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Zhang Z, Jin J, Paluzzi VE, Jin Z, Wen Y, Huang CZ, Li CM, Mao C, Zuo H. AMP Aptamer Programs DNA Tile Cohesion without Canonical Base Pairing. J Am Chem Soc 2023; 145:19503-19507. [PMID: 37638713 DOI: 10.1021/jacs.3c06260] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Tile-based DNA self-assembly provides a versatile approach for the construction of a wide range of nanostructures for various applications such as nanomedicine and advanced materials. The inter-tile interactions are primarily programmed by base pairing, particularly Watson-Crick base pairing. To further expand the tool box for DNA nanotechnology, herein, we have designed DNA tiles that contain both ligands and aptamers. Upon ligand-aptamer binding, tiles associate into geometrically well-defined nanostructures. This strategy has been demonstrated by the assembly of a series of DNA nanostructures, which have been thoroughly characterized by gel electrophoresis and atomic force microscopy. This new inter-tile cohesion could bring new potentials to DNA self-assembly in the future. For example, the addition of free ligand could modulate the nanostructure formation. In the case of biological ligands, DNA self-assembly could be related to the presence of certain ligands.
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Affiliation(s)
- Zhe Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Jin Jin
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Victoria E Paluzzi
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zhuoer Jin
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Yuandong Wen
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | | | - Chun Mei Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Chengde Mao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Hua Zuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
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Zhang C, Paluzzi VE, Sha R, Jonoska N, Mao C. Implementing Logic Gates by DNA Crystal Engineering. Adv Mater 2023; 35:e2302345. [PMID: 37220213 DOI: 10.1002/adma.202302345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/03/2023] [Indexed: 05/25/2023]
Abstract
DNA self-assembly computation is attractive for its potential to perform massively parallel information processing at the molecular level while at the same time maintaining its natural biocompatibility. It has been extensively studied at the individual molecule level, but not as much as ensembles in 3D. Here, the feasibility of implementing logic gates, the basic computation operations, in large ensembles: macroscopic, engineered 3D DNA crystals is demonstrated. The building blocks are the recently developed DNA double crossover-like (DXL) motifs. They can associate with each other via sticky-end cohesion. Common logic gates are realized by encoding the inputs within the sticky ends of the motifs. The outputs are demonstrated through the formation of macroscopic crystals that can be easily observed. This study points to a new direction of construction of complex 3D crystal architectures and DNA-based biosensors with easy readouts.
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Affiliation(s)
- Cuizheng Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Victoria E Paluzzi
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Ruojie Sha
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Natasha Jonoska
- Department of Mathematics and Statistics, University of South Florida, Tampa, FL, 33620, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
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Paluzzi VE, Zhang C, Mao C. Near-Quantitative Preparation of Short Single-Stranded DNA Circles. Angew Chem Int Ed Engl 2023; 62:e202218443. [PMID: 36652628 DOI: 10.1002/anie.202218443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/19/2023]
Abstract
Small, single-stranded DNA (ssDNA) circles have many applications, such as templating rolling circle amplification (RCA), capturing microRNAs, and scaffolding DNA nanostructures. However, it is challenging to prepare such ssDNA circles, particularly when the DNA size becomes very small (e.g. a 20 nucleotide (nt) long ssDNA circle). Often, such short ssDNA dominantly form concatemers (either linear or circular) due to intermolecular ligation, instead of forming monomeric ssDNA circles by intramolecular ligation. Herein, a simple method to overcome this problem by designing the complementary linker molecules is reported. It is demonstrated that ssDNA, as short as 16 nts, can be enzymatically ligated (by the commonly used T4 DNA ligase) into monomeric ssDNA circles at high concentration (100 μM) with high yield (97 %). This method does not require any special sequence, thus, it is expected to be generally applicable. The experimental protocol is identical to regular DNA ligation, thus, is expected to be user friendly for general chemists and biologists.
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Affiliation(s)
- Victoria E Paluzzi
- Purdue University, Department of Chemistry, West Lafayette, IN-47907, USA
| | - Cuizheng Zhang
- Purdue University, Department of Chemistry, West Lafayette, IN-47907, USA
| | - Chengde Mao
- Purdue University, Department of Chemistry, West Lafayette, IN-47907, USA
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Mao D, Paluzzi VE, Zhang C, Mao C. DNA conformational equilibrium enables continuous changing of curvatures. Nanoscale 2023; 15:470-475. [PMID: 36515101 DOI: 10.1039/d2nr05404c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Assembly of complex structures from a small set of tiles is a common theme in biology. For example, many copies of identical proteins make up polyhedron-shaped, viral capsids and tubulin can make long microtubules. This inspired the development of tile-based DNA self-assembly for nanoconstruction, particularly for structures with high symmetries. In the final structure, each type of motif will adopt the same conformation, either rigid or with defined flexibility. For structures that have no symmetry, their assembly remains a challenge from a small set of tiles. To meet this challenge, algorithmic self-assembly has been explored driven by computational science, but it is not clear how to implement this approach to one-dimensional (1D) structures. Here, we have demonstrated that a constant shift of a conformational equilibrium could allow 1D structures to evolve. As shown by atomic force microscopy imaging, one type of DNA tile successfully assembled into DNA spirals and concentric circles, which became less and less curved from the structure's center outward. This work points to a new direction for tile-based DNA assembly.
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Affiliation(s)
- Dake Mao
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA.
| | - Victoria E Paluzzi
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA.
| | - Cuizheng Zhang
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA.
| | - Chengde Mao
- Purdue University, Department of Chemistry, West Lafayette, IN 47907, USA.
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Zhang C, Paluzzi VE, Mao C. Tomography of DNA tiles influences the kinetics of surface-mediated DNA self-assembly. Biophys J 2022; 121:4909-4914. [PMID: 35923101 PMCID: PMC9808542 DOI: 10.1016/j.bpj.2022.07.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/28/2022] [Accepted: 07/19/2022] [Indexed: 01/07/2023] Open
Abstract
This manuscript studies the impact of extruding hairpins on two-dimensional self-assembly of DNA tiles on solid surface. Hairpins are commonly used as tomographic markers in DNA nanostructures for atomic force microscopy imaging. In this study, we have discovered that hairpins play a more active role. They modulate the adsorption of the DNA tiles onto the solid surface, thus changing the tile assembly kinetics on the solid surface. Based on this discovery, we were able to promote or slow down DNA self-assembly on the surface by changing the hairpin locations on the DNA tiles. This knowledge gained will be helpful for the future design of DNA self-assembly on surface.
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Affiliation(s)
- Cuizheng Zhang
- Department of Chemistry, Purdue University, West Lafayette, Indiana
| | | | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, Indiana.
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Zheng M, Li Z, Liu L, Li M, Paluzzi VE, Hyun Choi J, Mao C. Kinetic DNA Self-Assembly: Simultaneously Co-folding Complementary DNA Strands into Identical Nanostructures. J Am Chem Soc 2021; 143:20363-20367. [PMID: 34808053 DOI: 10.1021/jacs.1c09925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA origami is a powerful method for constructing DNA nanostructures. It requires long single-stranded DNAs. The preparation of such long DNA strands is often quite tedious and has a limited production yield. In contrast, duplex DNAs can be easily prepared via enzymatic reactions in large quantities. Thus, we ask a question: can we design DNA nanostructures in such a way that the two complementary strands can simultaneously fold into the designed structures in the same solution instead of hybridizing with each other to form a DNA duplex? By engineering DNA interaction kinetics, herein we are able to provide multiple examples to concretely demonstrate a positive answer to this question. The resulting DNA nanostructures have been thoroughly characterized by electrophoresis and atomic force microscopy imaging. The reported strategy is compatible with the DNA cloning method and thus would provide a convenient method for the large-scale production of the designed DNA nanostructures.
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Zheng M, Li Q, Li Q, Paluzzi VE, Choi JH, Mao C. Engineering the Nanoscaled Morphologies of Linear DNA Homopolymers. Macromol Rapid Commun 2021; 42:e2100217. [PMID: 34173292 DOI: 10.1002/marc.202100217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/24/2021] [Indexed: 12/26/2022]
Abstract
Supramolecular polymers have unique characteristics such as self-healing and easy processing. However, the scope of their structures is limited to mostly either flexible, random coils or rigid, straight chains. By broadening this scope, novel properties, functions, and applications can be explored. Here, DNA is used as a model system to engineer innovative, nanoscaled morphologies of supramolecular polymers. Each polymer chain consists of multiple copies of the same short (38-46 nucleotides long) DNA strand. The component DNA strands first dimerize into homo-dimers, which then further assemble into long polymer chains. By subtly tuning the design, a range of polymer morphologies are obtained; including straight chains, spirals, and closed rings with finite sizes. Such structures are confirmed by AFM imaging and predicted by molecular coarse simulation.
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Affiliation(s)
- Mengxi Zheng
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Qian Li
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.,College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Qian Li
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Victoria E Paluzzi
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Jong Hyun Choi
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
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