Article
Biochemical Research Methods
Esau Medina, Eric J. Yik, Piet Herdewijn, John C. Chaput
Summary: XNA polymerases have great potential in synthetic biology, but little is known about their biochemical properties. This study compared various evolved polymerases and found that mutations for XNA synthesis increased substrate tolerance but could affect protein folding stability. Additionally, reverse transcriptase activity on different XNA substrates varied among polymerases. These findings can help in the development of new polymerase variants with improved activity and specificity.
ACS SYNTHETIC BIOLOGY
(2021)
Review
Biochemical Research Methods
Joakim Bohlin, Michael Matthies, Erik Poppleton, Jonah Procyk, Aatmik Mallya, Hao Yan, Petr Sulc
Summary: Molecular simulation is essential in DNA/RNA nanotechnology research, improving the precision of nanoscaffolds and diagnostic tools. oxView is a design tool for visualizing, designing, editing, and analyzing simulations of DNA, RNA, and nucleic acid-protein nanostructures, providing an accessible software platform for researchers to integrate simulation and 3D visualization into their projects.
Article
Chemistry, Multidisciplinary
Zhichu Xiang, Jian Zhao, Deyu Yi, Zhenghan Di, Lele Li
Summary: The study introduces a protease-activatable aptamer system for molecular sensing and imaging in a tumor-specific manner. By utilizing a PNA-peptide-PNA triblock copolymer to lock the structure-switching activity of the aptamer, protease-mediated cleavage of the peptide substrate can reduce binding affinity and recover the biosensing function. This work demonstrates the potential of bridging the gap between functional DNA and peptides for precise biomedical applications.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Review
Chemistry, Multidisciplinary
Bang Lin Li, Hang Zhang, Nian Bing Li, Hang Qian, David Tai Leong
Summary: This review provides a comprehensive materialistic background on the interaction of nucleic acids with non-nucleic acid-based materials. By combining the unique properties of nucleic acids with these materials, synergistic characteristics can be achieved, leading to attractive applications in bio-imaging, sensing, therapies, and information storage.
ADVANCED FUNCTIONAL MATERIALS
(2022)
Article
Chemistry, Multidisciplinary
Xiaokang Zhang, Yuan Liu, Bin Wang, Shihua Zhou, Peijun Shi, Ben Cao, Yanfen Zheng, Qiang Zhang, Kirilov Kasabov Nikola
Summary: The rise of DNA nanotechnology is driving the development of molecular security devices and bringing about important changes in information security technology. However, developing a secure and reliable access control strategy remains a challenge.
Article
Chemistry, Multidisciplinary
Zhibei Qu, Yinan Zhang, Zheze Dai, Yaya Hao, Yichi Zhang, Jianlei Shen, Fei Wang, Qian Li, Chunhai Fan, Xiaoguo Liu
Summary: The limitations in engineering electric double layers in physiological fluids have hindered the extensive study of long-range electrostatic interactions beyond biomolecular interaction interfaces. However, experimental and theoretical studies have shown that long-range Coulomb interactions play a crucial role in DNA hybridizations. Encapsulating protein and gold nanoparticles with different charges allows for modulation of hybridization kinetics, potentially leading to new strategies for gene regulation and nucleic acid detection.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemistry & Molecular Biology
Narjiss Seddaoui, Noemi Colozza, Ludovica Gullo, Fabiana Arduini
Summary: In recent years, the use of paper as a smart support in electrochemical sensors has significantly improved. The foldability and porosity of paper enable the design of reagent and equipment-free multi-analysis devices. Paper surface engineering has been utilized to immobilize different bioreceptors, boosting the customization of paper-based electrochemical biosensors. Additionally, the integration of different analytical processes in an eco-designed analytical tool using paper has been highlighted.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Review
Nanoscience & Nanotechnology
Yanfei Qu, Fengyun Shen, Ziyi Zhang, Qi Wang, Hao Huang, Yufei Xu, Qian Li, Xiaoli Zhu, Lele Sun
Summary: In recent years, DNA-based nanoscale or microscale functional materials have shown great potential in immunotherapy as superior delivery carriers. These materials have programmable and addressable structures that enable precise assembly of molecules or nanoparticles. DNA hydrogels with predictable structures and adjustable mechanical strength are advantageous for controlled release of cargos. DNA aptamers have been screened for specific recognition of ions, molecules, and cells using systematic evolution of ligands by exponential enrichment technology. Chemical modifications further enhance the functionalities of DNA. These functional DNA materials have unique advantages in immunomodulation and have shown great potential in fighting against diseases like cancer, viral infection, and inflammation.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Chemistry, Analytical
Zhao-Kun Wang, Zhen-Xuan Yuan, Chen Qian, Xian-Wei Liu
Summary: In this study, a plasmonic method was developed to probe the hybridization process at a single base pair resolution and study the relationship between the complementarity of DNA analytes and DNA hybridization behaviors. Single-molecule hybridization events were measured in real time, revealing stable and transient adsorption as two types of hybridization behaviors, which were correlated with the length of the complementary sequences and could distinguish DNA analytes with different complementary sequences.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Lan Mei, Bo Chen, Rangrang Fan, Min Wu, Chengxin Weng, Aiping Tong, Bingwen Zou, Hui Yang, Chunlai Nie, Gang Guo
Summary: This study constructs DNase-resistant and tumor-distinguishing DNA nano-assemblies based on crossover motifs, and found that 3HB equipped with three aptamers shows the best tumor discriminating ability.
ADVANCED FUNCTIONAL MATERIALS
(2022)
Review
Chemistry, Multidisciplinary
Seungheon Lee, Shivudu Godhulayyagari, Shadler T. Nguyen, Jasmine K. Lu, Sasha B. Ebrahimi, Devleena Samanta
Summary: The use of DNA-based nanostructures as probes has led to significant advances in chemical and biological sensing, allowing the detection of analytes in complex media, the understanding of fundamental biological processes, and the ability to diagnose diseases based on molecular signatures.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Sitao Xie, Zhimin Wang, Ting Fu, Liyan Zheng, Hui Wu, Lei He, Huidong Huang, Cai Yang, Ruowen Wang, Xu Qian, Liping Qiu, Weihong Tan
Summary: Aptamers are a promising tool in cancer-targeted theranostics, but their in vivo stability has been a critical issue. To address this, researchers developed an environment-responsive stabilization strategy for enhancing the stability of aptamers in the tumor microenvironment.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Review
Pharmacology & Pharmacy
Matthew Stephens
Summary: Nucleic acid aptamers, refined from random sequences, have the ability to bind to various targets and possess advantages over protein-based therapeutics. Despite these advantages and the approval of several nucleic acid-based therapeutics, conventional biologics still dominate the field. Recent research has identified potential aptamers that could reshape medicine as diagnostic tools and treatments.
PHARMACOLOGY & THERAPEUTICS
(2022)
Article
Chemistry, Analytical
Jiaqing Li, Yangyang Liu, Dongdong Liu, Tong Xu, Chen Zhang, Jianjun Li, Zhuo A. Wang, Yuguang Du
Summary: Glycans are promising for disease diagnosis due to their significant changes in disease states. By developing a simulation-based approach, the interactions between glycans and ssDNA aptamers were studied, revealing the preference for paromomycin to bind aptamers with base-restricted stem structures. Combined experiments and simulations identified optimal mutant aptamers, providing a potential strategy for accelerating aptamer screening using glycan-binding rRNA genes. This in silico workflow could also be applied for the development and application of RNA-templated ssDNA aptamers targeting glycans.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Richard L. Redman, Isaac J. Krauss
Summary: Carbohydrate binding proteins are important targets in medicine and biology, and multivalency plays a key role in high-affinity interactions. A novel platform for designing multivalent carbohydrate cluster ligands by directed evolution using serum-stable 2'-fluoro modified RNA backbones has been developed. This method was validated by selecting oligomannose glycan clusters that bind to broadly neutralizing HIV antibody 2G12 with affinities ranging from 13 to 36 nM from a large sequence pool.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Juan Jin, Emily G. Baker, Christopher W. Wood, Jonathan Bath, Derek N. Woolfson, Andrew J. Turberfield
Article
Chemistry, Multidisciplinary
Devin Daems, Iene Rutten, Jonathan Bath, Deborah Decrop, Hans Van Gorp, Elena Perez Ruiz, Steven De Feyter, Andrew J. Turberfield, Jeroen Lammertyn
Article
Multidisciplinary Sciences
Natalie E. C. Haley, Thomas E. Ouldridge, Ismael Mullor Ruiz, Alessandro Geraldini, Ard A. Louis, Jonathan Bath, Andrew J. Turberfield
NATURE COMMUNICATIONS
(2020)
Article
Chemistry, Multidisciplinary
Katherine G. Young, Behnam Najafi, William M. Sant, Sonia Contera, Ard A. Louis, Jonathan P. K. Doye, Andrew J. Turberfield, Jonathan Bath
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2020)
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
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.
Article
Robotics
Erik Benson, Rafael Carrascosa Marzo, Jonathan Bath, Andrew J. Turberfield
Summary: This study demonstrates the successful creation of a nanoscale robotic printer using DNA nanotechnology, which can be applied in surface manufacturing, biophysical studies, and templated chemistry.
Article
Chemistry, Multidisciplinary
Gunnar Kloes, Timothy J. D. Bennett, Alma Chapet-Batlle, Ali Behjatian, Andrew J. Turberfield, Madhavi Krishnan
Summary: This study reports on an experimental investigation into the effect of molecular shape on long-range electrostatic interactions in solution. Using DNA nanostructures with different three-dimensional conformations but approximately equal total charge, it is demonstrated that the geometry of the charge distribution in a molecule has a significant impact on its electrical interactions. Escape-time electrometry (ETe) is shown to provide a rapid and easy method for screening and identifying the 3D conformations of charged biomolecules or molecular complexes in solution.
Article
Chemistry, Multidisciplinary
Joakim Bohlin, Andrew J. Turberfield, Ard A. Louis, Petr Sulc
Summary: We explored the design space for self-assembled multicomponent objects, ranging from unique building blocks to minimum number of distinct building blocks defining the target structure. By using patchy particle simulations, we analyzed the assembly dynamics of different solutions and their influence on the kinetics and yield of the target assembly. Our findings show that resource-saving solutions with minimum distinct blocks can perform just as well or faster than designs with unique building blocks. We also designed multifarious structures by sharing building blocks between different targets, and investigated the realization of multicomponent shapes using DNA nanostructures as building blocks through coarse-grained DNA simulations.
Article
Nanoscience & Nanotechnology
Christina Jayachandran, Arindam Ghosh, Meenakshi Prabhune, Jonathan Bath, Andrew J. J. Turberfield, Lara Hauke, Jorg Enderlein, Florian Rehfeldt, Christoph F. F. Schmidt
Summary: Mechanical forces play a critical role in various biological processes, including wound healing, tumor formation, cell migration, and differentiation. This study presents a FRET-based DNA-protein tension sensor designed to measure transient forces in actin networks. The sensor utilizes two actin-binding motifs with a fast off-rate attached to a central DNA hairpin loop. The conformational state of the sensor is determined using fluorescence lifetime imaging, enabling robust measurements even with intensity variations. The sensor's potential is demonstrated through confocal microscopy and monitoring of crosslinking activity in vitro using bulk rheology.
ACS APPLIED NANO MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Seham Helmi, Andrew J. Turberfield
Summary: Nanoscience aims to imitate nature's control over functional molecular assemblies. This study presents a templating technique that allows efficient attachment of two different oligonucleotides to a homobifunctional molecule, enabling its controlled and programmable placement within a DNA nanostructure. The technique is demonstrated with various organic molecules with different conjugation chemistries and water solubilities, showing the ability to control both position and orientation within a self-assembled three-dimensional DNA origami nanostructure. The study also shows the dynamic control over the environment of the target molecule using strand-displacement reactions.
