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
Multidisciplinary Sciences
Pierre Stoemmer, Henrik Kiefer, Enzo Kopperger, Maximilian N. Honemann, Massimo Kube, Friedrich C. Simmel, Roland R. Netz, Hendrik Dietz
Summary: The study successfully created an artificial macromolecular transport system where molecular pistons diffusively move through micrometer-long, hollow filaments, achieving high diffusivities and displacement ranges. Single-molecule fluorescence microscopy and Langevin simulations were used to analyze the motion of the pistons along the tubes, revealing details of the free energy surface that directs their movements. The system can also be influenced by electric fields to create a nanoscale electric rail system, showing great potential for future molecular transportation networks.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Victor Pan, Wen Wang, Ian Heaven, Tanxi Bai, Yongxin Cheng, Chunlai Chen, Yonggang Ke, Bryan Wei
Summary: The study presents a simple and robust method for multiplexed molecular probing using fluorescent DNA barcodes generated from hierarchically assembled DNA origami superstructures. Machine learning algorithm was successfully utilized for high precision processing and identification of barcodes. The increase in the number of combinations was achieved through various methods, showcasing the potential for applications in target nucleic acid sequence capture and simultaneous characterization of binding kinetics of multiple complementary nucleic acids.
Article
Chemistry, Multidisciplinary
Stefan Krause, Evelyn Ploetz, Johann Bohlen, Patrick Schuler, Renukka Yaadav, Florian Selbach, Florian Steiner, Izabela Kaminska, Philip Tinnefeld
Summary: Researchers screened 10 preparation methods for graphene-on-glass and presented an optimized protocol for single-molecule and super-resolution imaging; they utilized DNA origami technology to detect graphene quality, showing discrepancies between conventional techniques such as light microscopy, atomic force microscopy, and Raman spectroscopy for graphene characterization.
Article
Chemistry, Multidisciplinary
Elke Hebisch, Martin Hjort, Diogo Volpati, Christelle N. Prinz
Summary: Fluorescent nanodiamonds (FND) are promising materials for long term cell labeling and tracking due to their stable fluorescence, biocompatibility, and amenability to functionalization. This study successfully achieved direct delivery of FND to the cytosol using nanostraws and low voltage electroporation pulses, showing efficient and rapid transport of FND into cells. Live cell STED microscopy revealed that cell membranes open entirely on top of nanostraws, supporting the hypothesis that many FND are delivered directly to the cytosol, avoiding endocytosis and lysosomal entrapment.
Article
Chemistry, Multidisciplinary
Weitao Wang, Peter R. Hayes, Xi Ren, Rebecca E. Taylor
Summary: Cell damage and death in bioengineering applications can be limited by cell encapsulation, which provides essential protection. In this study, researchers cross-linked two layers of DNA nanorods on the cellular plasma membrane to form a modular and programmable nanoshell, targeting the cell-surface glycocalyx. The DNA origami nanoshell modulates the biophysical properties of cell membranes, enhances membrane stiffness, lowers lipid fluidity, and protects cells against mechanical stress, enabling effective and robust multicellular assembly.
Article
Biotechnology & Applied Microbiology
Guo-Teng Liang, Cuixin Lai, Zejun Yue, Hanbin Zhang, Danyang Li, Zhong Chen, Xingyu Lu, Liang Tao, Fedor V. Subach, Kiryl D. Piatkevich
Summary: In this study, a pair of engineered flavin-binding fluorescent proteins, miniGFP1 and miniGFP2, were developed. These miniGFPs showed improved photochemical properties and high sensitivity to transition metal ions, making them potential fluorescent biosensors for live cell imaging and metal ion detection.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Joschka Hellmeier, Rene Platzer, Vanessa Muehlgrabner, Magdalena C. Schneider, Elke Kurz, Gerhard J. Schuetz, Johannes B. Huppa, Eva Sevcsik
Summary: DNA origami structures provide flexible scaffolds for organizing biomolecules with nanometer precision, but functionalizing them with proteins while maintaining stoichiometry and protein functionality remains challenging. This study systematically evaluated different strategies for site-specific decoration of DNA origami structures, with a focus on efficiency, stoichiometry, and protein functionality. The study found that using charge-neutral peptide nucleic acid emerged as the best strategy for achieving high yield and preserving protein functionality.
Article
Chemistry, Multidisciplinary
Fatih N. Gur, Susanne Kempter, Florian Schueder, Christoph Sikeler, Maximilian J. Urban, Ralf Jungmann, Philipp C. Nickels, Tim Liedl
Summary: The study demonstrates a DNA origami switch that utilizes the transition from double-stranded DNA to single-stranded DNA to drive a reversible conformational change. By using the unique properties of DNA, the switch exerts a contractive force produced by the extended single-stranded DNA to achieve large-scale motion. The operation of this switch is shown through various microscopy techniques, illustrating the intricate forces at play in nanoscale physical systems operating in fluids.
ADVANCED MATERIALS
(2021)
Article
Chemistry, Multidisciplinary
Cameron W. Evans, Diwei Ho, Joshua B. Marlow, Jessica J. King, Charmaine Hee, Lucas N. Wong, Rob Atkin, Nicole M. Smith, Gregory G. Warr, Marck Norret, K. Swaminathan Iyer
Summary: Non-viral delivery is an important strategy for gene therapy, immunization, and RNA interference, but the efficiency of current non-viral carriers is limited. Researchers have developed dendronized bottlebrush polymers with controlled defects, showing that synthetic macromolecular complexes can communicate intracellularly. This challenges the assumption that delivery agents act as bystanders and improves the design of non-viral delivery agents for genome engineering, vaccines, and nucleic acid-based therapies.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Marcel Hanke, Niklas Hansen, Emilia Tomm, Guido Grundmeier, Adrian Keller
Summary: The study investigated the denaturation of DNA origami nanostructures by different Gdm salts, with guanidinium thiocyanate being the most potent denaturant. The results also revealed a non-monotonous temperature dependence of DNA origami denaturation in guanidinium sulfate, emphasizing the complexity of Gdm-DNA interaction.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
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
Biochemistry & Molecular Biology
Wenchao Zhu, Shiori Takeuchi, Shosei Imai, Tohru Terada, Takumi Ueda, Yusuke Nasu, Takuya Terai, Robert E. Campbell
Summary: Molecular fluorescent indicators based on chemigenetic combination of synthetic ion-recognition motifs and protein-based fluorophores are versatile tools for dynamic imaging of biological systems. This design enables the development of chemigenetic indicators with ion or molecular specificities that have not been realized with fully protein-based indicators.
NATURE CHEMICAL BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Xinpei Dai, Xiaoliang Chen, Xinxin Jing, Yinan Zhang, Muchen Pan, Mingqiang Li, Qian Li, Pi Liu, Chunhai Fan, Xiaoguo Liu
Summary: Integrating dissimilar materials at the nanoscale is crucial for modern electronics and optoelectronics. Researchers have developed a DNA origami-encoded strategy for integrating silica-metal heterostructures and revealed the underlying mechanisms. By programming the densities and lengths of protruding dsDNA strands on DNA origami, high site-addressability of material deposition was achieved.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
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
Lea Messager, Jonathan R. Burns, Jungyeon Kim, Denis Cecchin, James Hindley, Alice L. B. Pyne, Jens Gaitzsch, Giuseppe Battaglia, Stefan Howorka
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2016)
Article
Chemistry, Multidisciplinary
Beata Klejevskaja, Alice L. B. Pyne, Matthew Reynolds, Arun Shivalingam, Richard Thorogate, Bart W. Hoogenboom, Liming Ying, Ramon Vilar
CHEMICAL COMMUNICATIONS
(2016)
Article
Chemistry, Multidisciplinary
Alice Pyne, Marc-Philipp Pfeil, Isabel Bennett, Jascindra Ravi, Patrizia Iavicoli, Baptiste Lamarre, Anita Roethke, Santanu Ray, Haibo Jiang, Angelo Bella, Bernd Reisinger, Daniel Yin, Benjamin Little, Juan C. Munoz-Garcia, Eleonora Cerasoli, Peter J. Judge, Nilofar Faruqui, Luigi Calzolai, Andre Henrion, Glenn J. Martyna, Chris R. M. Grovenor, Jason Crain, Bart W. Hoogenboom, Anthony Watts, Maxim G. Ryadnov
Article
Multidisciplinary Sciences
Paulina D. Rakowska, Haibo Jiang, Santanu Ray, Alice Pyne, Baptiste Lamarre, Matthew Carr, Peter J. Judge, Jascindra Ravi, Ulla I. M. Gerling, Beate Koksch, Glenn J. Martyna, Bart W. Hoogenboom, Anthony Watts, Jason Crain, Chris R. M. Grovenor, Maxim G. Ryadnov
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2013)
Article
Chemistry, Multidisciplinary
Alice Pyne, Ruth Thompson, Carl Leung, Debdulal Roy, Bart W. Hoogenboom
Article
Multidisciplinary Sciences
Marc-Philipp Pfeil, Alice L. B. Pyne, Valeria Losasso, Jascindra Ravi, Baptiste Lamarre, Nilofar Faruqui, Hasan Alkassem, Katharine Hammond, Peter J. Judge, Martyn Winn, Glenn J. Martyna, Jason Crain, Anthony Watts, Bart W. Hoogenboom, Maxim G. Ryadnov
SCIENTIFIC REPORTS
(2018)
Article
Biochemistry & Molecular Biology
Dani A. C. Heesterbeek, Bart W. Bardoel, Edward S. Parsons, Isabel Bennett, Maartje Ruyken, Dennis J. Doorduijn, Ronald D. Gorham, Evelien T. M. Berends, Alice L. B. Pyne, Bart W. Hoogenboom, Suzan H. M. Rooijakkers
Correction
Multidisciplinary Sciences
Marc-Philipp Pfeil, Alice L. B. Pyne, Valeria Losasso, Jascindra Ravi, Baptiste Lamarre, Nilofar Faruqui, Hasan Alkassem, Katharine Hammond, Peter J. Judge, Martyn Winn, Glenn J. Martyna, Jason Crain, Anthony Watts, Bart W. Hoogenboom, Maxim G. Ryadnov
SCIENTIFIC REPORTS
(2018)
Article
Multidisciplinary Sciences
Edward S. Parsons, George J. Stanley, Alice L. B. Pyne, Adrian W. Hodel, Adrian P. Nievergelt, Anais Menny, Alexander R. Yon, Ashlea Rowley, Ralf P. Richter, Georg E. Fantner, Doryen Bubeck, Bart W. Hoogenboom
NATURE COMMUNICATIONS
(2019)
Article
Chemistry, Multidisciplinary
Isabel Bennett, Alice L. B. Pyne, Rachel A. McKendry
Article
Multidisciplinary Sciences
Alice L. B. Pyne, Agnes Noy, Kavit H. S. Main, Victor Velasco-Berrelleza, Michael M. Piperakis, Lesley A. Mitchenall, Fiorella M. Cugliandolo, Joseph G. Beton, Clare E. M. Stevenson, Bart W. Hoogenboom, Andrew D. Bates, Anthony Maxwell, Sarah A. Harris
Summary: Researchers used atomic force microscopy and atomistic molecular dynamics simulations to resolve the structures of negatively-supercoiled DNA minicircles, revealing that superhelical stress can induce local variations in the DNA structure, affecting the overall structure and flexibility of DNA. Furthermore, the study demonstrates that the energetics of triplex formation is governed by a delicate balance between electrostatics and bonding interactions.
NATURE COMMUNICATIONS
(2021)
Review
Engineering, Biomedical
Kavit H. S. Main, James I. Provan, Philip J. Haynes, Geoffrey Wells, John A. Hartley, Alice L. B. Pyne
Summary: Atomic force microscopy (AFM) is a powerful imaging technique that allows for structural characterization of single biomolecules with nanoscale resolution in their native states. Innovations and optimizations in AFM imaging have advanced our understanding of DNA structure, mechanics, and interactions, providing insights into biological interactions and DNA-protein interactions. AFM also plays a broader role in translational cancer research by imaging DNA with chemotherapeutic ligands for clinical applications.
APL BIOENGINEERING
(2021)
Article
Chemistry, Analytical
Georgina Benn, Alice L. B. Pyne, Maxim G. Ryadnov, Bart W. Hoogenboom
Article
Chemistry, Multidisciplinary
Bernice Akpinar, Philip J. Haynes, Nicholas A. W. Bell, Katharina Brunner, Alice L. B. Pyne, Bart W. Hoogenboom
