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
Nanoscience & Nanotechnology
Klaus F. Wagenbauer, Nhi Pham, Adrian Gottschlich, Benjamin Kick, Viktorija Kozina, Christopher Frank, Daniela Trninic, Pierre Stoemmer, Ruth Gruenmeier, Emanuele Carlini, Christina Angeliki Tsiverioti, Sebastian Kobold, Jonas J. Funke, Hendrik Dietz
Summary: A synthetic nanocarrier based on DNA origami chassis allows for precise control of antibodies in anticancer immunotherapy, enabling simultaneous engagement with immune signalling pathways, checkpoint inhibition, and targeted co-stimulation. Through modular and programmable assembly, specific T-cell engagers were identified and tested for their ability to activate T cells and induce lysis of target cells, both in vitro and in vivo. This approach provides a rapid and efficient method for the generation, screening, and testing of multi-specific antibodies in preclinical pharmaceutical development.
NATURE NANOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Daniel Fu, Raghu Pradeep Narayanan, Abhay Prasad, Fei Zhang, Dewight Williams, John S. Schreck, Hao Yan, John Reif
Summary: We have developed an automated design tool that can be applied to curved geometries for encapsulating three-dimensional DNA nanostructures. This research is significant in solving previous design challenges and expanding the application of DNA nanostructure design.
Article
Multidisciplinary Sciences
Chunyang Zhou, Donglei Yang, Sebastian Sensale, Pranav Sharma, Dongfang Wang, Lei Yu, Gaurav Arya, Yonggang Ke, Pengfei Wang
Summary: This study reports a design method for controllable DNA molecular structures through controlled base stacking. Precise control over molecular conformation and transformation is achieved by programming stacking bonds within the junction. Dynamic transformations between different conformations are achieved through specific environmental and molecular stimulations.
Article
Nanoscience & Nanotechnology
Christopher M. M. Wintersinger, Dionis Minev, Anastasia Ershova, Hiroshi M. M. Sasaki, Gokul Gowri, Jonathan F. F. Berengut, F. Eduardo Corea-Dilbert, Peng Yin, William M. M. Shih
Summary: Living systems can self-assemble at different length scales, and DNA origami techniques have enabled the self-assembly of submicron-scale shapes. By extending the crisscross polymerization strategy to DNA origami slats, custom multi-micron shapes with nanoscale surface patterning can be fabricated. This method allows for the production of complex structures composed of thousands of sophisticated and precisely designed origami slats.
NATURE NANOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Bo-Young Lee, Jaewon Lee, Dong June Ahn, Seungwoo Lee, Min-Kyu Oh
Summary: Reducing the expression of phage protein V was found to significantly enhance the production throughput of scaffold DNA. Reprogramming rolling circle amplification in Escherichia coli can lead to a substantial improvement in scaffold DNA production efficiency.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Wouter Engelen, Christian Sigl, Karoline Kadletz, Elena M. Willner, Hendrik Dietz
Summary: This study presents a strategy for controlling DNA nanodevices based on IgG antibodies sensing antigens, allowing for antigen-triggered disassembly and release of molecular payload. The method is applicable in various DNA nanostructures and IgG-antigen combinations.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biochemistry & Molecular Biology
Enrique Lin-Shiao, Wolfgang G. Pfeifer, Brian R. Shy, Mohammad Saffari Doost, Evelyn Chen, Vivasvan S. Vykunta, Jennifer R. Hamilton, Elizabeth C. Stahl, Diana M. Lopez, Cindy R. Sandoval Espinoza, Alexander E. Deyanov, Rachel J. Lew, Michael G. Poirer, Alexander Marson, Carlos E. Castro, Jennifer A. Doudna
Summary: DNA nanostructures are a promising tool for delivering molecular payloads to cells, but effectively delivering genetic material to the nucleus has been a challenge. This study successfully integrated gene material into cells using DNA nanostructures as HDR templates, with increased entry into the nucleus through CRISPR technology. These nanostructured templates showed lower toxicity and higher insertion efficiency compared to unstructured DNA templates.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Robotics
Namita Sarraf, Kellen R. Rodriguez, Lulu Qian
Summary: The power of natural evolution lies in the adaptability of biological organisms, but it is limited by the time scale of genetics and reproduction. Engineering artificial molecular machines that have adaptability as a core feature and operate at a faster time scale could revolutionize synthetic cells. We developed a tile displacement mechanism in DNA origami assemblies to achieve modular reconfiguration, and we established design principles for simultaneous reconfigurations using complex invaders with distinct shapes.
Article
Chemistry, Multidisciplinary
Yan Li, Jin Pei, Xuehe Lu, Yunfei Jiao, Fengsong Liu, Xiaohui Wu, Jianbing Liu, Baoquan Ding
Summary: The DNA origami technique offers a programmable way to assemble nanostructures with arbitrary shapes, limited only by the scaffold strand length. A new strategy has been developed to efficiently organize multiple DNA origami tiles into super-DNA origami using a flexible and covalent-bound branched DNA structure. Compared to traditional DNA junctions, this approach yields higher efficiency and more compact structures, enabling precise organization of gold nanoparticles into various patterns.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Multidisciplinary
Jing Yang, Yuan Liang, Xiang Li, Yongpeng Zhang, Long Qian, Yonggang Ke, Cheng Zhang
Summary: The programmable assembly of gold nanoparticle superstructures with precise spatial arrangement has attracted attention for their unique characteristics in plasmonics and biomedicine. This article presents a strategy of using a spatially programmable enzymatic nanorobot arm to modulate the anisotropic assembly of DNA/AuNP superstructures.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Multidisciplinary Sciences
Longfei Liu, Qiancheng Xiong, Chun Xie, Frederic Pincet, Chenxiang Lin
Summary: The triggered formation of membrane tubes in response to specific DNA signals allows for spatial and temporal control of membrane dynamics in an artificial system. The conformational change of DNA clamps can modulate the timing, efficiency, and width of vesicle tubulation.
Article
Chemistry, Multidisciplinary
Jianbing Liu, Baoquan Ding, Xiaohui Wu, Changping Yang, Hong Wang, Xuehe Lu, Yingxu Shang, Qing Liu, Jing Fan
Summary: DNA origami has been widely used in biomedical applications such as biosensing, bioimaging, and drug delivery. In this study, a new strategy for constructing genetically encoded DNA origami was presented using complementary DNA strands. The genetically encoded DNA origami could efficiently penetrate cell membranes and induce successful gene expression. By modifying the origami with tumor-targeting groups, effective tumor therapy could be achieved through upregulation of specific proteins in tumor cells. This combination of folding and coating strategies offers a promising avenue for the development of gene therapy.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Katsuhiko Abe, Hiroshi Sugiyama, Masayuki Endo
Summary: The study demonstrates photo-controlled sequence-selective dsDNA cleavage using a DNA origami structure with Cas9 nuclease. The activity of Cas9 was suppressed inside the ring-shaped DNA origami and restored after photoirradiation.
CHEMICAL COMMUNICATIONS
(2021)
Article
Chemistry, Analytical
Mengke Su, Shixuan Yang, Min Xu, Shanshan Du, Liqin Zheng, Xian Wang, Cheng Qu, Honglin Liu
Summary: In this study, a novel SERS probe was developed using nucleic acid-peptide conjugates for high-specific profiling of abnormal protein levels in cancer patients. The probe showed rapid, simple, and multisignal detection capabilities. The effect of low-temperature storage time on blood samples was also analyzed, and it was found that plasma samples stored at 4°C for more than 2 days could generate false negative results due to TB hydrolysis, highlighting the importance of clinical sample analysis. This nucleic acid-peptide conjugate provides new ideas for future SERS sensing strategies.
ANALYTICAL CHEMISTRY
(2023)
Article
Biophysics
Hui-Yan Li, Fang-Fei Yin, Xin-Yi Li, Wan-Nan Jia, Jia Ding, Li Zhang, Zhong-Hua Wang, Qin-Qin Hu, Jie-Liang Zuo, Hu-Liang Jia, Li-Hua Wang, Chun-Hai Fan, Hong-Zhou Gu, Jian Wu
Summary: In this study, an aptamer AP32 specific to SHh was obtained by SELEX technology and a novel aptamer-based assay was successfully developed. The method exhibited a broad detection range, high sensitivity, and could be used to predict early metastasis and poor prognosis in HCC, even in AFP-negative cases.
BIOSENSORS & BIOELECTRONICS
(2021)
Article
Chemistry, Analytical
Qingting Li, Shu Zhang, Wei Li, Zhilei Ge, Chunhai Fan, Hongzhou Gu
Summary: By utilizing an intramolecular terminal hybridization strategy, the efficiency of CircLigase in circularizing single-stranded DNA was significantly improved, achieving over 75% yield of byproduct-free monomeric rings and enabling intermolecular strand joining. This strategy also enhanced the preparation, quantity, and quality of DNA topologies using premade DNA rings. These insights may further advance nucleic acid biotechnology and nanotechnology.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Xinyu Du, Xiaoqin Cheng, Wei Li, Zhilei Ge, Chunjiu Zhong, Chunhai Fan, Hongzhou Gu
Summary: The study engineered RNA sensors to quantitatively measure TPP concentrations in whole blood samples, demonstrating the potential for clinical research and providing convenience.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Yang Yang, Zhenyong Wu, Laurie Wang, Kaifeng Zhou, Kai Xia, Qiancheng Xiong, Longfei Liu, Zhao Zhang, Edwin R. Chapman, Yong Xiong, Thomas J. Melia, Erdem Karatekin, Hongzhou Gu, Chenxiang Lin
Summary: A new sorting technique using cholesterol-modified DNA is reported, which can separate liposomes into six to eight homogeneous populations. These uniform and leak-resistant liposomes are ideal for studying how membrane curvature affects membrane protein activities, benefiting research in membrane biology and the development of liposomal drug-delivery systems.
Article
Chemistry, Multidisciplinary
Youli Jia, Liman Chen, Jin Liu, Wei Li, Hongzhou Gu
Summary: This study presents an efficient and cost-effective method for producing large quantities of single-stranded DNA nanostructures using DNA enzymes. By designing self-cleaving deoxyribozymes, the desired DNA structures are successfully amplified and released, providing a convenient approach for mass production.
Article
Biochemistry & Molecular Biology
Canyu Zhang, Qingting Li, Tianbin Xu, Wei Li, Yungang He, Hongzhou Gu
Summary: This study identified two new classes of DNA-hydrolyzing deoxyribozymes by programming a terminal hybridization stem, in addition to the previously reported classes, using the old selection strategy. These new deoxyribozymes can specifically hydrolyze DNA in the presence of Zn2+ and may have potential applications in engineering DNA-responsive DNA hydrolyzers for detecting target ssDNA sequences.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Chemistry, Multidisciplinary
Qingting Li, Zongxuan Tong, Yichun Cao, Hongzhou Gu
Summary: DNA nanotechnology utilizes DNA as a material to assemble nanostructures with precise sizes and geometries, while also harnessing DNA's ability to catalyze chemical reactions, especially in cleaving DNA/RNA. By blending these two types of DNA, the construction dimensions of DNA nanostructures have been expanded, leading to new applications across various fields.
Article
Chemistry, Analytical
Tianbin Xu, Canyu Zhang, Kai Xia, Wei Li, Yichun Cao, Hongzhou Gu
Summary: The discovery of two small DNAs that can specifically bind Ni2+ and discriminate against similar ions opens up a new avenue for biosensing of metal. These DNAs, when engineered into nanosized particles, can act as nanosponges to specifically adsorb Ni2+ from artificial wastewater, showing their potential for high-quality nickel enrichment and detection.
ANALYTICAL CHEMISTRY
(2021)
Review
Pharmacology & Pharmacy
Ayesha Younas, Hongzhou Gu, Yongxing Zhao, Nan Zhang
Summary: The knee joint is susceptible to injuries due to activities, diseases, or accidents. Various drug delivery systems like nanoparticles have been used to treat knee joint injuries by improving function and alleviating symptoms.
INTERNATIONAL JOURNAL OF PHARMACEUTICS
(2021)
Review
Oncology
Lulan Chen, Yue He, Xiangdong Wang, Junbo Ge, Hua Li
Summary: Cardiac voltage-gated ion channels are crucial for maintaining normal heart excitability and contraction. Studying VGICs can help identify new targets for heart disease and drug evaluation.
CLINICAL AND TRANSLATIONAL MEDICINE
(2021)
Article
Chemistry, Multidisciplinary
Jin Liu, Liman Chen, Tingting Zhai, Wei Li, Yuehua Liu, Hongzhou Gu
Summary: The programmability and modifiability of DNA allows scientists to control cholesterol-DNA assembly, expanding the range of molecular interactions and control that can be achieved with DNA.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Qiao Zhang, Kai Xia, Meng Jiang, Qingting Li, Weigang Chen, Mingzhe Han, Wei Li, Rongqin Ke, Fei Wang, Yongxing Zhao, Yuehua Liu, Chunhai Fan, Hongzhou Gu
Summary: This study presents a new method called PECAN (paired-end cutting assisted by DNAzymes), which allows for the mass production of high-quality single-stranded DNA with arbitrary sequences. The method utilizes self-hydrolyzing DNAzymes to generate precursor DNA, which can then be amplified and processed to release large quantities of target DNA. PECAN offers high customizability, purity, and scalability, making it suitable for a wide range of applications.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Nanoscience & Nanotechnology
Xiao Chu, Xinyu Du, Longhua Yang, Ziyi Wang, Yi Zhang, Xiaonan Wang, Lijun Dai, Jiangnan Zhang, Jie Liu, Nan Zhang, Yongxing Zhao, Hongzhou Gu
Summary: Nucleic acid-based aptamers targeting TNFR1 have been identified as potential candidates for treating Rheumatoid Arthritis (RA). These aptamers, obtained through SELEX, can inhibit TNF alpha activity by binding to TNFR1. Enhanced anti-inflammatory effects were achieved using divalent aptamer constructs.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Review
Nanoscience & Nanotechnology
Pengchao Sun, Jingjing Su, Xiaonan Wang, Mo Zhou, Yongxing Zhao, Hongzhou Gu
Summary: This review summarizes the applications of therapeutic RNAs developed through RNA interference (RNAi), nucleic acid aptamers, DNA nanostructures-based drug delivery systems, and nucleic acid vaccines for the treatment and diagnosis of rheumatoid arthritis. The prospects of nucleic acids for rheumatoid arthritis therapy are also intensively discussed.
ACS APPLIED BIO MATERIALS
(2022)
Review
Multidisciplinary Sciences
Qinqin Hu, Zheyan Fang, Junbo Ge, Hua Li
Summary: Nanotechnology has shown great potential in the diagnosis and treatment of coronary artery diseases (CADs), including improving the sensitivity and specificity of biosensors and molecular imaging techniques, and engineering nanomaterials as drug carriers targeting pathological sites. Some nanomaterials can also be regarded as pharmaceuticals for the treatment of atherosclerosis due to their intrinsic characteristics.
