Article
Nanoscience & Nanotechnology
Xiaoxing Chen, Bin Jia, Zhangwei Lu, Libing Liao, Hanyang Yu, Zhe Li
Summary: The study introduced a strategy to produce customized scaffolds with integrated aptamer sequences for the direct construction of functional DNA origami structures. Results showed efficient and stable integration of various aptamers in the scaffolds, leading to increased binding efficiency and stronger resistance to degradation. This scalable method provides a new way to construct more stable and functionally robust DNA origami structures for broader applications.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Multidisciplinary Sciences
David Melancon, Benjamin Gorissen, Carlos J. Garcia-Mora, Chuck Hoberman, Katia Bertoldi
Summary: This passage discusses the design of large-scale structures with deployability, presenting two main strategies historically used and their limitations. Drawing inspiration from the Japanese art of paper folding, a novel design approach is proposed to construct large-scale inflatable systems that can lock in place after deployment.
Article
Chemistry, Multidisciplinary
Lei Yu, Jin Cheng, Dongfang Wang, Victor Pan, Shuai Chang, Jie Song, Yonggang Ke
Summary: Programmable DNA nanotechnology has been widely used in various applications, and minimizing mechanical stress is an important design rule for DNA nanostructures. This study compares the self-assembly of a canonical DNA gridiron with a new design that has a higher degree of mechanical stress. The interweaving DNA gridiron exhibits lower yield but promotes the formation of a two-dimensional crystalline lattice. Tuning the design of interweaving gridiron leads to changes in crystal size and regularity. The discovery of the new role of mechanical stress provides useful knowledge for future DNA nanostructure design.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Md. Sirajul Islam, Gerrit David Wilkens, Karol Wolski, Szczepan Zapotoczny, Jonathan Gardiner Heddle
Summary: The DNA origami technique allows for the design and production of three-dimensional shapes, and multi-functionality can be achieved by connecting different 3D building blocks with left-handed and right-handed forms. This enables the formation of regular arrays with alternating chirality.
NANOSCALE ADVANCES
(2021)
Article
Multidisciplinary Sciences
Muren Hu, Chang Feng, Qianqin Yuan, Chenbin Liu, Bujun Ge, Fenyong Sun, Xiaoli Zhu
Summary: mRNA delivery has shown great potential in the treatment of various diseases. Here, the authors develop a lantern-shaped flexible origami for the nanolization of single mRNA molecules and demonstrate efficient delivery of Smad4 mRNA, achieving the suppression of colorectal cancer tumor growth.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Kosti Tapio, Charlotte Kielar, Johannes M. Parikka, Adrian Keller, Heini Jarvinen, Karim Fahmy, J. Jussi Toppari
Summary: In recent years, DNA has been used as a promising material for fabricating hierarchical nanostructures due to its self-assembly properties and functionalization schemes. This study demonstrates the assembly of a two-dimensional fishnet-type lattice on a silicon substrate using cross-shaped DNA origami. The effects of environmental and structural factors on lattice assembly are investigated, and a methodology for producing closely-spaced DNA origami lattices on silicon substrate is developed.
CHEMISTRY OF MATERIALS
(2023)
Article
Chemistry, Analytical
Xiaotong Shen, Qingwen Ouyang, Hongwei Tan, Jin Ouyang, Na Na
Summary: Researchers designed stable single-stranded DNA (ssDNA) nanorobots by examining the dynamic folding of ssDNA in self-assemblies via molecular dynamics simulations. Two ssDNA strands were successfully assembled into nanorobots using two functional siRNAs, enabling multiple applications. The nanorobots were demonstrated to be stable, flexible, highly utilized, and low in folding errors. This study provides a computational pathway for constructing flexible and multifunctional ssDNA frameworks, expanding the biological application of nucleic acid nanostructures.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Yunxiang Lei, Zhichao Mei, Yuanfang Chen, Ning Deng, Yulin Li
Summary: This study presents a fast and convenient method for simultaneously purifying and concentrating DNA origami objects through ethanol precipitation. The method is simple and efficient, and is expected to be applicable to the scalable production of pure and dense DNA origami solutions.
Article
Nanoscience & Nanotechnology
Sonja Schmid, Pierre Stoemmer, Hendrik Dietz, Cees Dekker
Summary: The NEOtrap, formed by a DNA-origami sphere docked onto a passivated solid-state nanopore, allows the trapping and observation of single proteins for hours with high sensitivity and resolution. It can distinguish between nucleotide-dependent protein conformations and is a promising tool for studying the molecular kinetics underlying protein function.
NATURE NANOTECHNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Erik Benson, Rafael Carrascosa Marzo, Jonathan Bath, Andrew J. Turberfield
Summary: Linear actuators based on DNA origami are demonstrated in this paper, providing nanoscale precision through bottom-up assembly at the molecular scale. Two assembly strategies and two positioning strategies are used to control the position of the slider on the rail with high yield and precision. These components have potential applications in molecular machinery and nanoscale manufacture, including programmed chemical synthesis.
Review
Biochemical Research Methods
Noemi Bellassai, Roberta D'Agata, Giuseppe Spoto
Summary: Nucleic acid nanotechnology focuses on designing and developing synthetic nucleic acid strands to create nanosized functional systems. The structural properties and conformational polymorphism of nucleic acid sequences make nucleic acid nanostructures attractive in biosensing applications. Recent advances in biosensing have been derived from molecular beacon and DNA origami structures, each offering unique characteristics and potentials in the field.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Kristina Huebner, Himanshu Joshi, Aleksei Aksimentiev, Fernando D. Stefani, Philip Tinnefeld, Guillermo P. Acuna
Summary: The study introduces a new technique to determine the orientation of single fluorophores in DNA origami structures, providing insights into the relationship between the fluorophores, environment, and structure. Results indicate that the orientation of fluorophores is influenced more by the specific molecular environment than the type of fluorophore.
Article
Biochemistry & Molecular Biology
Emma Silvester, Benjamin Vollmer, Vojtech Prazak, Daven Vasishtan, Emily A. Machala, Catheryne Whittle, Susan Black, Jonathan Bath, Andrew J. Turberfield, Kay Gruenewald, Lindsay A. Baker
Summary: Electron cryotomography (cryoET) has revolutionized our understanding of biological function by revealing molecular details of membranes, viruses, and cells. A new tagging strategy using DNA origami allows for precise identification of individual protein complexes in tomograms without relying on metal clusters, making it suitable for a wide range of biological surfaces in cryoET studies.
Article
Nanoscience & Nanotechnology
Esra Oktay, Joshua Bush, Merlyn Vargas, Dylan Valerio Scarton, Bailey O'Shea, Amber Hartman, Christopher M. Green, Kayla Neyra, Carolina M. Gomes, Igor L. Medintz, Divita Mathur, Remi Veneziano
Summary: Functional DNA origami nanoparticles (DNA-NPs) are used as nanocarriers in biomedical applications. A simple and robust strategy based on asymmetric polymerase chain reaction (aPCR) allows direct synthesis of custom-length scaffolds that can be randomly or precisely modified.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Chemistry, Multidisciplinary
Yongkang Jiang, Yingtian Li, Ke Liu, Hongying Zhang, Xin Tong, Diansheng Chen, Lei Wang, Jamie Paik
Summary: This study presents an ultra-tunable bistable structure that offers a wide range of tunable energy barriers. Various functional robots, including an ultra-sensitive robotic flytrap and a fast catcher, were prototyped using these structures. This work expands the possibilities for bistable structure design and has significant implications for robotics, biomedical engineering, architecture, and kinetic art.
CELL REPORTS PHYSICAL SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
David Kutak, Erik Poppleton, Haichao Miao, Petr Sulc, Ivan Barisic
Summary: This paper proposes a Unified Nanotechnology Format (UNF) specifically designed for biomimetic nanotechnology field. UNF enables storage of both design and simulation data in a single file and aims to become a widely accepted and used file format, facilitating the work of researchers and software developers. The paper also provides a set of converters from existing file formats to UNF and showcases several use cases visualizing different types of data that UNF can handle.
Article
Biochemistry & Molecular Biology
David Kutak, Lucas Melo, Fabian Schroeder, Zoe Jelic-Matosevic, Natalie Mutter, Branimir Bertosa, Ivan Barisic
Summary: Significant advances have been made in the rational design of proteins, DNA, and other organic nanostructures in the last decade. The ability to engineer molecular structures precisely has resulted in a wide range of applications in fields such as biotechnology and medicine. However, the increasing complexity and size of artificial molecular systems require computational design support. This study presents Catana, a web-based modelling environment for proteins and DNA nanostructures, which allows users to create and modify recombinant fusion proteins, predict protein structures, and manipulate DNA origami structures.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Computer Science, Software Engineering
Mickael Sereno, Stephane Gosset, Lonni Besancon, Tobias Isenberg
Summary: This paper explores the use of tangible touch tablets combined with Augmented Reality Head-Mounted Displays (AR-HMDs) for spatial 3D selections. The study shows that tablets can be used as tangible objects in the AR space, but their touch displays are separate from the AR-HMD, raising research questions.
COMPUTER GRAPHICS FORUM
(2022)
Article
Computer Science, Cybernetics
Xiyao Wang, Lonni Besancon, Mehdi Ammi, Tobias Isenberg
Summary: This study focuses on the interaction needs for scientific data exploration and evaluates people's performance with different combinations of input devices and output displays. The results suggest that the mouse remains a good choice, especially for tasks that require high accuracy, and can be complemented with other 3D interaction devices.
INTERNATIONAL JOURNAL OF HUMAN-COMPUTER STUDIES
(2022)
Editorial Material
Computer Science, Software Engineering
Tobias Isenberg, Stefan Bruckner
Summary: The article introduces a special session at EuroVis conference where authors of visualization-related articles can present their work to improve its visibility.
COMPUTERS & GRAPHICS-UK
(2022)
Article
Computer Science, Software Engineering
Sarkis Halladjian, David Kouril, Haichao Miao, M. Eduard Groeller, Ivan Viola, Tobias Isenberg
Summary: Multiscale Unfolding is an interactive technique for visually illustrating multiple hierarchical scales of DNA in a single view. It allows viewers to see the genome at different scales and demonstrates how one scale spatially folds into the next.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2022)
Article
Microbiology
Branka Bedenic, Vesna Bratic, Slobodan Mihaljevic, Anita Lukic, Karlo Vidovic, Kresimir Reiner, Silvia Schoeenthaler, Ivan Barisic, Gernot Zarfel, Andrea Grisold
Summary: A study conducted in a COVID-19 hospital in Zagreb during November to December 2020 found a high rate of COVID-19-associated pneumonia with bacterial superinfections, primarily caused by multidrug-resistant (MDR) pathogens. Among the 118 patients hospitalized in the intensive care unit (ICU), 39% developed serious bacterial infections, resulting in a mortality rate of 70%. The predominant bacterium was carbapenem-resistant (CRAB) Acinetobacter baumannii. This highlights the importance of local epidemiology in determining causative agents and the need for infection prevention measures in overcrowded ICUs.
Article
Computer Science, Software Engineering
David Kutak, Pere-Pau Vazquez, Tobias Isenberg, Michael Krone, Marc Baaden, Jan Byska, Barbora Kozlikova, Haichao Miao
Summary: Visualization is crucial in molecular and structural biology, and has been successfully applied in various tasks. Challenges in this area can be overcome with advanced visualization techniques, but some are limited by the hardware devices used. Researchers are exploring the potential of immersive virtual environments to enhance molecular visualization. This review comprehensively covers the applications of molecular visualization in immersive virtual environments, categorizes existing research, and discusses potential future directions.
COMPUTER GRAPHICS FORUM
(2023)
Article
Computer Science, Software Engineering
Mathis Brossier, Robin Skanberg, Lonni Besancon, Mathieu Linares, Tobias Isenberg, Anders Ynnerman, Alexander Bock
Summary: Moliverse is a software that integrates the molecular visualization framework VIAMD into the astronomical visualization software OpenSpace, allowing the display of gas composition in planetary atmospheres and molecular structures in comet trails at an astronomical scale. It can be used for educational exhibitions and science presentations.
COMPUTERS & GRAPHICS-UK
(2023)
Article
Computer Science, Software Engineering
David Kouril, Ondrej Strnad, Peter Mindek, Sarkis Halladjian, Tobias Isenberg, M. Eduard Groller, Ivan Viola
Summary: We propose a method to generate documentary-style content using real-time scientific visualization, specifically in the field of molecular biology. Our approach, called molecumentaries, combines adaptable methods with scientific visualization to create engaging visual presentations enriched with verbal explanations. By integrating scientific knowledge and storytelling techniques, we provide insights and guide the audience through a narrative that showcases molecular structures.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2023)
Article
Computer Science, Software Engineering
Ruwayda Alharbi, Ondrej Strnad, Laura R. Luidolt, Manuela Waldner, David Kouril, Ciril Bohak, Tobias Klein, Eduard Groeller, Ivan Viola
Summary: This article proposes a new visibility and guidance approach called Nanotilus for exploring crowded three-dimensional structures. Unlike traditional methods, Nanotilus provides an inside-out experience, preserving immersion in virtual reality. The approach combines scene sparsification and camera path planning, and includes additional features such as animation control, textual annotation, and text-to-visualization conversion to enhance the guided tour experience.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2023)
Article
Computer Science, Software Engineering
Ziga Lesar, Ruwayda Alharbi, Ciril Bohak, Ondrej Strnad, Christoph Heinzl, Matija Marolt, Ivan Viola
Summary: This system allows users to form groups of objects and control the visibility of each group on a per-instance basis, effectively exploring crowded volumetric data.
Article
Computer Science, Software Engineering
Ngan Nguyen, Ciril Bohak, Dominik Engel, Peter Mindek, Ondrej Strnad, Peter Wonka, Sai Li, Timo Ropinski, Ivan Viola
Summary: Cryo-electron tomography (cryo-ET) is a new 3D imaging technique that has the potential to resolve submicron structural details. To enhance the visualization of noisy volumes, we propose leveraging soft segmentation as an explicit component. Our approach combines the strengths of weak and deep-learning-based segmentation algorithms. The proposed visualization method utilizes deep-learning-based segmentation for segmentation-aware transfer function design.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2023)
Article
Microbiology
Valentino D'Onofrio, Reinoud Cartuyvels, Peter E. A. Messiaen, Ivan Barisic, Inge C. Gyssens
Summary: This study investigated the correlation between virulence factors of clinical E. coli isolates and sepsis outcome in a large cohort. The results showed that microcins, toxins, and fimbriae were associated with disease severity, while adhesins and iron uptake proteins seemed to be protective. In addition, two genes were associated with worse clinical outcomes.