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Gubu A, Zhang X, Lu A, Zhang B, Ma Y, Zhang G. Nucleic acid amphiphiles: Synthesis, properties, and applications. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:144-163. [PMID: 37456777 PMCID: PMC10345231 DOI: 10.1016/j.omtn.2023.05.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Nucleic acid amphiphiles, referring to nucleic acids modified with large hydrophobic groups, have been widely used in programmable bioengineering. Since nucleic acids are intrinsically hydrophilic, the hydrophobic groups endow nucleic acid amphiphiles with unique properties, such as self-assembling, interactions with artificial or biological membranes, and transmembrane transport. Importantly, the hybridization or target binding capability of oligonucleotide itself supplies nucleic acid amphiphiles with excellent programmability. As a result, this type of molecule has attracted considerable attention in academic studies and has enormous potential for further applications. For a comprehensive understanding of nucleic acid amphiphiles, we review the reported research on nucleic acid amphiphiles from their molecular design to final applications, in which we summarize the synthetic strategies for nucleic acid amphiphiles and draw much attention to their unique properties in different contexts. Finally, a summary of the applications of nucleic acid amphiphiles in drug development, bioengineering, and bioanalysis are critically discussed.
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Affiliation(s)
- Amu Gubu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Aptacure Therapeutics Limited, Kowloon, Hong Kong SAR, China
| | - Xueli Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, No. 38 Xueyuan Road, Beijing, China
| | - Aiping Lu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen 518000, China
| | - Baoting Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yuan Ma
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen 518000, China
| | - Ge Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen 518000, China
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2
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Emissive‐Dye/Cucurbit[n]uril‐Based Fluorescence Probes for Sensing Applications. ChemistrySelect 2023. [DOI: 10.1002/slct.202204833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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3
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Kankanamalage DVDW, Tran JHT, Beltrami N, Meng K, Zhou X, Pathak P, Isaacs L, Burin AL, Ali MF, Jayawickramarajah J. DNA Strand Displacement Driven by Host-Guest Interactions. J Am Chem Soc 2022; 144:16502-16511. [PMID: 36063395 PMCID: PMC9479067 DOI: 10.1021/jacs.2c05726] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Base-pair-driven toehold-mediated strand displacement (BP-TMSD) is a fundamental concept employed for constructing DNA machines and networks with a gamut of applications─from theranostics to computational devices. To broaden the toolbox of dynamic DNA chemistry, herein, we introduce a synthetic surrogate termed host-guest-driven toehold-mediated strand displacement (HG-TMSD) that utilizes bioorthogonal, cucurbit[7]uril (CB[7]) interactions with guest-linked input sequences. Since control of the strand-displacement process is salient, we demonstrate how HG-TMSD can be finely modulated via changes to the structure of the input sequence (including synthetic guest head-group and/or linker length). Further, for a given input sequence, competing small-molecule guests can serve as effective regulators (with fine and coarse control) of HG-TMSD. To show integration into functional devices, we have incorporated HG-TMSD into machines that control enzyme activity and layered reactions that detect specific microRNA.
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Affiliation(s)
| | - Jennifer H T Tran
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125, United States
| | - Noah Beltrami
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Kun Meng
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Xiao Zhou
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Pravin Pathak
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Alexander L Burin
- Department of Chemistry, Tulane University, 2015 Percival Stern Hall, New Orleans, Louisiana 70118, United States
| | - Mehnaaz F Ali
- Department of Chemistry, Xavier University of Louisiana, 1 Drexel Drive, New Orleans, Louisiana 70125, United States
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Kuang H, Wang D, Schneiderman Z, Tsapatsis M, Kokkoli E. Supramolecular Assembly of Single-Tail ssDNA-Amphiphiles through π-π Interactions. Bioconjug Chem 2022; 33:2035-2040. [PMID: 35699360 DOI: 10.1021/acs.bioconjchem.2c00090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work, we demonstrate the formation of supramolecular architectures from the assembly of single-tail single stranded DNA (ssDNA)-amphiphiles. Short ssDNA sequences of 10 nucleotides that were either unstructured or formed G-quadruplex secondary structures were conjugated to a single 4-(hexadecyloxy)benzamide tail, either directly or through a polycarbon (C12) spacer. Conjugation of the ssDNA to the tail did not interfere with the G-quadruplex secondary structure of the ssDNA sequence. The ssDNA-amphiphiles self-assembled into ellipsoidal micelles, vesicles, nanotapes, and nanotubes. These nanotubes appeared to be formed by the rolling up of nanotapes. The increase of the hydrophobic block of the ssDNA-amphiphiles through the addition of a C12 spacer led to an increase in wall thickness and nanotube diameter. The presence of π-π interactions, through the benzoic group, was verified via X-ray diffraction (XRD) and played a critical role in the formation of the different nanostructures. In contrast, ssDNA-amphiphiles with a single heptadecanoic acid tail self-assembled only into ellipsoidal micelles.
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Affiliation(s)
- Huihui Kuang
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Danyu Wang
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Zachary Schneiderman
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Michael Tsapatsis
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Applied Physics Laboratory, Johns Hopkins University, Laurel, Maryland 20723, United States
| | - Efrosini Kokkoli
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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Carbajo‐Gordillo AI, López‐Fernández J, Benito JM, Blanco JLJ, Santana‐Armas ML, Marcelo G, Giorgio CD, Przybylski C, Mellet CO, Ilarduya CT, Mendicuti F, Fernández JMG. Enhanced Gene Delivery Triggered by Dual pH/Redox Responsive Host‐Guest Dimerization of Cyclooligosaccharide Star Polycations. Macromol Rapid Commun 2022; 43:e2200145. [DOI: 10.1002/marc.202200145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/23/2022] [Indexed: 11/10/2022]
Affiliation(s)
| | - José López‐Fernández
- Instituto de Investigaciones Químicas (IIQ) C/ Américo Vespucio 49 Sevilla 41092 Spain
| | - Juan M. Benito
- Instituto de Investigaciones Químicas (IIQ) C/ Américo Vespucio 49 Sevilla 41092 Spain
| | - José L. Jiménez Blanco
- Department of Organic Chemistry Faculty of Chemistry University of Seville C/ Profesor García González 1 Seville 41012 Spain
| | - María L. Santana‐Armas
- Department of Pharmaceutical Technology and Chemistry, School of Pharmacy and Nutrition University of Navarra Pamplona 31080 Spain
| | - Gema Marcelo
- Department of Analytical Chemistry Physical Chemistry and Chemical Engineering Faculty of Chemistry University of Alcalá Alcalá de Henares Madrid Spain
| | - Christophe Di Giorgio
- Institut de Chimie Nice UMR 7272 Université Côte d'Azur 28, Avenue de Valrose Nice F‐06108 France
| | - Cédric Przybylski
- Institut Parisien de Chimie Moléculaire (IPCM) CNRS Sorbonne Université Paris France
| | - Carmen Ortiz Mellet
- Department of Organic Chemistry Faculty of Chemistry University of Seville C/ Profesor García González 1 Seville 41012 Spain
| | - Conchita Tros Ilarduya
- Department of Pharmaceutical Technology and Chemistry, School of Pharmacy and Nutrition University of Navarra Pamplona 31080 Spain
| | - Francisco Mendicuti
- Department of Analytical Chemistry Physical Chemistry and Chemical Engineering Faculty of Chemistry University of Alcalá Alcalá de Henares Madrid Spain
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Li B, Xuan L, Wu L. Polyoxometalate-Containing Supramolecular Gels. Macromol Rapid Commun 2022; 43:e2200019. [PMID: 35102624 DOI: 10.1002/marc.202200019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 01/27/2022] [Indexed: 11/08/2022]
Abstract
Supramolecular gels are important soft materials with various applications, which are fabricated through hydrogen bonding, π-π stacking, electrostatic or host-guest interactions. Introducing functional groups, especially inorganic components, is an efficient strategy to obtain gels with robust architecture and high performance. Polyoxometalates (POMs), as a class of negatively-charged clusters, have defined structures and multiple interaction sites, resulting in their potential as building blocks for constructing POM-containing supramolecular gels. The introduction of POMs into gels not only provides strong driving forces for the formation of gels due to the characteristics of charged cluster and oxygen-rich surface, but also brings new properties sourcing from unique electronic structures of POMs. Though many POM-containing gels have been reported, a comprehensive review is still absent. Herein, the concept of POM-containing gels is discussed, following with the design strategies and driving forces. To better understand the results in the literature, detailed examples, which are classified into several categories based on the types of organic components, are presented to illustrate the gelation process and gel structures. Moreover, applications of POM-containing gels in energy chemistry, sustainable chemistry and other aspects are also reviewed, as well as the future developments of this field. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Bao Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
| | - Luyun Xuan
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
| | - Lixin Wu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, P. R. China
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Fan S, Liu X, Yu S, Wang J, Li C, Cheng S, Hong M. Aptamer-functionalized fluorine-containing DNAsomes for targeted drug delivery to cancer cells. NEW J CHEM 2022. [DOI: 10.1039/d2nj00967f] [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
A drug-loaded aptamer functionalized fluorine-containing DNAsome was reported here, which can deliver doxorubicin into cancer cells in a targeted manner through receptor mediated endocytosis and induce the apoptosis of cancer cells.
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Affiliation(s)
- Shuhua Fan
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252059, Shandong, China
| | - Xiaoyan Liu
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252059, Shandong, China
| | - Shuxian Yu
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252059, Shandong, China
| | - Juan Wang
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252059, Shandong, China
| | - Chuan Li
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252059, Shandong, China
| | - Shuang Cheng
- School of Agriculture, Liaocheng University, Liaocheng, 252059, Shandong, China
| | - Min Hong
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252059, Shandong, China
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Mobley EB, Byrd N, Yim MG, Gariepy R, Rieder M, Ward S. Glutathione sensitive vesicles prepared from supramolecular amphiphiles. SOFT MATTER 2021; 17:9664-9669. [PMID: 34633020 DOI: 10.1039/d1sm01238j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Glutathione (GSH) sensitive vesicles were prepared by the self-assembly of amphiphilic inclusion complexes. These novel chemically sensitive supramolecular amphiphiles are anticipated to have applications in drug delivery; the nanocarriers can protect the encapsulated cargo and release it via triggered degradation in high concentrations of GSH. Additionally, the sensitivity of the vesicles to GSH indicates that the dynamic covalent disulfide bond at the vesicle surface can be used for post-modification of the nanocarrier via a thiol-disulfide exchange, a strategy that can be exploited to introduce targeting moieties to increase treatment specificity. Supramolecular amphiphiles containing a dynamic covalent disulfide bond were prepared via the host-guest inclusion complexes between alkylated β-cyclodextrin (β-CD) hosts and adamantane terminated polyethylene glycol derivatives. The significant difference between the critical micelle concentrations of the supramolecular amphiphiles and the individual host and guest components confirmed that a unique supramolecular amphiphile was formed. Fluorescence experiments and dynamic light scattering (DLS) revealed that the supramolecular amphiphiles self-assembled into vesicles of 130 nm diameter which were stable for 8 months. Degradation of the vesicles after incubation with GSH was monitored using DLS and by the release of encapsulated 5,6-carboxyfluorescein (CF), observed by an increase in fluorescence intensity. Degradation of the nanocarrier was faster at intracellular GSH concentrations than at extracellular GSH concentrations.
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Affiliation(s)
- Emily B Mobley
- Department of Chemistry and Biochemistry, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California, 93401, USA.
| | - Natalie Byrd
- Department of Chemistry and Biochemistry, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California, 93401, USA.
| | - Matthew G Yim
- Department of Chemistry and Biochemistry, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California, 93401, USA.
| | - Rachel Gariepy
- Department of Chemistry and Biochemistry, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California, 93401, USA.
| | - Maya Rieder
- Department of Chemistry and Biochemistry, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California, 93401, USA.
| | - Sandra Ward
- Department of Chemistry and Biochemistry, California Polytechnic State University, 1 Grand Avenue, San Luis Obispo, California, 93401, USA.
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Zhou J, Wu R, Chen Y, Tan Y. Triple stimulation-responsive behavior of pseudorotaxane polymer assembled by amphiphilic polymer and cucurbit[7]uril in aqueous solution. Colloids Surf A Physicochem Eng Asp 2021. [DOI: 10.1016/j.colsurfa.2021.126271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Abstract
The preparation and applications of DNA containing polymers are comprehensively reviewed, and they are in the form of DNA−polymer covalent conjugators, supramolecular assemblies and hydrogels for advanced materials with promising features.
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Affiliation(s)
- Zeqi Min
- School of Materials Science & Engineering
- Department of Polymer Materials
- Shanghai University
- Shanghai 200444
- China
| | - Biyi Xu
- School of Materials Science & Engineering
- Department of Polymer Materials
- Shanghai University
- Shanghai 200444
- China
| | - Wen Li
- School of Materials Science & Engineering
- Department of Polymer Materials
- Shanghai University
- Shanghai 200444
- China
| | - Afang Zhang
- School of Materials Science & Engineering
- Department of Polymer Materials
- Shanghai University
- Shanghai 200444
- China
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Chernikova EY, Berdnikova DV. Cucurbiturils in nucleic acids research. Chem Commun (Camb) 2020; 56:15360-15376. [PMID: 33206072 DOI: 10.1039/d0cc06583h] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
During the past ten years, the importance of cucurbiturils (CB[n]) as macrocyclic hosts in supramolecular assemblies with various types of natural and synthetic nucleic acids (NAs) has increased explosively. As a component of such systems, CB[n] macrocycles can play a wide spectrum of roles from drug and gene delivery vehicles to catalysts/inhibitors of biochemical reactions and even building blocks for NA-based materials. The aim of this highlight article is to describe the development of the CB[n] applications in nucleic acids research and to outline the current situation and perspectives of this fascinating synergistic combination of supramolecular chemistry of CB[n] and NAs.
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Affiliation(s)
- Ekaterina Y Chernikova
- Laboratory of Photoactive Supramolecular Systems, A. N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, Russia.
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