Article
Biochemistry & Molecular Biology
Zhichao Mei, Lingjun Wan, Mengzhou Wei, Yulin Li
Summary: We reported a facile, base-sequence-independent strategy for logically controlling DNA self-assembly through external molecules. The INHIBIT and XOR logic controls over the assembly/disassembly of DNA polyhedra were realized through cystamine (Cyst) and ethylenediamine (EN) respectively. Our work provides a sequence-independent strategy for logically controlling DNA self-assembly, opening up new possibilities for dynamic DNA nanotechnology.
Article
Chemistry, Multidisciplinary
Xiangyuan Ouyang, Yongli Wu, Linjie Guo, Le Li, Mo Zhou, Xinyi Li, Ting Liu, Yawen Ding, Huaiyu Bu, Gang Xie, Jianlei Shen, Chunhai Fan, Lihua Wang
Summary: In this study, the ordered self-assembly of CuNCs using DNA nanoribbon as the template (DNR/CuNCs) was found to improve the electrochemiluminescence (ECL) properties of CuNCs compared with individual CuNCs. The DNR/CuNCs showed a high ECL yield of 46.8% in K2S2O8, which was approximately 68 times higher than that of individual CuNCs. This strategy was also successfully applied to other ECL emitters, such as gold nanoclusters and the Ru(bpy)(3)(2+)/TPrA system. Furthermore, a DNR/CuNC-based ECL biosensor with higher sensitivity was constructed for dopamine determination, showing the potential of DNR/CuNCs as a new type of superior luminophore candidate in ECL bioanalysis.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Engineering, Biomedical
Jinpeng Han, Yuchen Cui, Zi Gu, Dayong Yang
Summary: The study developed a nanocarrier system that can efficiently release drugs in cells while minimizing side effects, utilizing polyphenol-DNA nanocomplexes. Through programmable assembly and disassembly processes, this method achieves precise release of multiple genes and drugs in cells.
Article
Multidisciplinary Sciences
Akiko Hatakeyama, Yuliia Shymko, Brigitte Hartmann, Romain Retureau, Claude Nogues, Marco Pasi, Malcolm Buckle
Summary: This study uses PhAST technology to investigate the structural changes of nucleosomes, revealing similarities and differences between nucleosome assembly and disassembly processes. The results suggest that the efficiency of DNA-histone binding is influenced by the DNA sequence and the amplitude of PhAST signals changes differently during assembly and disassembly. These findings provide new insights into the role of DNA sequence in gene expression regulation and shed light on how the intrinsic properties of DNA are integrated into the control of chromatin structure.
Review
Biochemistry & Molecular Biology
Ke Li, Yanfei Liu, Beibei Lou, Yifu Tan, Liwei Chen, Zhenbao Liu
Summary: In the past decades, DNA has been widely utilized in the field of nanostructures due to its programmable properties. This review presents different strategies for the functionalization of DNA on nanoparticle surfaces and discusses the roles of DNA in the assembly of nanostructures as well as the influencing factors. The biomedical applications of DNA-assembled nanostructures are also summarized. This review provides new insights into the application of DNA in nanostructure assembly.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Chemistry, Analytical
Zhipeng Xie, Simin Liu, Yueming Zhai
Summary: This study focuses on the translocation characteristics of DNA tetrahedrons to evaluate their self-assembly process and the advantage of tetrahedral DNA nanostructures as a signal amplification label.
JOURNAL OF ELECTROANALYTICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Yuyan Wang, Xin Huang, Xinxing Zhang
Summary: The study presents a robust self-healing material with high strength, toughness, and healing efficiency by incorporating high density noncovalent bonds at the interfaces between nanosheets and matrix, overturning the traditional notion that high mechanical strength and healing ability are mutually exclusive in noncovalent bonding materials.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Hiroaki Konishi, Eiji Nakata, Futa Komatsubara, Takashi Morii
Summary: Cellular compartmentalization is crucial for organizing biochemical reactions, but synthesizing compartments to encapsulate materials with precise control remains challenging. This study evaluated a liposome-encapsulated compartment with potential to locate and control materials of interest. A nanoliposome was constructed inside a ring-shaped DNA skeleton, equipped with a double-stranded DNA platform to isolate molecules from the outer environment.
Article
Chemistry, Multidisciplinary
Jae-Myoung Kim, Chungyeon Lee, Yeonhee Lee, Jinhaeng Lee, So-Jung Park, Sungho Park, Jwa-Min Nam
Summary: Plasmonic gap nanostructures have attracted extensive research due to their strongly enhanced optical responses, but the reproducible and controlled preparation of highly uniform nanogaps and the prediction, understanding, and control of their optical properties remain challenging.
ADVANCED MATERIALS
(2021)
Article
Chemistry, Multidisciplinary
Yun Liu, Weihua Fu, Zhongsheng Xu, Liang Zhang, Tao Sun, Mengmeng Du, Xun Kang, Shilin Xiao, Chunyu Zhou, Mingfu Gong, Dong Zhang
Summary: This paper presents a novel method for direct reversible self-assembly and dis-assembly of Au nanoparticles in water driven by pH stimuli. By controlling the condensation and decomposition of 3-aminopropyltriethoxysilane, plasmonic color switching among adjacent AuNPs can be achieved, offering a new avenue for regulating plasmonic properties of nanoparticles.
FRONTIERS IN CHEMISTRY
(2021)
Review
Chemistry, Multidisciplinary
Yongzheng Xing, Alexia Rottensteiner, Jonah Ciccone, Stefan Howorka
Summary: Membrane-spanning nanopores have diverse applications in label-free single-molecule sensing, nucleic acid sequencing, and research in biology and biophysics. The limitations of naturally occurring and synthetic inorganic nanopores can be overcome by functionalizing existing pores with DNA strands and creating a new class of DNA nanopores. This review focuses on the progress and potential applications of functional DNA nanopores.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Nanoscience & Nanotechnology
Congzhou Chen, Tingting Lin, Mingyuan Ma, Xiaolong Shi, Xin Li
Summary: This study demonstrates the assembly and visualization of a hexagonal DNA origami ring using atomic force microscopy. The flexible origami structure shows potential applications in dynamic pattern recognition and structural calibration.
Article
Chemistry, Multidisciplinary
Fangzhi Yu, Xiangfei Li, Jian Zhao, Yuliang Zhao, Lele Li
Summary: In this study, an optically triggered DNA assembly and disassembly strategy was developed to regulate the cGAS-STING signaling pathway. By using light activation, the DNA hairpins can form long linear structures and stimulate the synthesis of cGAMP for STING stimulation. The temporal dose of stimulation can be efficiently controlled through remote photo-triggering.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Multidisciplinary Sciences
Daichi Hayakawa, Thomas E. Videbaek, Douglas M. Hall, Huang Fang, Christian Sigl, Elija Feigl, Hendrik Dietz, Seth Fraden, Michael F. Hagan, Gregory M. Grason, W. Benjamin Rogers
Summary: This article explores new design principles for making self-limiting architectures using self-assembly. The authors use DNA origami to create triangular subunits with specific interactions and binding angles, and study their assembly into tubules with a self-limited width. They demonstrate that the tubules can reach significant lengths and that their width can be controlled through geometric programming. They also find that the width and chirality of the tubules can be manipulated by increasing the number of subunit species. These findings provide insights into the role of assembly complexity and geometry in self-limiting assembly and have potential applications in other self-limiting architectures.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Robotics
Anuruddha Bhattacharjee, Yitong Lu, Aaron T. Becker, MinJun Kim
Summary: The study introduces a design of reconfigurable modular robots with high reconfigurability and controllability for mesoscale manufacturing applications. The platform can create programmable patterns through wireless control and assembly-disassembly techniques. Experimental results demonstrate robust and reproducible behavior, showing promise for mesoscale manufacturing.
IEEE TRANSACTIONS ON ROBOTICS
(2022)
Article
Chemistry, Multidisciplinary
Simona Ranallo, Daniela Sorrentino, Elisabetta Delibato, Gianfranco Ercolani, Kevin W. Plaxco, Francesco Ricci
Summary: Here we report the design and optimization of an antibody-responsive, DNA-based device that enables communication between non-interacting proteins. The device recognizes and binds a specific antibody, causing a conformational change that releases a DNA strand regulating the activity of a target protein. We demonstrate the antibody-induced control of thrombin and Taq DNA polymerase, showcasing the versatility of this strategy in regulating protein-protein communication in artificial networks.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Alessia Amodio, Marco Cassani, Liviana Mummolo, Christina Cortez-Jugo, Sukhvir Kaur Bhangu, Jori Symons, Chantelle L. Ahlenstiel, Giancarlo Forte, Francesco Ricci, Anthony D. Kelleher, Sharon R. Lewin, Francesca Cavalieri, Frank Caruso
Summary: This study develops a strategy combining DNA nanotechnology and super-resolution expansion microscopy (ExM) to detect and image HIV-1 RNA in infected cells. By using a chimeric locked nucleic acid (LNA)-DNA sensor and physically trapping the viral RNA, nanoscale imaging is achieved.
Article
Chemistry, Multidisciplinary
Erica Del Grosso, Patrick Irmisch, Serena Gentile, Leonard J. Prins, Ralf Seidel, Francesco Ricci
Summary: This study presents a general approach to achieve dissipative control over toehold-mediated strand-displacement, a widely used reaction in DNA nanotechnology. By re-engineering the classic reaction, the high-energy invader strand is converted into a low-energy waste product, allowing the system to spontaneously return to its original state over time. This method enables unique temporal activation of DNA systems and is reversible and highly controllable.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Aitor Patino Diaz, Sara Bracaglia, Simona Ranallo, Tania Patino, Alessandro Porchetta, Francesco Ricci
Summary: This study developed a cell-free in vitro transcription system for the detection of specific target antibodies. The system uses programmable antigen-conjugated DNA-based conformational switches that can trigger cell-free transcription upon binding to a target antibody, resulting in the production of a light-up fluorescence-activating RNA aptamer. The system combines the programmability and responsiveness of DNA-based systems with the specificity and sensitivity offered by in vitro genetic circuitries and commercially available transcription kits. The study demonstrates that cell-free transcriptional switches can efficiently measure antibody levels directly in blood serum and can be adapted to different antibodies.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Lorena Baranda Pellejero, Minke A. D. Nijenhuis, Francesco Ricci, Kurt Gothelf
Summary: DNA-templated chemical reactions have various applications, such as drug discovery, nucleic acid detection, and targeted drug delivery. This study introduces a new system that translates protein-protein binding events into DNA-templated reactions, resulting in covalent product formation. Using two DNA-antibody conjugates, two protein-templated reactions can occur simultaneously in the same solution without any interference.
Article
Chemistry, Multidisciplinary
Nada Farag, Gianfranco Ercolani, Erica Del Grosso, Francesco Ricci
Summary: In this study, we demonstrate the use of DNA repair enzymes to control the assembly of DNA-based structures. By designing responsive nucleic acid modules and utilizing specific enzyme repair activity, we were able to achieve the self-assembly of DNA tiles into tubular structures. This approach is programmable, specific, and orthogonal, allowing for accurate prediction of tile distribution. Additionally, we show that BER-enzyme inhibitors can be used to control DNA-tile assembly in a specific and concentration-dependent manner.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Review
Chemistry, Multidisciplinary
Erica Del Grosso, Elisa Franco, Leonard J. Prins, Francesco Ricci
Summary: DNA nanotechnology is a powerful tool for designing and controlling molecular systems. Dissipative DNA nanotechnology aims to build life-like systems by combining programmable reactions with energy-dissipating processes.
Article
Biochemistry & Molecular Biology
Marianna Rossetti, Rosa Merlo, Neda Bagheri, Danila Moscone, Anna Valenti, Aakash Saha, Pablo R. Arantes, Rudy Ippodrino, Francesco Ricci, Ida Treglia, Elisabetta Delibato, John van der Oost, Giulia Palermo, Giuseppe Perugino, Alessandro Porchetta
Summary: By using hairpin DNA as FRET-based reporters, we have enhanced the trans-cleavage activity of Cas12a enzymes, allowing for faster detection of clinically relevant double stranded DNA targets.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Yuyang Wu, Simona Ranallo, Erica Del Grosso, Alejandro Chamoro-Garcia, Herbert L. Ennis, Nenad Milosavic, Kyungae Yang, Tod Kippin, Francesco Ricci, Milan Stojanovic, Kevin W. Plaxco
Summary: Electrochemical aptamer-based (EAB) sensors utilize conformational changes to transduce target recognition into electrochemical output, supporting high-frequency molecular measurements and working in complex environments. However, modification of the aptamer is required to achieve the necessary conformational change and balance affinity and signal gain.
BIOCONJUGATE CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Juliette Bucci, Patrick Irmisch, Erica Del Grosso, Ralf Seidel, Francesco Ricci
Summary: In this study, a strategy for programmable delayed onset of toehold-mediated DNA strand displacement reactions (SDRs) is demonstrated. The strategy involves the use of blocker strands to inhibit strand displacement initially, followed by enzymatic degradation of the blocker strand to enable SDR. The kinetics of the blocker enzymatic degradation controls the timing of SDR initiation. The strategy is versatile and can be orthogonally controlled by different enzymes targeting specific blocker strands.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Alejandro Chamorro-Garcia, Claudio Parolo, Gabriel Ortega, Andrea Idili, Joshua Green, Francesco Ricci, Kevin W. Plaxco
Summary: Biosensors and bioassays that use proteins and nucleic acids to detect specific molecular targets have limitations in sensitivity to small variations in target concentration. This study introduces the sequestration mechanism to improve the responsiveness of these technologies, narrowing the dynamic range and enhancing the ability to measure small changes in target concentration.
