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Zhao W, Du H, Xia Y, Xie S, Huang YP, Xu T, Zhang J, Gao YQ, Wan X. Accelerating supramolecular aggregation by molecular sliding. Phys Chem Chem Phys 2022; 24:23840-23848. [PMID: 36165176 DOI: 10.1039/d2cp04064f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Diffusion-based translocation along DNA or RNA molecules is essential for genome regulatory proteins to execute their biological functions. The reduced dimensionality of the searching process makes the proteins bind specific target sites at a "faster-than-diffusion-controlled rate". We herein report a photoresponsive slider-track diffusion system capable of self-assembly rate acceleration, which consists of (-)-camphorsulfonic acid, 4-(4'-n-octoxylphenylazo)benzenesulfonic acid, and isotactic poly(2-vinylpyridine). The protonated pyridine rings act as the footholds for anionic azo sliders to diffusively bind and slide along polycationic tracks via electrostatic interactions. Ultraviolet light triggers the trans to cis isomerization and aggregation of azo sliders, which can be monitored by multiple spectroscopic methods without labeling. The presence of vinyl polymer track increases the aggregation rate of cis azobenzene up to ∼20 times, depending on the stereoregularity of the polymer chain, the acid/base ratio and the addition of salt. This system has a feature of simplicity, monitorability, controllability, and could find applications in designing molecular machines with desired functionalities.
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Affiliation(s)
- Wenjing Zhao
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Hongxu Du
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Yijie Xia
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Siyu Xie
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Yu-Peng Huang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Tieqi Xu
- State Key Laboratory of Fine Chemicals, College of Chemistry, Dalian University of Technology, Dalian 116024, China
| | - Jie Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Yi Qin Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Xinhua Wan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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Catalytic transport of molecular cargo using diffusive binding along a polymer track. Nat Chem 2019; 11:359-366. [DOI: 10.1038/s41557-018-0204-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 12/04/2018] [Indexed: 01/17/2023]
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Shi J, Liu W, Fu Y, Yin N, Zhang H, Chang J, Zhang Z. “US-detonated nano bombs” facilitate targeting treatment of resistant breast cancer. J Control Release 2018; 274:9-23. [DOI: 10.1016/j.jconrel.2018.01.030] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Revised: 01/17/2018] [Accepted: 01/29/2018] [Indexed: 12/16/2022]
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Xiong K, Blainey PC. A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA. J Vis Exp 2017. [PMID: 28994817 PMCID: PMC5752354 DOI: 10.3791/55923] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We describe a simple, robust and high throughput single molecule flow-stretching assay for studying 1D diffusion of molecules along DNA. In this assay, glass coverslips are functionalized in a one-step reaction with silane-PEG-biotin. Flow cells are constructed by sandwiching an adhesive tape with pre-cut channels between a functionalized coverslip and a PDMS slab containing inlet and outlet holes. Multiple channels are integrated into one flow cell and the flow of reagents into each channel can be fully automated, which significantly increases the assay throughput and reduces hands-on time per assay. Inside each channel, biotin-λ-DNAs are immobilized on the surface and a laminar flow is applied to flow-stretch the DNAs. The DNA molecules are stretched to >80% of their contour length and serve as spatially extended templates for studying the binding and transport activity of fluorescently labeled molecules. The trajectories of single molecules are tracked by time-lapse Total Internal Reflection Fluorescence (TIRF) imaging. Raw images are analyzed using streamlined custom single particle tracking software to automatically identify trajectories of single molecules diffusing along DNA and estimate their 1D diffusion constants.
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Affiliation(s)
- Kan Xiong
- Broad Institute, Massachusetts Institute of Technology and Harvard Medical School; Dept. of Biological Engineering, Massachusetts Institute of Technology
| | - Paul C Blainey
- Broad Institute, Massachusetts Institute of Technology and Harvard Medical School; Dept. of Biological Engineering, Massachusetts Institute of Technology;
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Zhang L, Zheng L, Meng Z, Balinin K, Loznik M, Herrmann A. Accelerating chemical reactions by molecular sledding. Chem Commun (Camb) 2017; 53:6331-6334. [PMID: 28548153 DOI: 10.1039/c7cc02500a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The speed-up of covalent bond formation was achieved between a sulfhydryl group and a 2-bromopropionic acid derivative by utilizing sliding peptide-modified substrates. Moreover, a new type of DNA cleaving reagent was developed, consisting of pVIc covalently coupled to verteporfin. This peptide-porphyrin conjugate allowed targeting of DNA and resulted in increased photodegradation of double-stranded nucleic acids.
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Affiliation(s)
- Lei Zhang
- Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
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