure height decrease or increase upon fast heavy ion irradiation in

Molecular architectonics of DNA for functional nanoarchitectures

• Debasis Ghosh,
• Lakshmi P. Datta and
• Thimmaiah Govindaraju

Beilstein J. Nanotechnol. 2020, 11, 124–140, doi:10.3762/bjnano.11.11

• the judicious exploitation of conventional and nonconventional base pairing interactions [12][13]. The field of DNA nanotechnology was further advanced by the DNA origami concept introduced by Rothemund and co-workers [14][15]. Intertwining and congregation of more than one DNA strand to produce DNA

• tiles or bricks, which staple in a programmed fashion to form crystalline assembly structures with well-defined geometries, constitute the guiding principles of specific nucleobase pairing-driven DNA nanostructures (DNA nanotechnology) [16][17]. In other words, DNA origami involves the programmed

• enabled the construction of complex architectonics through DNA origami [37]. The self-recognition characteristics of DNA allows the development of a wide array of DNA-based nanoarchitectures by employing an array of designer sequences and motifs. In the earliest designs, the Holliday junction structure of

Materials nanoarchitectonics at two-dimensional liquid interfaces

• Katsuhiko Ariga,
• Michio Matsumoto,
• Taizo Mori and
• Lok Kumar Shrestha

Beilstein J. Nanotechnol. 2019, 10, 1559–1587, doi:10.3762/bjnano.10.153

• , various materials such as molecular machines, molecular receptors, block-copolymer, DNA origami, nanocarbon, phages, and stem cells were assembled at liquid interfaces by using various useful techniques. This review overviews techniques such as conventional Langmuir–Blodgett method, vortex Langmuir

• materials for the fabrication of two-dimensionally structures. As depicted in Figure 8, Yonamine et al. successfully demonstrated the one-dimensional supramolecular polymerization of DNA origami pieces upon repeated mechanical compression and expansion of the two-dimensional air–water interface [219]. The

• used DNA origami pieces had a rectangle shape with 90 × 65 nm2, according to theoretical calculations, and were complexed with counter-cationic lipids to be soluble in organic solvents. The resulting organic solution of the DNA origami pieces was then spread on the air–water interface to form a

Dumbbell gold nanoparticle dimer antennas with advanced optical properties

• Janning F. Herrmann and
• Christiane Höppener

Beilstein J. Nanotechnol. 2018, 9, 2188–2197, doi:10.3762/bjnano.9.205

• , DNA origami-structures provide a high versatility of the formed structures, however, the gap sizes on the sub-nanometer scale are difficult to control. Recently, we succeeded in the formation of dumbbell dimer antennas by means of the electrostatic interaction of positively charged 40 nm AuNPs and

Review on nanoparticles and nanostructured materials: history, sources, toxicity and regulations

• Jaison Jeevanandam,
• Ahmed Barhoum,
• Yen S. Chan,
• Alain Dufresne and
• Michael K. Danquah

Beilstein J. Nanotechnol. 2018, 9, 1050–1074, doi:10.3762/bjnano.9.98

Mechanistic insights into plasmonic photocatalysts in utilizing visible light

• Kah Hon Leong,
• Azrina Abd Aziz,
• Lan Ching Sim,
• Pichiah Saravanan,
• Min Jang and
• Detlef Bahnemann

Beilstein J. Nanotechnol. 2018, 9, 628–648, doi:10.3762/bjnano.9.59

• capsids and DNA origami as biological scaffolds to increase fluorescence intensity by tuning the distance between capsid and Au NPs [155]. In recent years, the phytochemicals present in plant-based and waste materials have been used as reducing and stabilizing agents to prepare plasmonic metals (Au and Ag

Increasing the stability of DNA nanostructure templates by atomic layer deposition of Al₂O₃ and its application in imprinting lithography

• Hyojeong Kim,
• Kristin Arbutina,
• Anqin Xu and
• Haitao Liu

Beilstein J. Nanotechnol. 2017, 8, 2363–2375, doi:10.3762/bjnano.8.236

• ]. A wide range of DNA nanostructures, including DNA nanotubes, 1D λ-DNA, 2D DNA brick crystals with 3D features, hexagonal DNA 2D arrays, and DNA origami triangles, were tested for the pattern replication process to poly(methyl methacrylate) (PMMA), poly(L-lactic acid) (PLLA), and photo-cross-linked

• conformational coating on complex patterns, DNA origami triangle nanostructures were employed as the master templates for the pattern transfer to the PLLA stamp. The DNA origami triangle is a single layer of DNA double strands and has a theoretical height of 2 nm (Figure S7, Supporting Information File 1) [8

• strands. There are three holes at each of the vertex and one large triangular hole in the center of the DNA origami triangle. AFM images show that the three holes at the vertex, the central triangular hole, and the dangling loop were clearly visible before and after ALD, and after replication process with

Photobleaching of YOYO-1 in super-resolution single DNA fluorescence imaging

• Joseph R. Pyle and
• Jixin Chen

Beilstein J. Nanotechnol. 2017, 8, 2296–2306, doi:10.3762/bjnano.8.229

• proteins, a necessary process for gene regulation and expression [22], characterizing DNA origami [23][24], and imaging the unpacking of DNA [25]. Two main categories of super-resolution techniques were developed in the past two decades: (1) using hardware to beat the diffraction limit, using methods such

Dielectrophoresis of gold nanoparticles conjugated to DNA origami structures

• Anja Henning-Knechtel,
• Matthew Wiens,
• Mathias Lakatos,
• Andreas Heerwig,
• Frieder Ostermaier,
• Nora Haufe and
• Michael Mertig

Beilstein J. Nanotechnol. 2016, 7, 948–956, doi:10.3762/bjnano.7.87

• conventional top-down fabrication methods in nanotechnology. Their positioning onto specific locations of a microstructured substrate is an important task towards this aim. Here we study manipulation and positioning of pristine and of gold nanoparticle-conjugated tubular DNA origami structures using ac

• hybrid structures. Keywords: gold nanoparticles; dielectrophoresis; DNA nanotechnology; DNA origami; self-assembly; Introduction The DNA origami method facilitates high throughput synthesis of identical and fully addressable two- (2D) or three-dimensional (3D) nanoscaled structures [1][2][3]. Such DNA

• ) notches with the shape and dimension corresponding to the DNA origami structure [12][13], or (ii) gold islands to align DNA nanostructures between two conducting pads [14]. An alternative route is the alignment of the DNA origami structures within a microelectrode contact array through hydrodynamic flow

Length-extension resonator as a force sensor for high-resolution frequency-modulation atomic force microscopy in air

• Hannes Beyer,
• Tino Wagner and
• Andreas Stemmer

Beilstein J. Nanotechnol. 2016, 7, 432–438, doi:10.3762/bjnano.7.38

• in air or liquid have been reported so far, for example on mica [13][15], Si(111) [16], on a grating [17], HOPG, and DNA origami [18]. Froning et al. [18] also discussed the influence of the environmental conditions on the sensor properties. Temperature and humidity changes lead to variations in

DNA origami deposition on native and passivated molybdenum disulfide substrates

• Xiaoning Zhang,
• Masudur Rahman,
• David Neff and
• Michael L. Norton

Beilstein J. Nanotechnol. 2014, 5, 501–506, doi:10.3762/bjnano.5.58

• Xiaoning Zhang Masudur Rahman David Neff Michael L. Norton Department of Chemistry, Marshall University, One John Marshall Drive, Huntington, West Virginia 25755, United States 10.3762/bjnano.5.58 Abstract Maintaining the structural fidelity of DNA origami structures on substrates is a

• prerequisite for the successful fabrication of hybrid DNA origami/semiconductor-based biomedical sensor devices. Molybdenum disulfide (MoS2) is an ideal substrate for such future sensors due to its exceptional electrical, mechanical and structural properties. In this work, we performed the first investigations

• into the interaction of DNA origami with the MoS2 surface. In contrast to the structure-preserving interaction of DNA origami with mica, another atomically flat surface, it was observed that DNA origami structures rapidly lose their structural integrity upon interaction with MoS2. In a further series