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)
Review
Pharmacology & Pharmacy
Fariba Mollarasouli, Ulya Badilli, Nurgul K. Bakirhan, Sibel A. Ozkan, Yalcin Ozkan
Summary: DNA nanotechnology combines DNA with nanomaterials to fabricate nanoscale devices and structures with potential drug delivery and biosensing applications. The development of DNA nanotechnologies, such as DNA nanomachines, has attracted increasing attention due to their small sizes and high biocompatibility, allowing the creation of hybrid delivery structures.
JOURNAL OF DRUG DELIVERY SCIENCE AND TECHNOLOGY
(2021)
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
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
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
Soumya Sethi, Kumi Hidaka, Hiroshi Sugiyama, Masayuki Endo
Summary: The extracellular matrix provides a dynamic and reversible environment crucial for cellular processes. Mimicking this system with reversible nanoscale cues can help understand cellular processes and manipulate cell function. A photoswitchable DNA mechanical nanostructure was developed to regulate spatial distance between adhesion peptides, leading to significant morphology changes of cells under UV and visible light irradiation.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
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
Aaron Michelson, Honghu Zhang, Shuting Xiang, Oleg Gang
Summary: This study demonstrates a method for creating nanoengineered 3D SiC architectures using DNA-based self-assembly and templating processes, resulting in highly structured and spatially prescribed SiC nanoarchitectures with significant enhancements in electrical conductivity.
Review
Chemistry, Multidisciplinary
Hong-Bo Cheng, Shuchun Zhang, Enying Bai, Xiaoqiao Cao, Jiaqi Wang, Ji Qi, Jun Liu, Jing Zhao, Liqun Zhang, Juyoung Yoon
Summary: Diarylethene (DAE) photoswitch, as a smart trigger, has shown superior performance in stimulus-responsive materials. The introduction of DAE into an assembly system has been an attractive strategy, enabling the manifestation of photochromic behavior at the system level, promoting the design and manufacture of advanced materials.
ADVANCED MATERIALS
(2022)
Review
Chemistry, Multidisciplinary
Anurag Mukherjee, Maximilian D. Seyfried, Bart Jan Ravoo
Summary: Aromatic units tethered with an azo functionality are molecular photoswitches that can reversibly transform between E- and Z-isomers in response to light. These photoswitches have been widely used in the preparation of dynamic self-assembled materials, optoelectronic devices, and responsive biomaterials. Recently, azoheteroarenes and cyclic azobenzenes have emerged as second generation molecular photoswitches with distinct photoswitching behavior and responsive properties, making them promising candidates for various applications. This minireview introduces the structural refinement and photoresponsive properties of azoheteroarenes and cyclic azobenzenes, and summarizes their applications in supramolecular assembly, material science, and photopharmacology.
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
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
Biochemistry & Molecular Biology
Yuan Liu, Jiaxin Wang, Lijun Sun, Bin Wang, Qiang Zhang, Xiaokang Zhang, Ben Cao
Summary: With the advancement of nanotechnology, DNA molecules have evolved from being solely carriers of genetic information to versatile materials with great potential in drug delivery and disease diagnosis. In this study, ladder-shaped drug carriers based on DNA nanoladders were developed. By incorporating nicks into each rung, the nanoladder structure was designed to counteract stability issues and provide drug loading sites. Experimental results showed that the designed drug-carrying function was feasible, demonstrating the potential application of this novel design approach in various fields such as bioimaging, biosensing, and targeted therapy.
Article
Biochemistry & Molecular Biology
Kaixuan Zhou, Zhichao Mei, Yunxiang Lei, Zhen Guan, Chengde Mao, Yulin Li
Summary: By substituting divalent magnesium ions with monovalent sodium ions, the researchers achieved high-yield assembly of DNA polyhedra. This method allows for at least 10 times higher concentration of DNA compared to previous reports, and it also overcomes the obstacle of large-scale production of DNA nanostructures.
Article
Biochemistry & Molecular Biology
Kamaludin Dingle, Fatme Ghaddar, Petr Sulc, Ard A. Louis
Summary: Developmental bias is the primary explanation for the occupation of the RNA secondary structure morphospace, with only the most frequent structures appearing in nature and a small number of random sequences needed to produce all observed RNA secondary structures. These patterns are accurately predicted by the likelihood of structures appearing upon a uniform random sampling of sequences.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Physics, Condensed Matter
John Russo, Flavio Romano, Lukas Kroc, Francesco Sciortino, Lorenzo Rovigatti, Petr Sulc
Summary: This study proposes a general framework for solving inverse self-assembly problems and successfully demonstrates the design and numerical simulation of a specific cubic diamond structure. The approach uses patchy particles as building blocks and transforms the problem into a Boolean satisfiability problem to determine the interaction rules between patches.
JOURNAL OF PHYSICS-CONDENSED MATTER
(2022)
Article
Biochemistry & Molecular Biology
Erik Poppleton, Aatmik Mallya, Swarup Dey, Joel Joseph, Petr Sulc
Summary: The database is an online resource for nucleic acid nanostructures, providing an upload interface, searching and database browsing capabilities. It includes conversion tools to encourage design file conversion, aiming to facilitate sharing and reuse of designs in the DNA/RNA nanotechnology community.
NUCLEIC ACIDS RESEARCH
(2022)
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
Chemistry, Medicinal
Zhengyue Zhang, Jiri Sponer, Giovanni Bussi, Vojtech Mlynsky, Petr Sulc, Chad R. Simmons, Nicholas Stephanopoulos, Miroslav Krepl
Summary: HJ is a crucial DNA structure involved in DNA repair, recombination, and DNA nanotechnology. Molecular dynamics simulations revealed complex conformational transitions of HJs, including previously unconsidered half-closed intermediates. This study provides detailed insights into the rearrangement process of HJs and opens up possibilities for more accurate computational studies of biological processes and nanomaterials involving HJs.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Camilla Beneduce, Diogo E. P. Pinto, Petr Sulc, Francesco Sciortino, John Russo
Summary: This study investigates the nucleation process of a binary mixture of patchy particles designed to nucleate into a diamond lattice. By combining Gibbs-ensemble simulations and direct nucleation simulations, the role of the liquid-gas metastable phase diagram on the nucleation process is revealed. The strongest enhancement of crystallization is found to occur at an azeotropic point with the same stoichiometric composition of the crystal.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Yue Tang, Hao Liu, Qi Wang, Xiaodong Qi, Lu Yu, Petr Sulc, Fei Zhang, Hao Yan, Shuoxing Jiang
Summary: Moleculartessellation research aims to understand intricate patterns in nature and leverage them to create precise structures. This study presents a general method for constructing DNA origami tiles that form precise tessellation patterns. The study demonstrates the applicability of the method with various tile designs and tessellation patterns, opening up new opportunities for applications in metamaterial engineering, nanoelectronics, and nanolithography.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Multidisciplinary Sciences
Diogo E. P. Pinto, Petr Sulc, Francesco Sciortino, John Russo
Summary: The control over self-assembly of complex structures, particularly at the colloidal scale, has been a significant challenge in material science. The formation of amorphous aggregates often disrupts the desired assembly pathway. In this study, we investigate the self-assembly problem of three Archimedean shells using patchy particles as model building blocks. By recasting the assembly problem as a Boolean satisfiability problem, we find effective designs and selectively suppress unwanted structures.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Nanoscience & Nanotechnology
Mathias Centola, Erik Poppleton, Sujay Ray, Martin Centola, Robb Welty, Julian Valero, Nils G. Walter, Petr Sulc, Michael Famulok
Summary: Molecular engineering aims to design nanoassemblies for complex tasks, but efficient chemical-fuel-driven nanoscale driver-follower systems have not been realized. In this study, a DNA nanomachine driven by the chemical energy of DNA-templated RNA-transcription-consuming nucleoside triphosphates was developed, generating rhythmic pulsating motion and successfully coupling with a passive follower.
NATURE NANOTECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Yen-Yu Hsu, Samuel J. J. Chen, Julio Bernal-Chanchavac, Bineet Sharma, Hossein Moghimianavval, Nicholas Stephanopoulos, Allen P. P. Liu
Summary: In this study, a calcium-triggered DNA-mediated membrane fusion strategy was developed, where fusion was regulated by surface-bound PEG chains that can be cleaved by the calcium-activated protease calpain-1.
CHEMICAL COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Chad R. Simmons, Alex Buchberger, Skylar J. W. Henry, Alexandra Novacek, Nour Eddine Fahmi, Tara Macculloch, Nicholas Stephanopoulos, Hao Yan
Summary: This study positions a variety of binding molecules in rationally designed and self-assembling DNA crystals and solves their structures via X-ray crystallography, providing insights into the design principles for the spatial arrangement of functional guests within lattices. It opens up new potential opportunities for the use of DNA crystals to display and structurally characterize small molecules, peptides, and ultimately proteins of unknown structure.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Lorenzo Rovigatti, John Russo, Flavio Romano, Michael Matthies, Lukas Kroc, Petr Sulc
Summary: In this study, we address the problems faced during the self-assembly of colloidal diamond crystals by using the SAT-assembly design framework. We demonstrate that the assembly of CD crystals only requires a binary mixture, and we test a promising DNA nanotechnology design using molecular dynamics simulations.
Article
Nanoscience & Nanotechnology
Alex Buchberger, Kyle Riker, Julio Bernal-Chanchavac, Raghu Pradeep Narayanan, Chad R. Simmons, Nour Eddine Fahmi, Ronit Freeman, Nicholas Stephanopoulos
Summary: The integration of bioactive fibronectin domain proteins with DNA nanostructures was achieved using genetic fusion and assembly techniques, resulting in the formation of nanofiber arrays with enhanced bioactivity.
ACS APPLIED BIO MATERIALS
(2022)
Article
Chemistry, Multidisciplinary
Tara MacCulloch, Alexandra Novacek, Nicholas Stephanopoulos
Summary: We have developed a proximity-enhanced method for synthesizing a peptide with two different oligonucleotide handles. This method involves sequential bioorthogonal reactions and partial hybridization of the second handle to the first. Using this approach, we were able to synthesize a protease-responsive DNA latch and a cyclic bioactive peptide.
CHEMICAL COMMUNICATIONS
(2022)
