Article
Chemistry, Multidisciplinary
Yuhang Dong, Feng Li, Zhaoyue Lv, Shuai Li, Meihe Yuan, Nachuan Song, Jinqiao Liu, Dayong Yang
Summary: Coupling materials chemistry systems with biological processes to modulate lysosomal functions provides a promising approach for lysosome interference. This study demonstrates a new way to achieve lysosome interference by coupling subcellular microenvironment with a precisely programmable assembly system.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Jiantong Dong, Yu Ouyang, Jianbang Wang, Michael P. O'Hagan, Itamar Willner
Summary: The study reveals the dynamic transient assembly and disassembly of G-quadruplex structures and DNAzymes, driven by functional DNA reaction modules. These processes could potentially offer a therapeutic approach for diseases related to gene expression perturbation.
Article
Chemistry, Multidisciplinary
Fang He, Meixia Wang, Jieyu Wang, Hong-Hui Wang, Zhou Nie
Summary: MicroRNAs (miRNAs) can be used as diagnostic biomarkers and therapeutic targets in diseases. However, there is a lack of effective strategies to use extracellular miRNAs as input signals for therapy. We developed a programmable miRNA-responsive DNA receptor that can autonomously activate receptors based on miRNA levels. This receptor system was demonstrated in a mouse model of liver injury, showing potential for precise cell therapy in regenerative medicine.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Yuxiang Dong, Jiliang Liu, Xuanzhao Lu, Jialin Duan, Liqi Zhou, Lizhi Dai, Min Ji, Ningning Ma, Yong Wang, Peng Wang, Jun-Jie Zhu, Qianhao Min, Oleg Gang, Ye Tian
Summary: Self-assembly processes are important for fabricating complexly organized nanomaterials, but often limited in creating structures with multiscale order. In this study, a two-stage assembly strategy is introduced to successfully form complexly organized nanoparticle crystals.
Review
Biochemistry & Molecular Biology
Shuang Wang, Xiaolin Xie, Zhi Chen, Ningning Ma, Xue Zhang, Kai Li, Chao Teng, Yonggang Ke, Ye Tian
Summary: The DNA-grafted nanoparticle serves as a programmable atom equivalent for assembling three-dimensional superlattice with novel properties, allowing for the exploration of assembly strategies and mechanisms, as well as future applications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Analytical
Yanxin Chu, Shou-Jun Xiao, Jun-Jie Zhu
Summary: Non-enzymatic nucleic acid catalytic systems based on branch migration have been developed and a scalable planetary cross-catalytic (PCC) system is built. Four levels of catalytic reactions are designed and examined in terms of their reaction products and intermediates. The PCC systems show potential applications in biological signal transduction, biocomputing, and rapid detection of nucleic acid probes.
ANALYTICAL CHEMISTRY
(2023)
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)
Article
Chemistry, Multidisciplinary
Jenny Le, Dino Osmanovic, Melissa Ann Klocke, Elisa Franco
Summary: This study demonstrates the use of mini-gels loaded with molecules and reactions to control the dynamic self-assembly of DNA nanotubes. The mini-gels can serve as storage compartments for DNA, controlling the assembly and disassembly of nanotubes. Additionally, mini-gels can host enzymatic reactions to activate the self-assembly process.
Article
Chemistry, Multidisciplinary
Raghu Pradeep Narayanan, Abhay Prasad, Alex Buchberger, Lei Zou, Julio Bernal-Chanchavac, Tara Macculloch, Nour Eddine Fahmi, Hao Yan, Fei Zhang, Matthew J. Webber, Nicholas Stephanopoulos
Summary: The combination of multiple orthogonal interactions enables hierarchical complexity in self-assembled nanoscale materials. This study demonstrates the efficient supramolecular polymerization of DNA origami nanostructures using a multivalent display of small molecule host-guest interactions, and exploits high-affinity CB[7]-adamantane interactions to enable responsive enzymatic actuation.
Article
Chemistry, Multidisciplinary
Arlin Rodriguez, Dhanush Gandavadi, Johnsi Mathivanan, Tingjie Song, Bharath Raj Madhanagopal, Hannah Talbot, Jia Sheng, Xing Wang, Arun Richard Chandrasekaran
Summary: The programmable nature of DNA allows the construction of custom-designed static and dynamic nanostructures. However, the high concentrations of magnesium ions required for assembly restrict their applications. In this study, we investigate the assembly of DNA nanostructures in various ions and successfully assemble a majority of these structures in Ca2+, Ba2+, Na+, K+ and Li+. We also find that structures assembled in monovalent ions exhibit significantly higher nuclease resistance compared to those assembled in divalent ions.
Article
Chemistry, Multidisciplinary
Jiajia Zou, Ashley C. Stammers, Andrea Taladriz-Sender, Jamie M. Withers, Iain Christie, Marina Santana Vega, Badri L. Aekbote, William J. Peveler, David A. Rusling, Glenn A. Burley, Alasdair W. Clark
Summary: An orthogonal, noncovalent approach is presented for the assembly of higher-order DNA origami nanostructures. By incorporating perfluorinated tags into DNA origami tiles, their hierarchical assembly is controlled via fluorous-directed recognition. This integrated catch-and-latch approach combining fluorous effect with base-pairing specificity enables increased assembly efficiency and requires fewer DNA sequences, providing a cheap and efficient means for producing discrete superstructures in DNA nanotechnology.
Article
Chemistry, Multidisciplinary
Shuoxing Jiang, Nibedita Pal, Fan Hong, Nour Eddine Fahmi, Huiyu Hu, Matthew Vrbanac, Hao Yan, Nils G. Walter, Yan Liu
Summary: Controlling the nucleation step of a self-assembly system is crucial for engineering structural complexity and dynamic behaviors. This study investigates the inherent dynamics of three general nucleation modes in DNA tile-based self-assembly and reveals temperature-dependent kinetics and a nucleation-growth model are key factors. The assembly of tiles can be externally regulated by the hosting frame and an UV-responsive trigger, offering a general strategy for controlling the self-assembly process.
Article
Chemistry, Multidisciplinary
Nada Farag, Milan Dordevic, Erica Del Grosso, Francesco Ricci
Summary: This paper demonstrates an approach to achieve dynamic and reversible decoration of DNA-based scaffolds. Engineered DNA tiles with enzyme-responsive strands conjugated to different molecular labels are used. These strands are designed to be recognized and degraded by specific enzymes, inducing the replacement of them with new strands attached to different labels. Multiple enzyme-responsive strands allow for dynamic, orthogonal, and reversible decoration of DNA structures. The approach enables the control of the distribution of different labels on the same scaffold without crosstalk, leading to DNA scaffolds with different antibody recognition patterns.
ADVANCED MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Yunlong Zhang, Donglei Yang, Pengfei Wang, Yonggang Ke
Summary: Structural DNA nanotechnology enables the fabrication of designer nanoscale artificial architectures. In this study, we developed a molecular assembly system where DNA tiles can assemble into tubes and then large one-dimensional DNA bundles. By incorporating a cohesive link into the tiles, we induced intertube binding and successfully formed DNA bundles with micrometer-length and nanometer-width, whose assembly was collectively determined by cationic strength and linker designs. Moreover, programmable spatial features and compositions of multicomponent DNA bundles were realized. Lastly, dynamic capability was implemented to achieve reversible reconfigurations among tile, tube, and bundles. This assembly strategy expands the toolbox of DNA nanotechnology and has broad applications in materials science, synthetic biology, biomedical science, and beyond.
Article
Chemistry, Multidisciplinary
Aleksandra K. Adamczyk, Teun A. P. M. Huijben, Miguel Sison, Andrea Di Luca, Stefano Vanni, Sophie Brasselet, Kim I. Mortensen, Fernando D. Stefani, Mauricio Pilo-Pais, Guillermo P. Acuna
Summary: This study demonstrates a controlled orientation of single molecules in DNA origami by linking them to oligonucleotide strands and leaving unpaired bases. The number of unpaired bases affects the stretching and orientation of the fluorophore linkers. These findings expand the application of DNA origami in the fabrication of nanodevices involving orientation-dependent molecular interactions.
Article
Biochemical Research Methods
Tianqi Song, Sudhanshu Garg, Reem Mokhtar, Hieu Bui, John Reif
ACS SYNTHETIC BIOLOGY
(2018)
Article
Chemistry, Multidisciplinary
Sudhanshu Garg, Shalin Shah, Hieu Bui, Tianqi Song, Reem Mokhtar, John Reif
Article
Chemistry, Multidisciplinary
Tianqi Song, Nikhil Gopalkrishnan, Abeer Eshra, Sudhanshu Garg, Reem Mokhtar, Hieu Bui, Harish Chandran, John Reif
Article
Chemistry, Multidisciplinary
Shalin Shah, Abhishek K. Dubey, John Reif
Article
Chemistry, Multidisciplinary
Hieu Bui, Carl W. Brown, Susan Buckhout-White, Sebastian A. Diaz, Michael H. Stewart, Kimihiro Susumu, Eunkeu Oh, Mario G. Ancona, Ellen R. Goldman, Igor L. Medintz
Article
Biochemical Research Methods
Shalin Shah, Abhishek K. Dubey, John Reif
ACS SYNTHETIC BIOLOGY
(2019)
Article
Nanoscience & Nanotechnology
Tianqi Song, Abeer Eshra, Shalin Shah, Hieu Bui, Daniel Fu, Ming Yang, Reem Mokhtar, John Reif
NATURE NANOTECHNOLOGY
(2019)
Review
Materials Science, Multidisciplinary
Hieu Bui, Sebastian A. Diaz, Jake Fontana, Matthew Chiriboga, Remi Veneziano, Igor L. Medintz
ADVANCED OPTICAL MATERIALS
(2019)
Article
Chemistry, Multidisciplinary
Tianqi Song, Shalin Shah, Hieu Bui, Sudhanshu Garg, Abeer Eshra, Daniel Fu, Ming Yang, Reem Mokhtar, John Reif
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2019)
Review
Chemistry, Analytical
Alana Torres Vidal, Igor L. Medintz, Hieu Bui
Article
Chemistry, Multidisciplinary
Divita Mathur, William P. Klein, Matthew Chiriboga, Hieu Bui, Eunkeu Oh, Rafaela Nita, Jawad Naciri, Paul Johns, Jake Fontana, Sebastian A. Diaz, Igor L. Medintz
Article
Engineering, Electrical & Electronic
Abeer Eshra, Shalin Shah, Tianqi Song, John Reif
IEEE TRANSACTIONS ON NANOTECHNOLOGY
(2019)