1
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Feng F, Zhang L, Zheng P, Xiao SJ. Construction of DNA Bilayer Tiles and Arrays Using Circular DNA Molecules as Scaffolds. Chembiochem 2023; 24:e202300420. [PMID: 37464981 DOI: 10.1002/cbic.202300420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 07/20/2023]
Abstract
Using oligonucleotides to weave 2D tiles such as double crossovers (DX) and multi-arm junction (mAJ) tiles and arrays is well-known, but weaving 3D tiles is rare. Here, we report the construction of two new bilayer tiles in high yield using small circular 84mer oligonucleotides as scaffolds. Further, we designed five E-tiling approaches to construct porous nanotubes of microns long in medium yield via solution assembly and densely covered planar microscale arrays via surface-mediated assembly.
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Affiliation(s)
- Feiyang Feng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Ling Zhang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
| | - Shou-Jun Xiao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China
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2
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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] [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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3
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Zhu L, Luo J, Ren K. Nucleic acid-based artificial nanocarriers for gene therapy. J Mater Chem B 2023; 11:261-279. [PMID: 36524395 DOI: 10.1039/d2tb01179d] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleic acid nanotechnology is a powerful tool in the fields of biosensing and nanomedicine owing to their high editability and easy synthesis and modification. Artificial nucleic acid nanostructures have become an emerging research hotspot as gene carriers with low cytotoxicity and immunogenicity for therapeutic approaches. In this review, recent progress in the design and functional mechanisms of nucleic acid-based artificial nano-vectors especially for exogenous siRNA and antisense oligonucleotide delivery is summarized. Different types of DNA nanocarriers, including DNA junctions, tetrahedrons, origami, hydrogels and scaffolds, are introduced. The enhanced targeting strategies to improve the delivery efficacy are demonstrated. Furthermore, RNA based gene nanocarrier systems by self-assembly of short strands, rolling circle transcription, chemical crosslinking and using RNA motifs and DNA-RNA hybrids are demonstrated. Finally, the outlook and potential challenges are highlighted. The nucleic acid-based artificial nanocarriers offer a promising and precise tool for gene delivery and therapy.
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Affiliation(s)
- Longyi Zhu
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
| | - Jun Luo
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
| | - Kewei Ren
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
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4
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Dong N, Sun Y, Sun G, Zhang L, Sun S. Chiral DNA Nanotubes Self-Assembled from Building Blocks with Tailorable Curvature and Twist. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2204996. [PMID: 36287092 DOI: 10.1002/smll.202204996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/04/2022] [Indexed: 06/16/2023]
Abstract
DNA nanotubes with prescribed geometry could allow for nanomaterial organization with designed optical or electrical function. As one of the dominating driving forces for DNA nanotube assembly, intrinsic curvature and twist of building blocks can be induced by bending deformation and twisting deformation. However, it is still unknown that how bending and twisting design on nanoscale building blocks affects the geometry of DNA tubes with micrometer length. Here, through targeted base pair deletion or insertion, the amount of bending deformation in building blocks is modulated by length gradient and the amount of twisting deformation is modulated by average twist density. This work systematically explores the independent effect and synergistic effect of two types of deformation on tube geometry, including diameter, chirality, and helical angles, via a streptavidin-labeling technique. The design rules enable the construction of DNA nanotubes with prescribed chirality and tailored diameters.
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Affiliation(s)
- Niuniu Dong
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China
| | - Yishan Sun
- School of Clinical Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China
| | - Geng Sun
- The College of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Sha Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China
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5
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Zhang W, Jiang C, Guo X, Muhammad Faran Ashraf Baig M, Ni C, Xiao SJ. 2D DNA lattices assembled from DX-coupled tiles. J Colloid Interface Sci 2022; 616:499-508. [DOI: 10.1016/j.jcis.2022.02.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/27/2022] [Accepted: 02/09/2022] [Indexed: 10/19/2022]
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6
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Chen YR, Sun S, Yin H, Wang W, Liu R, Xu H, Yang Y, Wu ZS. Tumor-targeting [2]catenane-based grid-patterned periodic DNA monolayer array for in vivo theranostic application. J Mater Chem B 2022; 10:1969-1979. [PMID: 35014661 DOI: 10.1039/d1tb01978c] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
DNA nanotechnology is often used to build various nano-structures for signaling and/or drug delivery, but it essentially suffers from several major limitations, such as a large number of DNA strands and limited targeting ligands. Moreover, there is no report on in vivo two-dimensional DNA arrays because of various technical challenges. By cross-catenating two palindromic DNA rings, herein, we demonstrate a catenane-based grid-patterned periodic DNA monolayer array ([2]GDA) capable of preferentially accumulating in tumor tissues without any targeting ligands, with a thickness equal to the double-helical DNA monolayer (nearly 2 nm). The structural flexibility of [2]GDA enabled it to fold into a spherical object in solution, favoring cellular uptake. Thus, its cellular internalization activity was comparable with that of the commercial lipofectamine 3000. Moreover, [2]GDA retained the structural integrity over 24 h incubation in biological solutions, achieving a 360-fold improvement in in vivo stability. Significantly, anticancer drug-loaded [2]GDA exhibits desirable therapeutic efficacy in tumor-bearing animals without detectable side effects.
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Affiliation(s)
- Yan-Ru Chen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Shujuan Sun
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Hongwei Yin
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Weijun Wang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Ran Liu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Huo Xu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Ya Yang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 305108, China
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7
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Sui Z, An R, Komiyama M, Liang X. Stepwise Strategy for One-Pot Synthesis of Single-Stranded DNA Rings from Multiple Short Fragments. Chembiochem 2020; 22:1005-1011. [PMID: 33124728 DOI: 10.1002/cbic.202000738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Indexed: 12/24/2022]
Abstract
Cyclic rings of single-stranded (ss) DNA have various unique properties, but wider applications have been hampered by their poor availability. This paper reports a convenient one-pot method in which these rings are efficiently synthesized by using T4 DNA ligase through convergent cyclization of easily available short DNA fragments. The key to the present method is to separate all the splint oligonucleotides into several sets, and add each set sequentially at an appropriate interval to the solutions containing all the short DNA fragments. Compared with simple one-pot strategies involving simultaneous addition of all the splints at the beginning of the reaction, both the selectivity and the yields of target ssDNA rings are greatly improved. This convergent method is especially useful for preparing large-sized rings that are otherwise hard to obtain. By starting from six short DNA fragments (71-82 nt), prepared by a DNA synthesizer, a ssDNA ring of 452-nt size was synthesized in 35 mol % yield and in high selectivity. Satisfactorily pure DNA rings were obtainable simply by treating the crude products with exonuclease.
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Affiliation(s)
- Zhe Sui
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China
| | - Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, P. R. China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, P. R. China
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8
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Baig MMFA, Lai WF, Akhtar MF, Saleem A, Mikrani R, Farooq MA, Ahmed SA, Tahir A, Naveed M, Abbas M, Ansari MT. Targeting folate receptors (α1) to internalize the bleomycin loaded DNA-nanotubes into prostate cancer xenograft CWR22R cells. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113785] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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9
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Dong Y, Yao C, Zhu Y, Yang L, Luo D, Yang D. DNA Functional Materials Assembled from Branched DNA: Design, Synthesis, and Applications. Chem Rev 2020; 120:9420-9481. [DOI: 10.1021/acs.chemrev.0c00294] [Citation(s) in RCA: 168] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Yuhang Dong
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Chi Yao
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Yi Zhu
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Lu Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Dan Luo
- Department of Biological & Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
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10
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DNA nanotechnology as a tool to develop molecular tension probes for bio-sensing and bio-imaging applications: An up-to-date review. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.nanoso.2020.100523] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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11
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Wang Y, Guo X, Kou B, Zhang L, Xiao SJ. Small Circular DNA Molecules as Triangular Scaffolds for the Growth of 3D Single Crystals. Biomolecules 2020; 10:biom10060814. [PMID: 32466440 PMCID: PMC7355631 DOI: 10.3390/biom10060814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/14/2020] [Accepted: 05/22/2020] [Indexed: 12/30/2022] Open
Abstract
DNA is a very useful molecule for the programmed self-assembly of 3D (three dimension) nanoscale structures. The organised 3D DNA assemblies and crystals enable scientists to conduct studies for many applications such as enzymatic catalysis, biological immune analysis and photoactivity. The first self-assembled 3D DNA single crystal was reported by Seeman and his colleagues, based on a rigid triangle tile with the tile side length of two turns. Till today, successful designs of 3D single crystals by means of programmed self-assembly are countable, and still remain as the most challenging task in DNA nanotechnology, due to the highly constrained conditions for rigid tiles and precise packing. We reported here the use of small circular DNA molecules instead of linear ones as the core triangle scaffold to grow 3D single crystals. Several crystallisation parameters were screened, DNA concentration, incubation time, water-vapour exchange speed, and pH of the sampling buffer. Several kinds of DNA single crystals with different morphologies were achieved in macroscale. The crystals can provide internal porosities for hosting guest molecules of Cy3 and Cy5 labelled triplex-forming oligonucleotides (TFOs). Success of small circular DNA molecules in self-assembling 3D single crystals encourages their use in DNA nanotechnology regarding the advantage of rigidity, stability, and flexibility of circular tiles.
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Affiliation(s)
- Yu Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China; (Y.W.); (X.G.); (L.Z.)
| | - Xin Guo
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China; (Y.W.); (X.G.); (L.Z.)
| | - Bo Kou
- School of Materials Science and Engineering, Nanjing Institute of Technology, Nanjing 211167, China;
| | - Ling Zhang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China; (Y.W.); (X.G.); (L.Z.)
| | - Shou-Jun Xiao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China; (Y.W.); (X.G.); (L.Z.)
- Correspondence:
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12
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Gubu A, Wang J, Jin H, Tang X. Synthesis and "DNA Interlocks" Formation of Small Circular Oligodeoxynucleotides. ACS APPLIED MATERIALS & INTERFACES 2020; 12:12584-12590. [PMID: 32100989 DOI: 10.1021/acsami.0c00923] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Circular oligodeoxynucleotides (c-ODNs) have their particular characteristics in topological properties. However, different from oligoribonucleotides, enzymatic synthesis of small c-ODNs is still challenging using conventional methods. Herein, we successfully achieved highly efficient cyclization of linear single-stranded ODNs using T4 DNA ligase simply through the frozen/lyophilization/cyclization (FLC) method. We successfully shortened the cyclization length of linear ODNs to 20 nt (l-ODN 20) with up to 63% yield, which was never achieved before through normal enzymatic methods. With the efficient FLC method, we further developed "DNA interlocks" which were intercross-linked with multiple c-ODNs using the one-pot FLC method. This FLC strategy provides a powerful, cheap, and convenient method to synthesize small c-ODNs for studying DNA nanotechnology and paves the way to achieve future deciphering of c-ODN functions.
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Affiliation(s)
- Amu Gubu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing 100191, China
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing 100191, China
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing 100191, China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38 Xueyuan Road, Beijing 100191, China
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13
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Abbas M, Baig MMFA, Zhang Y, Yang YS, Wu S, Hu Y, Wang ZC, Zhu HL. A DNA-based nanocarrier for efficient cancer therapy. J Pharm Anal 2020; 11:330-339. [PMID: 34277121 PMCID: PMC8264464 DOI: 10.1016/j.jpha.2020.03.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 03/02/2020] [Accepted: 03/05/2020] [Indexed: 02/08/2023] Open
Abstract
The study aimed to achieve enhanced targeted cytotoxicity and cell-internalization of cisplatin-loaded deoxyribonucleic acid-nanothread (CPT-DNA-NT), mediated by scavenger receptors into HeLa cells. DNA-NT was developed with stiff-topology utilizing circular-scaffold to encapsulate CPT. Atomic force microscopy (AFM) characterization of the DNA-NT showed uniformity in the structure with a diameter of 50-150 nm and length of 300-600 nm. The successful fabrication of the DNA-NT was confirmed through native-polyacrylamide gel electrophoresis analysis, as large the molecular-weight (polymeric) DNA-NT did not split into constituting strands under applied current and voltage. The results of cell viability confirmed that blank DNA-NT had the least cytotoxicity at the highest concentration (512 nM) with a viability of 92% as evidence of its biocompatibility for drug delivery. MTT assay showed superior cytotoxicity of CPT-DNA-NT than that of the free CPT due to the depot release of CPT after DNA-NT internalization. The DNA-NT exhibited targeted cell internalizations with the controlled intracellular release of CPT (from DNA-NT), as illustrated in confocal images. Therefore, in vitro cytotoxicity assessment through flow cytometry showed enhanced apoptosis (72.7%) with CPT-DNA-NT (compared to free CPT; 64.4%). CPT-DNA-NT, being poly-anionic, showed enhanced endocytosis via scavenger receptors.
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Affiliation(s)
- Muhammad Abbas
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, PR China
| | - Mirza Muhammad Faran Ashraf Baig
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, PR China
| | - Yaliang Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, PR China
| | - Yu-Shun Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, PR China
| | - Songyu Wu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, PR China
| | - Yiqiao Hu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, PR China.,Institute of Drug Research and Development, Medical School of Nanjing University, Nanjing, 210093, PR China
| | - Zhong-Chang Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, PR China
| | - Hai-Liang Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210023, PR China
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14
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Baig MMFA, Lai WF, Mikrani R, Jabeen M, Naveed M, Abbas M, Farooq MA, Ahsan A, Kassim SA, Khan GJ, Ansari MT. Synthetic NRG-1 functionalized DNA nanospindels towards HER2/neu targets for in vitro anti-cancer activity assessment against breast cancer MCF-7 cells. J Pharm Biomed Anal 2020; 182:113133. [PMID: 32004770 DOI: 10.1016/j.jpba.2020.113133] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 01/14/2020] [Accepted: 01/24/2020] [Indexed: 02/08/2023]
Abstract
DNA based nano-carriers synthesized from short circular scaffolds (circular DNA nanotechnology) attains stiffer topology for ligand functionalization (neuregulin-1/NRG-1 ligand) and biological applications (targeted drug delivery). Daunorubicin (DR) is a hydrophobic chemical that requires robust vectors to efficiently encapsulate and avoid its free dispersion in water, biological media and cell culture. Here we design DNA nanospindels (DNA-NS) to efficiently load DR and target the (highly expressed) HER2/neu receptors on the plasma membrane of drug-resistant MCF-7 (breast cancer) cells. DNA-NS were synthesized by polymerizing the DNA-triangles (utilizing 84-nt short circular scaffold strand) into larger DNA nano-ribbons characterized by the native-PAGE testing. AFM results revealed the spinning of DNA nanoribbons on its (own) axis because of the intrinsic curvature of the DNA double helix resulting in the formation of the firm and twisted DNA-NS with the diameter (50-70 nm) and length (0.5-4 μm). DA loading onto DNA-NS was confirmed by the UV shift analysis. The MTT results with the blank DNA-NS evidenced its biocompatibility (remained value of 93%) compared to the decreased viability of the MCF-7 cells after treatment with DNA-NS (DR loaded). These findings were further supported by the analysis of cell proliferation/apoptosis through flow cytometry showing 64% apoptosis after treating with the DR loaded DNA-NS. Hence, through the short circular DNA nanotechnology, we have achieved a stiffer, uniform, and biocompatible DNA-NS for applications in the targeted therapy.
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Affiliation(s)
- Mirza Muhammad Faran Ashraf Baig
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, PR China; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Bahauddin Zakariya University, Multan 60000, Pakistan.
| | - Wing-Fu Lai
- Department of Applied Biology and Chemical Technology, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, PR China; School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, PR China
| | - Reyaj Mikrani
- Department of Pharmaceutics, Basic medicine, and Clinical Pharmacy, School of Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 211198, PR China
| | - Mehreen Jabeen
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Bahauddin Zakariya University, Multan 60000, Pakistan
| | - Muhammad Naveed
- School of Pharmacy, Nanjing Medical University, Jiangsu Province, Nanjing 211166, PR China
| | - Muhammad Abbas
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Muhammad Asim Farooq
- Department of Pharmaceutics, Basic medicine, and Clinical Pharmacy, School of Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu 211198, PR China
| | - Anam Ahsan
- College of Animal Science & Veterinary Medicine, Shanxi Agricultural University, Taigu, PR China
| | - Said Abasse Kassim
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, PR China
| | - Ghulam Jilany Khan
- Faculty of Pharmacy, University of Central Punjab, Lahore, 54570, Pakistan
| | - Muhammad Tayyab Ansari
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Bahauddin Zakariya University, Multan 60000, Pakistan
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15
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Zhang Y, Chen X, Kang G, Peng R, Pan V, Sundaresan R, Wang P, Ke Y. Programming DNA Tube Circumference by Tile Offset Connection. J Am Chem Soc 2019; 141:19529-19532. [PMID: 31793775 DOI: 10.1021/jacs.9b08921] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
DNA tubes with prescribed circumferences are appealing for numerous multidisciplinary applications. The DNA single-stranded tiles (SSTs) assembly method has demonstrated an unprecedented capability for programming the circumferences of DNA tubes in a modular fashion. Nevertheless, a distinct set of SSTs is typically required to assemble DNA tube of a specific circumference, with wider tubes requiring higher numbers of tiles of unique sequences, which not only increases the expense and design complexity but also hampers the assembly yield. Herein, we introduce "offset connection" to circumvent such challenges in conventional SST tube assembly. In this new connection scheme, the boundary SST tiles in an SST array are designed to connect in an offset manner. To compensate for the offset, the SST array has to grow wider until the array can close to form a wide tube with a tolerable degree of twist. Using this strategy, we have successfully assembled DNA tubes with prescribed circumferences consisting of 8, 12, 14, 16, 20, 24, 28, 32, 36, 42, 56, or 70 helices from two distinct sets of SSTs composed of 19×4 or 19×14 tiles.
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Affiliation(s)
- Yingwei Zhang
- State Key Laboratory of Chemical Resource Engineering, College of Materials Science and Engineering , Beijing University of Chemical Technology , Beijing 100082 , China
| | - Xianhui Chen
- State Key Laboratory of Chemical Resource Engineering, College of Materials Science and Engineering , Beijing University of Chemical Technology , Beijing 100082 , China
| | - Guangjie Kang
- State Key Laboratory of Chemical Resource Engineering, College of Materials Science and Engineering , Beijing University of Chemical Technology , Beijing 100082 , China
| | - Ruizi Peng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China.,Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory University , Atlanta , Georgia 30322 , United States
| | - Victor Pan
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory University , Atlanta , Georgia 30322 , United States
| | - Ranjani Sundaresan
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory University , Atlanta , Georgia 30322 , United States
| | - Pengfei Wang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine , Shanghai Jiao Tong University , Shanghai 200127 , China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering , Georgia Institute of Technology and Emory University , Atlanta , Georgia 30322 , United States.,Department of Chemistry , Emory University , Atlanta , Georgia 30322 , United States
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16
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Sun S, Yang Y, Li D, Zhu J. Large Chiral Nanotubes Self-Assembled by DNA Bricks. J Am Chem Soc 2019; 141:19524-19528. [PMID: 31789023 DOI: 10.1021/jacs.9b08737] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Synthesizing tubes of large diameters is important for materials science and nanotechnology but remains a largely unsolved challenge. We report herein an approach to program the width of DNA helical tubes by controlling the rigidity and curvature of repeating units via single-stranded bricks strategy. The rigidity of repeating units can be controlled by its thickness, and the curvature can be tuned by double-helical twist density. A single-step annealing allows for the fabrication of helical tubes with defined chirality and widths ranging from ∼50 to ∼550 nm.
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Affiliation(s)
- Sha Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences , Xi'an Jiaotong University Health Science Center , Xi'an 710061 , China
| | - Yuxuan Yang
- Department of Clinical Medicine , Xi'an Jiaotong University Health Science Center , Xi'an 710061 , China
| | - Dongmin Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences , Xi'an Jiaotong University Health Science Center , Xi'an 710061 , China
| | - Jin Zhu
- Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, State Key Laboratory of Coordination Chemistry , Nanjing University , Nanjing 210023 , China
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17
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Liu X, Zhao Y, Liu P, Wang L, Lin J, Fan C. Biomimetische DNA‐Nanoröhren: Gezielte Synthese und Anwendung nanoskopischer Kanäle. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201807779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Xiaoguo Liu
- School of Chemistry and Chemical Engineering, and Institute of Molecular MedicineRenji HospitalSchool of MedicineShanghai Jiao Tong University Shanghai 201240 China
- Division of Physical Biology & Bioimaging CenterShanghai Synchrotron Radiation FacilityCAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
| | - Yan Zhao
- Division of Physical Biology & Bioimaging CenterShanghai Synchrotron Radiation FacilityCAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
| | - Pi Liu
- State Key Laboratory of Medicinal Chemical BiologyCollege of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University Tianjin 300353 China
- Biodesign CenterTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging CenterShanghai Synchrotron Radiation FacilityCAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical BiologyCollege of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University Tianjin 300353 China
- Biodesign CenterTianjin Institute of Industrial BiotechnologyChinese Academy of Sciences Tianjin 300308 China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular MedicineRenji HospitalSchool of MedicineShanghai Jiao Tong University Shanghai 201240 China
- Division of Physical Biology & Bioimaging CenterShanghai Synchrotron Radiation FacilityCAS Key Laboratory of Interfacial Physics and TechnologyShanghai Institute of Applied PhysicsChinese Academy of Sciences Shanghai 201800 China
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18
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Liu X, Zhao Y, Liu P, Wang L, Lin J, Fan C. Biomimetic DNA Nanotubes: Nanoscale Channel Design and Applications. Angew Chem Int Ed Engl 2019; 58:8996-9011. [PMID: 30290046 DOI: 10.1002/anie.201807779] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/25/2018] [Indexed: 01/04/2023]
Abstract
Biomacromolecular nanotubes play important physiological roles in transmembrane ion/molecule channeling, intracellular transport, and inter-cellular communications. While genetically encoded protein nanotubes are prevalent in vivo, the in vitro construction of biomimetic DNA nanotubes has attracted intense interest with the rise of structural DNA nanotechnology. The abiotic use of DNA assembly provides a powerful bottom-up approach for the rational construction of complex materials with arbitrary size and shape at the nanoscale. More specifically, a typical DNA nanotube can be assembled either with parallel-aligned DNA duplexes or by closing DNA tile lattices. These artificial DNA nanotubes can be tailored and site-specifically modified to realize biomimetic functions including ionic or molecular channeling, bioreactors, drug delivery, and biomolecular sensing. In this Minireview, we aim to summarize recent advances in design strategies, including the characterization and applications of biomimetic DNA nanotubes.
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Affiliation(s)
- Xiaoguo Liu
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 201240, China.,Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Yan Zhao
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Pi Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University, Tianjin, 300353, China.,Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University, Tianjin, 300353, China.,Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 201240, China.,Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
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19
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Ali M, Afshan N, Jiang C, Xiao SJ. DNA dumbbell tiles with uneven widths for 2D arrays. Org Biomol Chem 2019; 17:1277-1283. [DOI: 10.1039/c8ob02709a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA dumbbell tiles of AO(E) and BO(E), with stem spans of 11 and 16 bp twisting two head loop motifs of each tile into parallel and antiparallel conformations respectively, were constructed to grow planar nanoribbon arrays and nanotubes as well.
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Affiliation(s)
- Mashooq Ali
- State Key Laboratory of Coordination Chemistry
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093
- China
| | - Noshin Afshan
- Institute of Molecular Medicine
- Renji Hospital Affiliated To Shanghai Jiao Tong University
- School of Medicine
- Shanghai 200001
- China
| | - Chuan Jiang
- State Key Laboratory of Coordination Chemistry
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093
- China
| | - Shou-Jun Xiao
- State Key Laboratory of Coordination Chemistry
- School of Chemistry and Chemical Engineering
- Nanjing University
- Nanjing 210093
- China
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20
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Two-Holder Strategy for Efficient and Selective Synthesis of Lk 1 ssDNA Catenane. Molecules 2018; 23:molecules23092270. [PMID: 30189687 PMCID: PMC6225352 DOI: 10.3390/molecules23092270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 08/31/2018] [Accepted: 09/05/2018] [Indexed: 11/23/2022] Open
Abstract
DNA catenanes are characterized by their flexible and dynamic motions and have been regarded as one of the key players in sophisticated DNA-based molecular machines. There, the linking number (Lk) between adjacent interlocked rings is one of the most critical factors, since it governs the feasibility of dynamic motions. However, there has been no established way to synthesize catenanes in which Lk is controlled to a predetermined value. This paper reports a new methodology to selectively synthesize Lk 1 catenanes composed of single-stranded DNA rings, in which these rings can most freely rotate each other due to minimal inter-ring interactions. To the mixture for the synthesis, two holder strands (oligonucleotides of 18–46 nt) were added, and the structure of the quasi-catenane intermediate was interlocked through Watson–Crick base pairings into a favorable conformation for Lk 1 catenation. The length of the complementary part between the two quasi-rings was kept at 10 bp or shorter. Under these steric constraints, two quasi-rings were cyclized with the use of T4 DNA ligase. By this simple procedure, the formation of undesired topoisomers (Lk ≥ 2) was almost completely inhibited, and Lk 1 catenane was selectively prepared in high yield up to 70 mole%. These Lk 1 catenanes have high potentials as dynamic parts for versatile DNA architectures.
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21
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Zhang Z, Liu S, Zhou T, Zhang H, Wang F, Zhang G, Wang X, Liu T. Salt-Induced Assembly Transformation of DNA-AuNP Conjugates Based on RCA Origami: From Linear Arrays to Nanorings. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:8904-8909. [PMID: 29945443 DOI: 10.1021/acs.langmuir.8b01505] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We developed a simple method to adjust the structural transformation of DNA-gold nanoparticles assemblies from linear arrays to nanorings by increasing salt concentrations. A DNA nanoladder constructing from RCA origami acted as templates to assemble periodic AuNPs arrays by a terminal thiol located on staple oligonucleotides. The linear AuNPs arrays could be transformed into nanorings only by changing the concentration of NaCl aqueous solution during the assembly process. It was proven that the electrostatic repulsion, being asymmetrically diminished by the high concentration of NaCl, caused the formation of nanoring architectures.
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Affiliation(s)
- Zhiqing Zhang
- College of Science , China University of Petroleum , Qingdao 266580 , China
| | - Shuzhen Liu
- College of Science , China University of Petroleum , Qingdao 266580 , China
| | - Ting Zhou
- College of Science , China University of Petroleum , Qingdao 266580 , China
| | - Hongzhi Zhang
- College of Science , China University of Petroleum , Qingdao 266580 , China
| | - Fang Wang
- College of Science , China University of Petroleum , Qingdao 266580 , China
| | - Guodong Zhang
- College of Science , China University of Petroleum , Qingdao 266580 , China
| | - Xiufeng Wang
- College of Science , China University of Petroleum , Qingdao 266580 , China
| | - Tingting Liu
- College of Science , China University of Petroleum , Qingdao 266580 , China
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22
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Chen T, Ren L, Liu X, Zhou M, Li L, Xu J, Zhu X. DNA Nanotechnology for Cancer Diagnosis and Therapy. Int J Mol Sci 2018; 19:ijms19061671. [PMID: 29874867 PMCID: PMC6032219 DOI: 10.3390/ijms19061671] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 05/27/2018] [Accepted: 06/01/2018] [Indexed: 01/03/2023] Open
Abstract
Cancer is one of the leading causes of mortality worldwide, because of the lack of accurate diagnostic tools for the early stages of cancer. Thus, early diagnosis, which provides important information for a timely therapy of cancer, is of great significance for controlling the development of the disease and the proliferation of cancer cells and for improving the survival rates of patients. To achieve the goals of early diagnosis and timely therapy of cancer, DNA nanotechnology may be effective, since it has emerged as a valid technique for the fabrication of various nanoscale structures and devices. The resultant DNA-based nanoscale structures and devices show extraordinary performance in cancer diagnosis, owing to their predictable secondary structures, small sizes, and high biocompatibility and programmability. In particular, the rapid development of DNA nanotechnologies, such as molecular assembly technologies, endows DNA-based nanomaterials with more functionalization and intellectualization. Here, we summarize recent progress made in the development of DNA nanotechnology for the fabrication of functional and intelligent nanomaterials and highlight the prospects of this technology in cancer diagnosis and therapy.
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Affiliation(s)
- Tianshu Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China.
- Institute of Biomedical Engineering, School of Communication and Information Engineering, Shanghai University, Shanghai 200444, China.
| | - Lingjie Ren
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Xiaohao Liu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Mengru Zhou
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Lingling Li
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Jingjing Xu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China.
- Institute of Biomedical Engineering, School of Communication and Information Engineering, Shanghai University, Shanghai 200444, China.
| | - Xiaoli Zhu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China.
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23
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Guo X, Wang XM, Wei S, Xiao SJ. Construction of a Holliday Junction in Small Circular DNA Molecules for Stable Motifs and Two-Dimensional Lattices. Chembiochem 2018; 19:1379-1385. [PMID: 29644789 DOI: 10.1002/cbic.201800122] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Indexed: 11/10/2022]
Abstract
Design rules for DNA nanotechnology have been mostly learnt from using linear single-stranded (ss) DNA as the source material. For example, the core structure of a typical DAO (double crossover, antiparallel, odd half-turns) tile for assembling 2D lattices is constructed from only two linear ss-oligonucleotide scaffold strands, similar to two ropes making a square knot. Herein, a new type of coupled DAO (cDAO) tile and 2D lattices of small circular ss-oligonucleotides as scaffold strands and linear ss-oligonucleotides as staple strands are reported. A cDAO tile of cDAO-c64nt (c64nt: circular 64 nucleotides), shaped as a solid parallelogram, is constructed with a Holliday junction (HJ) at the center and two HJs at both poles of a c64nt; similarly, cDAO-c84nt, shaped as a crossed quadrilateral composed of two congruent triangles, is formed with a HJ at the center and four three-way junctions at the corners of a c84nt. Perfect 2D lattices were assembled from cDAO tiles: infinite nanostructures of nanoribbons, nanotubes, and nanorings, and finite nanostructures. The structural relationship between the visible lattices imaged by AFM and the corresponding invisible secondary and tertiary molecular structures of HJs, inclination angle of hydrogen bonds against the double-helix axis, and the chirality of the tile can be interpreted very well. This work could shed new light on DNA nanotechnology with unique circular tiles.
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Affiliation(s)
- Xin Guo
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, P.R. China
| | - Xue-Mei Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, P.R. China
| | - Shuai Wei
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Shou-Jun Xiao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, P.R. China.,State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096, P.R. China
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24
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Afshan N, Ali M, Wang M, Baig MMFA, Xiao SJ. DNA nanotubes assembled from tensegrity triangle tiles with circular DNA scaffolds. NANOSCALE 2017; 9:17181-17185. [PMID: 29091094 DOI: 10.1039/c7nr04869f] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Using small circular DNA molecules of different lengths as scaffolds, we successfully synthesised DNA nanotubes consisting of Mao's DNA tensegrity triangle tiles with four-arm junctions (Holliday junctions) at all vertices. Due to the intrinsic curvature of the triangle tile and the consecutive tile alignment, the 2D arrays are organised in the form of nanotubes. Two sized triangle tiles with equilateral side lengths of 1.5 and 2.5 full helical turns are connected by the sticky ended cohesion of a duplex with a length of 2.5 helical turns respectively, and their parallel lozenge tiling lattices were demonstrated by high resolution AFM images, where the former lozenge unit cell has a lattice constant of 13.6 nm, and the latter has a larger lattice constant of 17.0 nm. Modification of the triangle tile with infinitesimal disturbance on side lengths and insertion of one thymine single stranded loop at every vertex resulted in comparably similar nanotubes.
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Affiliation(s)
- Noshin Afshan
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, Jiangsu, China.
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25
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Baig MMFA, Khan S, Naeem MA, Khan GJ, Ansari MT. Vildagliptin loaded triangular DNA nanospheres coated with eudragit for oral delivery and better glycemic control in type 2 diabetes mellitus. Biomed Pharmacother 2017; 97:1250-1258. [PMID: 29145151 DOI: 10.1016/j.biopha.2017.11.059] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/31/2017] [Accepted: 11/10/2017] [Indexed: 11/18/2022] Open
Abstract
Diabetes mellitus type 2 is a multidimensional disease associated with poor glycemic control through compromised sensitivity of pancreatic islet α and β cells against glucose and dwindled secretion of insulin which is linked with the quantity of incretin hormones that are abridged by dipeptidyl peptidase-4 (DPP-4) in diseased condition. Vildagliptin (VG) inhibits DPP-4 therefore regulates the incretins that conversely maintains glycemic control. The safe reach and absorption of VG from intestine was dubious. Therefore we used Electrostatic Attraction Method to develop drug loaded DNA nanotechnology triangles coated by Eudragit (Eud) to make stable nanospheres of Vildagliptin (VG). We further analyzed the formulated nanospheres by AFM, XRD, DSC, SEM, TGA, ATR-FTIR and native PAGE. Additionally the efficacy of formulated nanospheres for drug release and glycemic control was assessed in Db/Db mouse. Our results showed that formulated nanospheres are smooth, spherical, stable and uniform in size ranging from 500 to 2000 nm with drug entrapment efficiency up to 95 ± 2% and extended drug release up to 15 ± 2 h. FTIR and DSC results confirmed the absence of VG-DNA-Eud interaction and XRD studies revealed a change in the crystalline status of the VG in nanospheres. Ex-vivo studies indicate that Eud-DNA-VG nanospheres effectively bypasses the acidic pH of the stomach and enhances glycemic control in Db/Db mouse without any risk of pancreatitis or pancreatic cancer. To the best of our knowledge, this is the first study conclusively reporting that VG loaded DNA Nano-architects coated with Eudragit are stable, safe and may improve therapeutic outcomes after oral delivery.
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Affiliation(s)
- Mirza Muhammad Faran Ashraf Baig
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan; School of Chemistry and Chemical Engineering, Nanjing University, PR China
| | - Sara Khan
- Department of Pharmaceutical Chemistry, University College of Pharmacy, University of the Punjab, Lahore Pakistan
| | - Muhammad Ahsan Naeem
- Department of Mechatronics and Control Engineering, University of Engineering and Technology, Lahore, Pakistan
| | - Ghulam Jilany Khan
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, PR China; Department of Pharmacology, Faculty of Pharmacy (FOP), University of Central Punjab, Lahore, Pakistan; Jiangsu Center for Pharmacodynamics Research and Evaluation, China Pharmaceutical University, Nanjing 210009, China.
| | - Muhammad Tayyab Ansari
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
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26
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Abstract
Transmembrane proteins are mostly nanochannels playing a highly important role in metabolism. Understanding their structures and functions is vital for revealing life processes. It is of fundamental interest to develop chemical devices to mimic biological channels. Structural DNA nanotechnology has been proven to be a promising method for the preparation of fine DNA nanochannels as a result of the excellent properties of DNA molecules. This review presents the development history and current situation of three different types of DNA nanochannel: tile-based nanotube, DNA origami nanochannel, and DNA bundle nanochannel.
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Affiliation(s)
- Dianming Wang
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Yiyang Zhang
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Dongsheng Liu
- Department of Chemistry, Tsinghua University, Beijing, China
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27
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Wang M, Huang H, Zhang Z, Xiao SJ. 2D DNA lattices constructed from two-tile DAE-O systems possessing circular central strands. NANOSCALE 2016; 8:18870-18875. [PMID: 27812582 DOI: 10.1039/c6nr06745j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We reported a classical two-tile system of DAE-O (doublecrossover, antiparallel, and even half-turns tiles with odd half-turns connection) to construct regular single crystalline 2D (two dimensional) DNA lattices, using pre-circularised oligonucleotides of 42-, 64-, and 84-nt (nucleotides) as the central looped strands in DAE tiles respectively. DAE tiles with 42- and 64-nt as central strands, either in circular form or in linear form, grew regular single crystalline lattices well. However DAE tiles including a circular 84-nt as the central strand grew single crystalline lattices, those including a linear 84-nt as the central strand grew polycrystalline 2D lattices. A subtle difference in the lateral rigidity of DAE tiles with regard to the duplex axis was suggested to be the cause of the morphological difference.
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Affiliation(s)
- Meng Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, Jiangsu, China.
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28
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Chen J, Klem S, Jones AK, Orr B, Banaszak Holl MM. Folate-Binding Protein Self-Aggregation Drives Agglomeration of Folic Acid Targeted Iron Oxide Nanoparticles. Bioconjug Chem 2016; 28:81-87. [DOI: 10.1021/acs.bioconjchem.6b00526] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Junjie Chen
- Department
of Chemistry, ‡Department of Biomedical Engineering, §Department of Physics, and ∥Program in Macromolecular
Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sarah Klem
- Department
of Chemistry, ‡Department of Biomedical Engineering, §Department of Physics, and ∥Program in Macromolecular
Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Alexis K. Jones
- Department
of Chemistry, ‡Department of Biomedical Engineering, §Department of Physics, and ∥Program in Macromolecular
Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bradford Orr
- Department
of Chemistry, ‡Department of Biomedical Engineering, §Department of Physics, and ∥Program in Macromolecular
Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Mark M. Banaszak Holl
- Department
of Chemistry, ‡Department of Biomedical Engineering, §Department of Physics, and ∥Program in Macromolecular
Science and Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
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29
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Bis-three-way junction nanostructure and DNA machineries for ultrasensitive and specific detection of BCR/ABL fusion gene by chemiluminescence imaging. Sci Rep 2016; 6:32370. [PMID: 27577607 PMCID: PMC5006031 DOI: 10.1038/srep32370] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 08/04/2016] [Indexed: 01/07/2023] Open
Abstract
A novel G-quadruplex DNAzyme-driven chemiluminescence (CL) imaging method has been developed for ultrasensitive and specific detection of BCR/ABL fusion gene based on bis-three-way junction (bis-3WJ) nanostructure and cascade DNA machineries. Bis-3WJ probes are designed logically to recognize BCR/ABL fusion gene, which forms the stable bis-3WJ nanostructure for the activation of polymerase/nicking enzyme machineries in cascade, resulting in synthesis of DNAzyme subunits. These DNAzyme subunits can form integrated DNAzyme by self-assembly to catalyze CL substrate, thus providing an amplified signal for the sensing events or outputs for AND logic operation. The imaging method achieved ultrasensitive detection of BCR/ABL fusion gene with a low detection limit down to 23 fM. And this method exhibited wide linear ranges over seven orders of magnitude and excellent discrimination ability toward target. In addition, an acceptable recovery was obtained in complex matrix. It is notable that this biosensing strategy possesses merits of homogenous, isothermal and label-free assay system. Therefore, these merits endow the developed imaging method with a potential tool for CML diagnosis.
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30
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Cecconello A, Kahn JS, Lu CH, Khosravi Khorashad L, Govorov AO, Willner I. DNA Scaffolds for the Dictated Assembly of Left-/Right-Handed Plasmonic Au NP Helices with Programmed Chiro-Optical Properties. J Am Chem Soc 2016; 138:9895-901. [PMID: 27428505 DOI: 10.1021/jacs.6b04096] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Within the broad interest of assembling chiral left- and right-handed helices of plasmonic nanoparticles (NPs), we introduce the DNA-guided organization of left- or right-handed plasmonic Au NPs on DNA scaffolds. The method involves the self-assembly of stacked 12 DNA quasi-rings interlinked by 30 staple-strands. By the functionalization of one group of staple units with programmed tether-nucleic acid strands and additional staple elements with long nucleic acid chains, acting as promoter strands, the promoter-guided assembly of barrels modified with 12 left- or right-handed tethers is achieved. The subsequent hybridization of Au NPs functionalized with single nucleic acid tethers yields left- or right-handed structures of plasmonic NPs. The plasmonic NP structures reveal CD spectra at the plasmon absorbance, and the NPs are imaged by HR-TEM. Using geometrical considerations corresponding to the left- and right-handed helices of the Au NPs, the experimental CD spectra of the plasmonic Au NPs are modeled by theoretical calculations.
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Affiliation(s)
- Alessandro Cecconello
- The Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Jason S Kahn
- The Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Chun-Hua Lu
- The Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | | | - Alexander O Govorov
- Department of Physics and Astronomy, Ohio University , Athens, Ohio 45701, United States
| | - Itamar Willner
- The Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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In-Phase Assembly of Slim DNA Lattices with Small Circular DNA Motifs via Short Connections of 11 and 16 Base Pairs. Chembiochem 2016; 17:1132-7. [DOI: 10.1002/cbic.201600054] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Indexed: 12/14/2022]
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Liang L, Zhang Z, Kong Z, Liu Y, Shen JW, Li D, Wang Q. Charge-tunable insertion process of carbon nanotubes into DNA nanotubes. J Mol Graph Model 2016; 66:20-5. [PMID: 27017425 DOI: 10.1016/j.jmgm.2016.03.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/20/2016] [Accepted: 03/22/2016] [Indexed: 12/16/2022]
Abstract
Control over interactions with biomolecules holds the key of the applications of carbon nanotubes (CNTs) in biotechnology. Here we report a molecule dynamics study on the encapsulation process of different charged CNTs into DNA nanotubes. Our results demonstrated that insertion process of CNTs into DNA nanotubes are charge-tunable. The positive charged CNTs could spontaneously encapsulate and confined in the hollow of DNA nanotubes under the combination of electrostatic and vdW interaction in our ns scale simulation. The conformation of DNA nanotubes is very stable even after the insertion of CNTs. For pristine CNTs, it could not entirely encapsulated by DNA nanotubes in simulation scale in this study. The encapsulation time of pristine CNTs into DNA nanotubes was estimated about 21.9s based on the potential of mean force along the reaction coordination of encapsulation process of CNTs into DNA nanotubes. In addition, the encapsulation process was also affected by the diameter of CNTs. These findings highlight the charge-tunable self-assembly process of nanomaterials and biomolecules. Our study suggests that the encapsulated CNTs-DNA nanotubes could be used as building blocks for constructing organic-inorganic hybrid materials and has the potential applications in the field of biosensor, drug delivery system and biomaterials etc.
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Affiliation(s)
- Lijun Liang
- College of Life Information Science and Instrument Engineering, Hangzhou Dianzi University, Hangzhou, People's Republic of China; Department of Chemistry, Zhejiang University, Hangzhou 310027, People's Republic of China
| | - Zhisen Zhang
- Research Institute for Soft Matter and Biomimetics, Department of Physics, Xiamen University, Xiamen 361005, People's Republic of China
| | - Zhe Kong
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, People's Republic of China
| | - Yong Liu
- School of Medicine, Hangzhou Normal University, Hangzhou 310016, People's Republic of China
| | - Jia-Wei Shen
- School of Medicine, Hangzhou Normal University, Hangzhou 310016, People's Republic of China.
| | - Debing Li
- College of Life Information Science and Instrument Engineering, Hangzhou Dianzi University, Hangzhou, People's Republic of China
| | - Qi Wang
- Department of Chemistry, Zhejiang University, Hangzhou 310027, People's Republic of China.
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Yang H, Seela F. Circular DNA by "Bis-Click" Ligation: Template-Independent Intramolecular Circularization of Oligonucleotides with Terminal Alkynyl Groups Utilizing Bifunctional Azides. Chemistry 2015; 22:1435-44. [PMID: 26685101 DOI: 10.1002/chem.201503615] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Indexed: 12/19/2022]
Abstract
A highly effective and convenient "bis-click" strategy was developed for the template-independent circularization of single-stranded oligonucleotides by employing copper(I)-assisted azide-alkyne cycloaddition. Terminal triple bonds were incorporated at both ends of linear oligonucleotides. Alkynylated 7-deaza-2'-deoxyadenosine and 2'-deoxyuridine residues with different side chains were used in solid-phase synthesis with phosphoramidite chemistry. The bis-click ligation of linear 9- to 36-mer oligonucleotides with 1,4-bis(azidomethyl)benzene afforded circular DNA in a simple and selective way; azido modification of the oligonucleotide was not necessary. Short ethynyl side chains were compatible with the circularization of longer oligonucleotides, whereas octadiynyl residues were used for short 9-mers. Compared with linear duplexes, circular bis-click constructs exhibit a significantly increased duplex stability over their linear counterparts. The intramolecular bis-click ligation protocol is not limited to DNA, but may also be suitable for the construction of other macrocycles, such as circular RNAs, peptides, or polysaccharides.
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Affiliation(s)
- Haozhe Yang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069, Osnabrück, Germany), Fax: (+49) 251-53406857
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149, Münster, Germany. .,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069, Osnabrück, Germany), Fax: (+49) 251-53406857.
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Afshan N, Zheng H, Xiao SJ. How Small DNA Minicircles Can Be Applied to Construct DNA Nanotubes? CHINESE J CHEM 2015. [DOI: 10.1002/cjoc.201500561] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Abstract
The specificity of DNA hybridization allows for the modular design of 2D and 3D shapes with wide-ranging applications including sensors, actuators, and even logic devices. The inherent biocompatibility of DNA and the ability to produce monodisperse structures of controlled shape and size make DNA nanostructures of interest as potential drug and gene delivery vehicles. In this review, we discuss several new approaches for the assembly of DNA nanostructures, advances in the modeling of these structures, and we highlight recent studies on the use of DNA nanotechnology for therapeutic applications such as drug delivery in tumor models.
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Affiliation(s)
- Laura A Lanier
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst MA 01003
| | - Harry Bermudez
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst MA 01003
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Pujari SS, Ingale SA, Seela F. High-density functionalization and cross-linking of DNA: "click" and "bis-click" cycloadditions performed on alkynylated oligonucleotides with fluorogenic anthracene azides. Bioconjug Chem 2014; 25:1855-70. [PMID: 25154019 DOI: 10.1021/bc5003532] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
High density functionalization of DNA with ethynyl and octadiynyl side chains followed by CuAAC "click labeling" with 9-azidomethylanthracene was performed. Alkynyl DNA was also cross-linked with fluorogenic 9,10-bis-azidomethylanthracene employing the "bis-click" reaction. By this means the fluorescence of the anthracene moiety was imparted to the virtually nonfluorescent DNA. Phosphoramidites of 8-aza-7-deaza-2'-deoxyadenosine with short and long linker arms in a steric nondemanding 7-position were utilized in solid phase oligodeoxynucleotide synthesis. High density alkynylated DNA-without anthracene residues-was found to be of comparable stability with both long and short linker arms. High density anthracene functionalized DNA became less stable with the short linker compared to that with the long linker connectivity. Interstrand cross-linked homodimers constructed from alkynylated oligonucleotides with fluorogenic 9,10-bis-azidomethylanthracene were hybridized with complementary strands to form double helices. They are more stable when the linker was located at a terminus than in a central position. Short linker anthracene adducts were destabilizing compared to long linker adducts. The fluorogenic anthracene residues not only have a significant effect on the duplex stability, but also impart fluorescence to the species. Fluorescence of cross-linked double helices with long linker connectivity was quenched when the cross-link was in a terminal position and was dequenched when the linker was connecting the two double helices at the center of the molecule. The fluorescence of the anthracene cross-linked double helices was strongly increased (dequenched) when the correct base pair was formed, while no change occurred upon mismatch formation.
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Affiliation(s)
- Suresh S Pujari
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology , Heisenbergstraße 11, 48149 Münster, Germany
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