1
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Alleva N, Eigen K, Ng DYW, Weil T. A Versatile and Efficient Method to Isolate DNA-Polymer Conjugates. ACS Macro Lett 2023; 12:1257-1263. [PMID: 37656875 PMCID: PMC10515633 DOI: 10.1021/acsmacrolett.3c00371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/29/2023] [Indexed: 09/03/2023]
Abstract
We present a facile and adaptable method to purify and isolate DNA-polymer conjugates from different uncharged homo, random, or block copolymer families. Anion exchange chromatography is used to separate the reaction solution and retrieve the excess unreacted polymer and oligonucleotide. The stationary phase has a high efficiency (25 nmol of DNA per run), facilitating the purification of large batches without compromising the peak shape and resolution. To demonstrate the versatility of this method, different types of polymers, including acrylates, methacrylates, and acrylamides containing hydrophilic and hydrophobic blocks, were purified with high yields. Additionally, DNA-polymer conjugates with various DNA block lengths were also successfully purified, further highlighting the broad applicability of this method.
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Affiliation(s)
- Nico Alleva
- Max Planck Institute for
Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Katharina Eigen
- Max Planck Institute for
Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - David Y. W. Ng
- Max Planck Institute for
Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Tanja Weil
- Max Planck Institute for
Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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2
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Mathur N, Singh N. Melting of dsDNA attached with AuNPs. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:58. [PMID: 37477744 DOI: 10.1140/epje/s10189-023-00318-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/05/2023] [Indexed: 07/22/2023]
Abstract
DNA-linked gold nanoparticles (DNA-AuNPs) are combined nanomaterials that contain the optical and electronic properties of AuNPs with the unique functions of DNA. These hybrid systems are used in various nanobiotechnology, medical, and pharmaceutical sciences (Löwe et al. in FEBS J 287(23):5039, 2020; Speer et al. in Annu Rev Biophys 51:267, 2022). In recent years, there has been an increasing interest in studying the behavior of DNA-AuNPs in the presence of molecular solvents. In the present work, we study the thermal melting of DNA-linked gold nanoparticles (DNA-AuNP). In the first part of the study, we find the melting profile of short heterogeneous DNA-linked AuNP in the presence of solvent in the solution. We also study the effect of the location of the gold nanoparticle attached to the DNA molecule. In this case, we move the location of the AuNP from one end to the other. We found that while the melting temperature is susceptible to the location of the AuNP when it is near the ends, there is a region in the middle section of the chain where the melting temperature remains constant.
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Affiliation(s)
- Neha Mathur
- BITS-Pilani, Pilani Campus, 333031, Pilani, India.
| | - Navin Singh
- BITS-Pilani, Pilani Campus, 333031, Pilani, India
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3
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Wang J, Pan T, Zhang S. Highly Selective, Single-Tube Colorimetric Assay for Detection of Multiple Mutations in the Epidermal Growth Factor Receptor Gene. J Mol Diagn 2023; 25:313-319. [PMID: 37125988 DOI: 10.1016/j.jmoldx.2023.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/30/2023] [Accepted: 02/24/2023] [Indexed: 05/02/2023] Open
Abstract
Many closed-tube methods are designed to detect DNA biomarkers. However, the utility of biomarkers such as a DNA mutation related to personalized medicine is limited as the operation of expensive detection instruments requires well-trained technicians. Therefore, we developed a simple and cheap colorimetric assay based on aggregation of silica-gold nanoparticle-modified probes, with linking probes, to detect mutations. This method consists of target amplification, sequence identification, and aggregation of the silica-gold nanoparticle-modified probes. All reactions are controlled by one individual and proceed sequentially, in a single tube, with no manual intervention. Approximately 10 copies of target DNA were detected with this assay, using 12 hot-spot mutations in exon 19 of EGFR gene as the example. In artificial samples, 0.1% mutant DNA can be distinguished from wild-type genomic DNA. The technology was tested on 104 clinical samples, which included 29 samples that were positive for an exon 19 deletion. The data were consistent with amplification refractory mutation system PCR, with the exception of one weakly positive sample, which was confirmed to be positive by digital PCR. The limit of detection of this colorimetric assay was verified to be better than that of amplification refractory mutation system PCR, and it provides a tool to discriminate multiple mutations in EGFR gene in clinical samples.
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Affiliation(s)
- Jianping Wang
- Research and Development Department, Guangzhou Biotron Biotechnology Co., Ltd., Guangzhou, China.
| | - Tengfei Pan
- Research and Development Department, Guangzhou Biotron Biotechnology Co., Ltd., Guangzhou, China
| | - Song Zhang
- Research and Development Department, Guangzhou Biotron Biotechnology Co., Ltd., Guangzhou, China
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4
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Hu Q, Wan J, Luo Y, Li S, Cao X, Feng W, Liang Y, Wang W, Niu L. Electrochemical Detection of Femtomolar DNA via Boronate Affinity-Mediated Decoration of Polysaccharides with Electroactive Tags. Anal Chem 2022; 94:12860-12865. [PMID: 36070236 DOI: 10.1021/acs.analchem.2c02894] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In view of their high efficiency and cost-effectiveness, polymers are of great promise as carriers for signal tags in amplified detection. Herein, we present a polysaccharide-amplified method for the electrochemical detection of a BRCA1 breast cancer gene-derived DNA target at the femtomolar levels. Briefly, peptide nucleic acid (PNA) with a complementary sequence was tethered as the capture probe for the DNA target, to which carboxyl group-containing polysaccharides were then attached via facile phosphate-Zr(IV)-carboxylate crosslinking, followed by the decoration of polysaccharide chains with electroactive ferrocene (Fc) signal tags via affinity coupling between a cis-diol site and phenylboronic acid (PBA) group. As the polysaccharide chain contains hundreds of cis-diol sites, boronate affinity can enable the site-specific decoration of each polysaccharide chain with hundreds of Fc signal tags, efficiently transducing each target capture event into the decoration of many Fc signal tags. As polysaccharides are cheap, renewable, ubiquitous, and biodegradable natural biopolymers, the use of polysaccharides for signal amplification offers the benefits of high efficiency, cost-effectiveness, excellent biocompatibility, and environmental friendliness. The linear range of the polysaccharide-amplified method for DNA detection was demonstrated to be from 10 fM to 10 nM (R2 = 0.996), with the detection limit as low as 2.9 fM. The results show that this method can also discriminate single base mismatch with satisfactory selectivity and can be applied to DNA detection in serum samples. In view of these merits, the polysaccharide-amplified PNA-based electrochemical method holds great promise in DNA detection with satisfactory sensitivity and selectivity.
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Affiliation(s)
- Qiong Hu
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Jianwen Wan
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Yilin Luo
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Shiqi Li
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Xiaojing Cao
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Wenxing Feng
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Yiyi Liang
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Wei Wang
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
| | - Li Niu
- Guangzhou Key Laboratory of Sensing Materials and Devices, Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, P. R. China
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5
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Alleva N, Winterwerber P, Whitfield CJ, Ng DYW, Weil T. Nanoscale patterning of polymers on DNA origami. J Mater Chem B 2022; 10:7512-7517. [PMID: 35699081 DOI: 10.1039/d2tb00812b] [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
The combination of DNA-origami and synthetic polymers paves the way to a new class of structurally precise biohybrid nanomaterials for diverse applications. Herein, we introduce the grafting to method with high conversions (70-90%) under ambient conditions to generate DNA-polymer conjugates, which can hybridized precisely to DNA-origami architectures. We generated homo and block copolymers from three different polymer families (acrylates, methacrylates and acrylamides), coupled them to single stranded DNA (ssDNA) and pattern different DNA-origami architectures to demonstrate the formation of precise surface nanopatterns.
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Affiliation(s)
- Nico Alleva
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
| | - Pia Winterwerber
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
| | - Colette J Whitfield
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
| | - David Y W Ng
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
| | - Tanja Weil
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
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6
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Cheng D, Zhou Z, Shang S, Wang H, Guan H, Yang H, Liu Y. Electrochemical immunosensor for highly sensitive detection of cTnI via in-situ initiated ROP signal amplification strategy. Anal Chim Acta 2022; 1219:340032. [DOI: 10.1016/j.aca.2022.340032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/25/2022] [Accepted: 06/02/2022] [Indexed: 11/27/2022]
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7
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Shao Y, Dong Y, Fan L, Xu W, Bin L, Wang L, Li D, Zhao S. A highly sensitive aptasensor based on 3D-rGO/AuNPs for Hg2+ determination using HCR amplification strategy triggered by T-Hg2+-T. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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8
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Ma N, Liu J, Liu B, Li L, Kong J, Zhang X. Coenzyme-catalyzed electroinitiated reversible addition fragmentation chain transfer polymerization for ultrasensitive electrochemical DNA detection. Talanta 2022; 236:122840. [PMID: 34635230 DOI: 10.1016/j.talanta.2021.122840] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 08/28/2021] [Accepted: 08/31/2021] [Indexed: 12/19/2022]
Abstract
Ultrasensitive detection of biomarkers at an early stage is generally limited by external influence factors such as high reaction temperature, complex operations, and sophisticated instruments. Here, we circumvent these problems by using nicotinamide adenine dinucleotide (NAD+) to control electroinitiated reversible addition fragmentation chain transfer (electro-RAFT) polymerization for biosensing that enables the detection of a few molecules of target DNA. In this coenzyme-catalyzed electro-RAFT polymerization, numerous ferrocenylmethyl methacrylate (FCMMA) as monomer with electrochemistry signal were linked to the biomarker on Au electrode. Afterwards, a strong oxidation peak appears at the potential of about 0.3 V that represents a typical oxidation potential of FCMMA. The sensitivity of this methodology was presented by detecting DNA from 10-1 to 104 fM concentration and detection limit (LOD) being down to 4.39 aM in 10 μL samples. This is lower by factors than detection limits of most other ultra-sensitive electrochemical DNA assays.
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Affiliation(s)
- Nan Ma
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu, 210094, PR China
| | - Jingliang Liu
- School of Environmental Science, Nanjing Xiaozhuang University, Nanjing, 211171, PR China
| | - Bang Liu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu, 210094, PR China
| | - Lianzhi Li
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252059, PR China
| | - Jinming Kong
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, Jiangsu, 210094, PR China.
| | - Xueji Zhang
- School of Biomedical Engineering, Shenzhen University Health Science Center, Shenzhen, Guangdong, 518060, PR China
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9
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Functionalized graphene oxide in situ initiated ring-opening polymerization for highly sensitive sensing of cytokeratin-19 fragment. Mikrochim Acta 2021; 188:123. [PMID: 33712913 DOI: 10.1007/s00604-021-04780-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/07/2021] [Indexed: 01/17/2023]
Abstract
Improving the sensitivity of detection is crucial to monitor biomarker, assess toxicity, and track therapeutic agent. Herein, a sensitivity-improved immunosensor is reported for the first time via functionalized graphene oxide (GO) and a "grafting-to" ring-opening polymerization (ROP) dual signal amplification strategy. Through the ROP reaction using 2-[(4-ferrocenylbutoxy)methyl] oxirane (FcEpo) as the monomer, lots of electroactive tags are linked in situ from multiple initiation sites on the GO surface modified with ethanol amine (GO-ETA), thereby achieving high sensitivity even in the case of trace amounts of tumor markers. The utmost important factor for achieving this high sensitivity is to select functionalized GO as the initiator that contains a large number of repeated hydroxyl functional groups so as to trigger additional ROP reaction. Under the optimal conditions, the high sensitivity and applicability is demonstrated by the use of GO-ETA-mediated ROP-based immunosensor to detect non-small cell lung cancer (NSCLC)-specific biomarker down to 72.58 ag/mL (equivalent to ~6 molecules in a 5 μL sample). Furthermore, the satisfactory results for the determination of biomarkers in clinical serum samples highlighted that this immunosensor holds a huge potential in practical clinical application. This work described an electrochemical immunosensor for ultrasensitive detection of CYFRA 21-1 via the functionalized graphene oxide (GO) and a "grafting-to" ring-opening polymerization (ROP) dual signal amplification strategy, which hold the merits of high sensitivity, applicability, selectivity, efficiency, easy operation and environmental friendliness.
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10
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Smart materials for point-of-care testing: From sample extraction to analyte sensing and readout signal generator. Biosens Bioelectron 2020; 170:112682. [PMID: 33035898 DOI: 10.1016/j.bios.2020.112682] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/30/2020] [Accepted: 10/02/2020] [Indexed: 12/20/2022]
Abstract
The last decade has seen a surge of technical developments in the field on point-of-care testing (POCT). While these developments are extremely diverse, the common aim is to implement improved methods for quick, reliable and inexpensive diagnosis of patients within the clinical setting. While examples of successful introduction and use of POCT techniques are growing, further developments are still necessary to create POCT devices with better portability, usability and performance. Advances in smart materials emerge as potentially valuable know-hows to provide a competitive edge to the development of next generation POCT devices. This review describes the key advantages of adopting smart material-based technologies at different analytical stages of a POCT platform. Under these analytical stages which involves sample pre-treatment, analyte sensing and readout signal generator, several concepts and approaches from contemporary research work in using smart material-based technologies will be the major focus in this review. Lastly, challenges and potential outlook in implementing materials technologies from the application point of view for POCT will be discussed.
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11
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Lückerath T, Koynov K, Loescher S, Whitfield CJ, Nuhn L, Walther A, Barner‐Kowollik C, Ng DYW, Weil T. DNA-Polymer Nanostructures by RAFT Polymerization and Polymerization-Induced Self-Assembly. Angew Chem Int Ed Engl 2020; 59:15474-15479. [PMID: 32301556 PMCID: PMC7496909 DOI: 10.1002/anie.201916177] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/01/2020] [Indexed: 01/06/2023]
Abstract
Nanostructures derived from amphiphilic DNA-polymer conjugates have emerged prominently due to their rich self-assembly behavior; however, their synthesis is traditionally challenging. Here, we report a novel platform technology towards DNA-polymer nanostructures of various shapes by leveraging polymerization-induced self-assembly (PISA) for polymerization from single-stranded DNA (ssDNA). A "grafting from" protocol for thermal RAFT polymerization from ssDNA under ambient conditions was developed and utilized for the synthesis of functional DNA-polymer conjugates and DNA-diblock conjugates derived from acrylates and acrylamides. Using this method, PISA was applied to manufacture isotropic and anisotropic DNA-polymer nanostructures by varying the chain length of the polymer block. The resulting nanostructures were further functionalized by hybridization with a dye-labelled complementary ssDNA, thus establishing PISA as a powerful route towards intrinsically functional DNA-polymer nanostructures.
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Affiliation(s)
- Thorsten Lückerath
- Synthesis of MacromoleculesMax Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Kaloian Koynov
- Synthesis of MacromoleculesMax Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Sebastian Loescher
- Institute for Macromolecular ChemistryFreiburg UniversityStefan Meier Str. 3179104FreiburgGermany
- Freiburg Institute for Interactive Materials and Bioinspired Technologies (FIT)Georges-Köhler-Allee 10579104FreiburgGermany
| | - Colette J. Whitfield
- Synthesis of MacromoleculesMax Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Lutz Nuhn
- Synthesis of MacromoleculesMax Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Andreas Walther
- Institute for Macromolecular ChemistryFreiburg UniversityStefan Meier Str. 3179104FreiburgGermany
- Freiburg Institute for Interactive Materials and Bioinspired Technologies (FIT)Georges-Köhler-Allee 10579104FreiburgGermany
| | - Christopher Barner‐Kowollik
- Centre for Materials Science, School of Chemistry and PhysicsQueensland University of Technology (QUT)2 George StreetQLD4000BrisbaneAustralia
- Macromolecular ArchitecturesInstitute for Chemical Technology and Polymer Chemistry (ITCP)Karlsruhe Institute of Technology (KIT)Engersserstraße 1876131KarlsruheGermany
| | - David Y. W. Ng
- Synthesis of MacromoleculesMax Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
| | - Tanja Weil
- Synthesis of MacromoleculesMax Planck Institute for Polymer ResearchAckermannweg 1055128MainzGermany
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12
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Lückerath T, Koynov K, Loescher S, Whitfield CJ, Nuhn L, Walther A, Barner‐Kowollik C, Ng DYW, Weil T. DNA‐Polymer‐Nanostrukturen durch RAFT‐Polymerisation und polymerisationsinduzierte Selbstassemblierung. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916177] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Thorsten Lückerath
- Synthese von Makromolekülen Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Kaloian Koynov
- Synthese von Makromolekülen Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Sebastian Loescher
- Institut für Makromolekulare Chemie Universität Freiburg Stefan Meier Straße 31 79104 Freiburg Deutschland
- Freiburger Zentrum für Interaktive Werkstoffe und Bioinspirierte Technologien (FIT) Georges-Köhler-Allee 105 79104 Freiburg Deutschland
| | - Colette J. Whitfield
- Synthese von Makromolekülen Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Lutz Nuhn
- Synthese von Makromolekülen Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Andreas Walther
- Institut für Makromolekulare Chemie Universität Freiburg Stefan Meier Straße 31 79104 Freiburg Deutschland
- Freiburger Zentrum für Interaktive Werkstoffe und Bioinspirierte Technologien (FIT) Georges-Köhler-Allee 105 79104 Freiburg Deutschland
| | - Christopher Barner‐Kowollik
- Centre for Materials Science School of Chemistry and Physics Queensland University of Technology (QUT) 2 George Street QLD 4000 Brisbane Australien
- Makromolekulare Architekturen Institut für Technische Chemie und Polymerchemie (ITCP) Karlsruher Institut für Technologie (KIT) Engesserstraße 18 76131 Karlsruhe Deutschland
| | - David Y. W. Ng
- Synthese von Makromolekülen Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
| | - Tanja Weil
- Synthese von Makromolekülen Max-Planck-Institut für Polymerforschung Ackermannweg 10 55128 Mainz Deutschland
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13
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Xiao F, Wei Z, Wang M, Hoff A, Bao Y, Tian L. Oligonucleotide-Polymer Conjugates: From Molecular Basics to Practical Application. Top Curr Chem (Cham) 2020; 378:24. [PMID: 32064539 DOI: 10.1007/s41061-020-0286-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/21/2020] [Indexed: 12/18/2022]
Abstract
DNA exhibits many attractive properties, such as programmability, precise self-assembly, sequence-coded biomedical functions, and good biocompatibility; therefore, DNA has been used extensively as a building block to construct novel nanomaterials. Recently, studies on oligonucleotide-polymer conjugates (OPCs) have attracted increasing attention. As hybrid molecules, OPCs exhibit novel properties, e.g., sophisticated self-assembly behaviors, which are distinct from the simple combination of the functions of DNA and polymer, making OPCs interesting and useful. The synthesis and applications of OPCs are highly dependent on the choice of the polymer block, but a systematic summary of OPCs based on their molecular structures is still lacking. In order to design OPCs for further applications, it is necessary to thoroughly understand the structure-function relationship of OPCs. In this review, we carefully categorize recently developed OPCs by the structures of the polymer blocks, and discuss the synthesis, purification, and applications for each category. Finally, we will comment on future prospects for OPCs.
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Affiliation(s)
- Fan Xiao
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd, Nanshan District, Shenzhen, 518055, Guangdong, People's Republic of China.,School of Materials Science and Engineering, Harbin Institute of Technology, Nangang District, Harbin, 150001, People's Republic of China
| | - Zixiang Wei
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd, Nanshan District, Shenzhen, 518055, Guangdong, People's Republic of China
| | - Maggie Wang
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225-9150, USA
| | - Alexandra Hoff
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225-9150, USA
| | - Ying Bao
- Department of Chemistry, Western Washington University, 516 High Street, Bellingham, WA, 98225-9150, USA.
| | - Leilei Tian
- Department of Materials Science and Engineering, Southern University of Science and Technology, 1088 Xueyuan Blvd, Nanshan District, Shenzhen, 518055, Guangdong, People's Republic of China.
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14
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Sun H, Qiu Y, Lu Y, Kong J, Zhang X. Ultrasensitive DNA electrochemical biosensor based on MnTBAP biomimetic catalyzed AGET ATRP signal amplification reaction. Chem Commun (Camb) 2020; 56:6636-6639. [DOI: 10.1039/d0cc02176h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this paper, an ultrasensitive, highly selective and green electrochemical biosensor for quantifying DNA sequences (aM DNA) based on a MnTBAP catalyst for AGET ATRP reaction is proposed.
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Affiliation(s)
- Haobo Sun
- Research Center for Biomedical and Health Science
- Anhui Science and Technology University
- Fengyang 233100
- P. R. China
- School of Environmental and Biological Engineering
| | - Yunliang Qiu
- Department of Criminal Science and Technology
- Nanjing Forest Police College
- Nanjing 210023
- P. R. China
| | - Yajie Lu
- Research Center for Biomedical and Health Science
- Anhui Science and Technology University
- Fengyang 233100
- P. R. China
| | - Jinming Kong
- School of Environmental and Biological Engineering
- Nanjing University of Science and Technology
- Nanjing 210094
- P. R. China
| | - Xueji Zhang
- School of Biomedical Engineering
- Shenzhen University Health Science Center
- Shenzhen
- P. R. China
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15
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Hu Q, Gan S, Bao Y, Zhang Y, Han D, Niu L. Controlled/“living” radical polymerization-based signal amplification strategies for biosensing. J Mater Chem B 2020; 8:3327-3340. [DOI: 10.1039/c9tb02419k] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Controlled/“living” radical polymerization-based signal amplification strategies and their applications in highly sensitive biosensing of clinically relevant biomolecules are reviewed.
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Affiliation(s)
- Qiong Hu
- Center for Advanced Analytical Science
- School of Chemistry and Chemical Engineering
- Guangzhou University
- Guangzhou 510006
- P. R. China
| | - Shiyu Gan
- Center for Advanced Analytical Science
- School of Chemistry and Chemical Engineering
- Guangzhou University
- Guangzhou 510006
- P. R. China
| | - Yu Bao
- Center for Advanced Analytical Science
- School of Chemistry and Chemical Engineering
- Guangzhou University
- Guangzhou 510006
- P. R. China
| | - Yuwei Zhang
- Center for Advanced Analytical Science
- School of Chemistry and Chemical Engineering
- Guangzhou University
- Guangzhou 510006
- P. R. China
| | - Dongxue Han
- Center for Advanced Analytical Science
- School of Chemistry and Chemical Engineering
- Guangzhou University
- Guangzhou 510006
- P. R. China
| | - Li Niu
- Center for Advanced Analytical Science
- School of Chemistry and Chemical Engineering
- Guangzhou University
- Guangzhou 510006
- P. R. China
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16
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Chakraborty G, Balinin K, Portale G, Loznik M, Polushkin E, Weil T, Herrmann A. Electrostatically PEGylated DNA enables salt-free hybridization in water. Chem Sci 2019; 10:10097-10105. [PMID: 32055364 PMCID: PMC6991176 DOI: 10.1039/c9sc02598g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 09/11/2019] [Indexed: 12/18/2022] Open
Abstract
Chemically modified nucleic acids have long served as a very important class of bio-hybrid structures. In particular, the modification with PEG has advanced the scope and performance of oligonucleotides in materials science, catalysis and therapeutics. Most of the applications involving pristine or modified DNA rely on the potential of DNA to form a double-stranded structure. However, a substantial requirement for metal-cations to achieve hybridization has restricted the range of applications. To extend the applicability of DNA in salt-free or low ionic strength aqueous medium, we introduce noncovalent DNA-PEG constructs that allow canonical base-pairing between individually PEGylated complementary strands resulting in a double-stranded structure in salt-free aqueous medium. This method relies on grafting of amino-terminated PEG polymers electrostatically onto the backbone of DNA, which results in the formation of a PEG-envelope. The specific charge interaction of PEG molecules with DNA, absolute absence of metal ions within the PEGylated DNA molecules and formation of a double helix that is significantly more stable than the duplex in an ionic buffer have been unequivocally demonstrated using multiple independent characterization techniques.
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Affiliation(s)
- Gurudas Chakraborty
- Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , The Netherlands .
- DWI-Leibniz Institute for Interactive Materials , Forckenbeckstraße 50 , 52056 Aachen , Germany
| | - Konstantin Balinin
- Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , The Netherlands .
- DWI-Leibniz Institute for Interactive Materials , Forckenbeckstraße 50 , 52056 Aachen , Germany
- Max Planck Institute for Polymer Research , Ackermannweg 10 , 55128 Mainz , Germany
| | - Giuseppe Portale
- Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , The Netherlands .
| | - Mark Loznik
- Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , The Netherlands .
- DWI-Leibniz Institute for Interactive Materials , Forckenbeckstraße 50 , 52056 Aachen , Germany
| | - Evgeny Polushkin
- Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , The Netherlands .
| | - Tanja Weil
- Max Planck Institute for Polymer Research , Ackermannweg 10 , 55128 Mainz , Germany
| | - Andreas Herrmann
- Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , The Netherlands .
- DWI-Leibniz Institute for Interactive Materials , Forckenbeckstraße 50 , 52056 Aachen , Germany
- Institute of Technical and Macromolecular Chemistry , RWTH Aachen University , Worringerweg 2 , 52074 Aachen , Germany
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17
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Fishman JM, Zwick DB, Kruger AG, Kiessling LL. Chemoselective, Postpolymerization Modification of Bioactive, Degradable Polymers. Biomacromolecules 2019; 20:1018-1027. [PMID: 30608163 PMCID: PMC6690479 DOI: 10.1021/acs.biomac.8b01631] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Degradable polymers promote sustainability, mitigate environmental impact, and facilitate biological applications. Tailoring degradable polymers is challenging because installing functional group-rich side chains is difficult when the backbone itself is susceptible to degradation. A convenient means of side chain installation is through postpolymerization modification (PPM). In functionalizing polyoxazinones, a class of degradable polymers generated by the ring-opening metathesis polymerization (ROMP), we predictably found PPM challenging. Even the versatile azide-alkyne cycloaddition click reaction was ineffective. To solve this problem, we screened PPM reactions whose efficiencies could be assessed using photochemistry (excimer formation). The mildest, pH-neutral process was functionalization of a ketone-containing polymer to yield either oxime (acid labile)- or alkyoxylamine (stable)-substituted polymers. Using this approach, we equipped polymers with fluorophores, reporter groups, and bioactive epitopes. These modifications imbued the polymers with distinctive spectral properties and biological activities. Thus, polyoxazinones are now tunable through a modular method to diversify these macromolecules' function.
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Affiliation(s)
- Joshua M. Fishman
- Department of Chemistry, University of Wisconsin
– Madison, Madison, WI 53706
| | - Daniel B. Zwick
- Department of Biochemisry, University of
Wisconsin – Madison, Madison, WI 53706
| | - Austin G. Kruger
- Department of Chemistry, University of Wisconsin
– Madison, Madison, WI 53706
| | - Laura L. Kiessling
- Department of Chemistry, University of Wisconsin
– Madison, Madison, WI 53706
- Department of Biochemisry, University of
Wisconsin – Madison, Madison, WI 53706
- Department of Chemistry, Massachusetts Institute
of Techology, Cambridge, MA 02139
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18
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Hu Q, Kong J, Han D, Niu L, Zhang X. Electrochemical DNA Biosensing via Electrochemically Controlled Reversible Addition-Fragmentation Chain Transfer Polymerization. ACS Sens 2019; 4:235-241. [PMID: 30620562 DOI: 10.1021/acssensors.8b01357] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Sensitive and selective sensing of biological molecules is fundamental to disease diagnosis and infectious disease surveillance. Herein, an ultrasensitive and highly selective electrochemical DNA biosensor is described by exploiting the electrochemically controlled reversible addition-fragmentation chain-transfer (eRAFT) polymerization as a signal amplification strategy and the peptide nucleic acid (PNA) probes as the recognition elements. Specifically, the PNA probes with a thiol at their 5'-terminals are anchored to a gold electrode surface (via gold-sulfur self-assembly) for sequence-specific recognition of target DNA (tDNA) fragments, of which the phosphate sites serve as the anchorages for the targeted labeling (via the well-established phosphate-Zr4+-carboxylate chemistry) of the carboxyl-group-containing chain-transfer agents (CTAs) for the succedent eRAFT polymerization, wherein the initiating radicals are generated through electrochemical reduction of aryl diazonium salts under a potentiostatic condition. In the presence of ferrocenylmethyl methacrylate (FcCH═CH2) as the monomer, the grafting of polymer chains from the CTA-anchored sites as a result of the eRAFT polymerization brings numerous electroactive Fc tags to the electrode surface, outputting a high electrochemical sensing signal even in the presence of trace amounts of tDNA fragments. Under the optimized conditions, the linear range of the described electrochemical DNA biosensor spans from 10 aM to 10 pM ( R2 = 0.998), with an attomolar detection limit (4.1 aM) being achieved. Moreover, the described electrochemical DNA biosensor is highly selective and applicable to the sensing of tDNA fragments in complex serum samples. Given its high efficiency, easy operation, and low cost, this biosensor shows great promise in real applications.
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Affiliation(s)
- Qiong Hu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, People’s Republic of China
- Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, School of Civil Engineering, Guangzhou University, Guangzhou 510006, People’s Republic of China
| | - Jinming Kong
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, People’s Republic of China
| | - Dongxue Han
- Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, School of Civil Engineering, Guangzhou University, Guangzhou 510006, People’s Republic of China
| | - Li Niu
- Center for Advanced Analytical Science, School of Chemistry and Chemical Engineering, School of Civil Engineering, Guangzhou University, Guangzhou 510006, People’s Republic of China
| | - Xueji Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, People’s Republic of China
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19
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Abdullah R, Xie S, Wang R, Jin C, Du Y, Fu T, Li J, Tan J, Zhang L, Tan W. Artificial Sandwich Base for Monitoring Single-Nucleobase Changes and Charge-Transfer Rates in DNA. Anal Chem 2019; 91:2074-2078. [PMID: 30543105 DOI: 10.1021/acs.analchem.8b04513] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Developing a convenient method to discriminate among different types of DNA nucleotides within a target sequence of the human genome is extremely challenging. We herein report an artificial ferrocene-base (Fe-base) that was synthesized and incorporated into different loci of a DNA strand. The Fe-base replacement on a nucleobase can interact with DNA bases and efficiently discriminate among A, T, G, and C DNA bases of the complementary locus on the basis of interacting electrochemical properties. Furthermore, cyclic-voltammetry (CV) studies demonstrated the electrochemical stability of DNA strands incorporated with Fe-bases and the reversibility of the incorporation. Square-wave voltammetry (SWV) was performed to measure current changes between Fe-bases and bases of interest in the DNA duplex. The changes in the charge-transfer rates appeared to be correlated with the position of the Fe-base in the DNA strand, allowing rapid and efficient sensing of single-nucleobase changes in DNA and showing promise for the design of Fe-oligomer chip technology as a tool for DNA sequencing.
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Affiliation(s)
- Razack Abdullah
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China.,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China
| | - Sitao Xie
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China
| | - Ruowen Wang
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Cheng Jin
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China
| | - Yulin Du
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China
| | - Ting Fu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China
| | - Juan Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China
| | - Lili Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China
| | - Weihong Tan
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering , Shanghai Jiao Tong University , Shanghai 200240 , China.,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China.,Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute , University of Florida , Gainesville , Florida 32611-7200 , United States
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20
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Hu X, Kim CJ, Albert SK, Park SJ. DNA-Grafted Poly(acrylic acid) for One-Step DNA Functionalization of Iron Oxide Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14342-14346. [PMID: 30392363 DOI: 10.1021/acs.langmuir.8b03119] [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
Here, we report one-step DNA functionalization of hydrophobic iron oxide nanoparticles (IONPs) using DNA-grafted poly(acrylic acid) (PAA- g-DNA). PAA- g-DNA was synthesized by coupling PAA to amine-modified oligonucleotides via solid-phase amide chemistry, which yielded PAA grafted with multiple DNA strands with high graft efficiencies. Synthesized PAA- g-DNA was utilized as a phase-transfer and DNA functionalization agent for hydrophobic IONPs, taking advantage of unreacted carboxylic acid groups. The resulting DNA-modified IONPs were well dispersed in aqueous solutions and possessed DNA binding properties characteristic of polyvalent DNA nanostructures, showing that this approach provides a simple one-step method for DNA functionalization of hydrophobic IONPs.
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Affiliation(s)
- Xiaole Hu
- Department of Chemistry and Nanoscience , Ewha Womans University , 52 Ewhayeodae-gil , Seodaemun-gu, Seoul 03760 , Korea
| | - Chan-Jin Kim
- Department of Chemistry and Nanoscience , Ewha Womans University , 52 Ewhayeodae-gil , Seodaemun-gu, Seoul 03760 , Korea
| | - Shine K Albert
- Department of Chemistry and Nanoscience , Ewha Womans University , 52 Ewhayeodae-gil , Seodaemun-gu, Seoul 03760 , Korea
| | - So-Jung Park
- Department of Chemistry and Nanoscience , Ewha Womans University , 52 Ewhayeodae-gil , Seodaemun-gu, Seoul 03760 , Korea
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21
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Gu H, Ciganda R, Castel P, Ruiz J, Astruc D. Living ROMP Synthesis and Redox Properties of Triblock Metallocopolymers Containing Side-Chain Iron and Cobalt Sandwich Complexes. MACROMOL CHEM PHYS 2018. [DOI: 10.1002/macp.201800384] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Haibin Gu
- Key Laboratory of Leather Chemistry and Engineering of Ministry of Education; Sichuan University; Chengdu 610065 China
| | - Roberto Ciganda
- Institute of Molecular Sciences; University of Bordeaux; UMR CNRS 5255 33405 Talence Cedex France
| | - Patricia Castel
- Institute of Molecular Sciences; University of Bordeaux; UMR CNRS 5255 33405 Talence Cedex France
| | - Jaime Ruiz
- Institute of Molecular Sciences; University of Bordeaux; UMR CNRS 5255 33405 Talence Cedex France
| | - Didier Astruc
- Institute of Molecular Sciences; University of Bordeaux; UMR CNRS 5255 33405 Talence Cedex France
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22
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Vyborna Y, Vybornyi M, Häner R. Functional DNA-grafted supramolecular polymers - chirality, cargo binding and hierarchical organization. Chem Commun (Camb) 2018; 53:5179-5181. [PMID: 28439588 DOI: 10.1039/c7cc00886d] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis, characterization and functionalization of DNA-grafted supramolecular polymers are described. Cargo loading of the helical supramolecular assemblies with gold nanoparticles is demonstrated.
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Affiliation(s)
- Yuliia Vyborna
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
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23
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Cai W, Xie S, Zhang J, Tang D, Tang Y. An electrochemical impedance biosensor for Hg2+ detection based on DNA hydrogel by coupling with DNAzyme-assisted target recycling and hybridization chain reaction. Biosens Bioelectron 2017; 98:466-472. [DOI: 10.1016/j.bios.2017.07.025] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/06/2017] [Accepted: 07/10/2017] [Indexed: 12/24/2022]
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24
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Otrin L, Marušič N, Bednarz C, Vidaković-Koch T, Lieberwirth I, Landfester K, Sundmacher K. Toward Artificial Mitochondrion: Mimicking Oxidative Phosphorylation in Polymer and Hybrid Membranes. NANO LETTERS 2017; 17:6816-6821. [PMID: 29067800 DOI: 10.1021/acs.nanolett.7b03093] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
For energy supply to biomimetic constructs, a complex chemical energy-driven ATP-generating artificial system was built. The system was assembled with bottom-up detergent-mediated reconstitution of an ATP synthase and a terminal oxidase into two types of novel nanocontainers, built from either graft copolymer membranes or from hybrid graft copolymer/lipid membranes. The versatility and biocompatibility of the proposed nanocontainers was demonstrated through convenient system assembly and through high retained activity of both membrane-embedded enzymes. In the future, the nanocontainers might be used as a platform for the functional reconstitution of other complex membrane proteins and could considerably expedite the design of nanoreactors, biosensors, and artificial organelles.
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Affiliation(s)
- Lado Otrin
- Max Planck Institute for Dynamics of Complex Technical Systems , Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Nika Marušič
- Max Planck Institute for Dynamics of Complex Technical Systems , Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Claudia Bednarz
- Max Planck Institute for Dynamics of Complex Technical Systems , Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Tanja Vidaković-Koch
- Max Planck Institute for Dynamics of Complex Technical Systems , Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Ingo Lieberwirth
- Max Planck Institute for Polymer Research , Ackermannweg 10, 55128 Mainz, Germany
| | - Katharina Landfester
- Max Planck Institute for Polymer Research , Ackermannweg 10, 55128 Mainz, Germany
| | - Kai Sundmacher
- Max Planck Institute for Dynamics of Complex Technical Systems , Sandtorstrasse 1, 39106 Magdeburg, Germany
- Otto von Guericke University , Universitaetsplatz 2, 39106 Magdeburg, Germany
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25
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Cho VY, Hong BJ, Kohlstedt KL, Schatz GC, Nguyen ST. The competing effects of core rigidity and linker flexibility in the nanoassembly of trivalent small molecule-DNA hybrids (SMDH 3s)-a synergistic experimental-modeling study. NANOSCALE 2017; 9:12652-12663. [PMID: 28825749 PMCID: PMC5804500 DOI: 10.1039/c7nr01931a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The nanoassembly behavior of trivalent small molecule-DNA hybrids (SMDH3s) was investigated as a function of core geometry and supramolecular flexibility through a synergistic experimental-modeling study. While complementary SMDH3s possessing a highly flexible tetrahedral trivalent core primarily assemble into nanoscale caged dimers, the nanoassemblies of SMDH3 comonomers with rigid pyramidal and trigonal cores yield fewer caged dimers and more large-oligomer networks. Specifically, the rigid pyramidal SMDH3 comonomers tend to form smaller nanosized aggregates (dimers, tetramers, and hexamers) upon assembly, attributable to the small (<109°) branch-core-branch angle of the pyramidal core. In contrast, the more-rigid trigonal planar SMDH3 comonomers have a larger (∼120°) branch-core-branch angle, which spaces their DNA arms farther apart, facilitating the formation of larger nanoassemblies (≥nonamers). The population distributions of these nanoassemblies were successfully captured by coarse-grained molecular dynamics (CGMD) simulations over a broad range of DNA concentrations. CGMD simulations can also forecast the effect of incorporating Tn spacer units between the hydridizing DNA arms and the rigid organic cores to increase the overall flexibility of the SMDH3 comonomers. Such "decoupling" of the DNA arms from the organic core was found to result in preferential formation of nanoscale dimers up to an optimal spacer length, beyond which network formation takes over due to entropic factors. This excellent agreement between the simulation and experimental results confirms the versatility of the CGMD model as a useful and reliable tool for elucidating the nanoassembly of SMDH-based building blocks.
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Affiliation(s)
- Vincent Y Cho
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA.
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26
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Yang ZH, Zhuo Y, Yuan R, Chai YQ. Amplified impedimetric aptasensor combining target-induced DNA hydrogel formation with pH-stimulated signal amplification for the heparanase assay. NANOSCALE 2017; 9:2556-2562. [PMID: 28150826 DOI: 10.1039/c6nr08353f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Herein, a novel electrochemical impedimetric biosensor for the heparanase (HPA) assay was developed based on target protein-induced DNA hydrogel formation, followed by pH-stimulation of the hydrogel density to increase the signal amplification. The method involved the synthesis of two different copolymer chains, consisting of two cooperatively functioning cross-linking elements, where one element was associated with the HPA-response and the other one with the pH-response. Initially, single-strand DNA as a capture probe was modified on the electrode surface. In the presence of HPA, the HPA-responsive element binding to HPA-induced DNA hybridization between the two copolymer chains and captured DNA, giving rise to the formation of a low-density polymer hydrogel film on the electrode surface and it obtaining an obvious impedimetric response. A significant signal enhancement was observed when changing the pH of the hydrogel film to 5.0, which could be ascribed to the fact that the pH-responsive element can fold into four-stranded i-motif structures at pH 5.0, leading to the increase in density of the hydrogel film. By implementing the DNA hydrogel to induce an impedimetric response change, this impedimetric biosensor exhibited an excellent analytical performance towards the HPA quantitative assay, with a low detection limit of 0.003 pg mL-1. This new method provides a versatile signal amplification method and paves a new way to construct impedimetric sensors for bioassays.
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Affiliation(s)
- Zhe-Han Yang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
| | - Ying Zhuo
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
| | - Ya-Qin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
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27
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Lee AW, Hsu CC, Liu YZ, Wei PL, Chen JK. Supermolecules of poly(N-isopropylacrylamide) complexating Herring sperm DNA with bio-multiple hydrogen bonding. Colloids Surf B Biointerfaces 2016; 148:422-430. [PMID: 27639492 DOI: 10.1016/j.colsurfb.2016.09.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 09/09/2016] [Accepted: 09/11/2016] [Indexed: 10/21/2022]
Abstract
In this study we used the poly(N-isopropylacrylamide) (PNIPAAm) as a medium to blend with an organic DNA, herring sperm DNA (HSD), to generate PNIPAAm-HSD supramolecular complexes. Bio-multiple hydrogen bonding (BMHB) between PNIPAAm and HSD was investigated that changed the temperature responsiveness of PNIPAAm relatively to the HSD concentrations. With blending the HSD into PNIPAAm matrix, the phase separation in solution is completely opposite from that of neat PNIPAAm. Surface property in static water contact angle (SWCA) is also opposite from that of pure PNIPAAm upon increasing HSD content over 60%. In addition, we found that the PNIPAAm and HSD self-assembled a specific triangle-like structure at a PNIPAAm-to-HSD weight ratio of 1:4 at 25°C; while the triangle-like structure disappeared with increasing temperature to 45°C. Furthermore, both PNIPAAm and HSD could be regarded as insulator, but it transformed into a semiconductive matter after blending with the HSD. Incorporation of organic DNA with hydrogel could significantly change their properties, which might facilitate their use as novel materials in bioelectronics.
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Affiliation(s)
- Ai-Wei Lee
- Department of Anatomy and Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan; Department of Materials Science and Engineering, National Taiwan University of Science and Technology, 43, Sec 4, Keelung Rd, Taipei 106, Taiwan
| | - Cheng-Chen Hsu
- Department of Anatomy and Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
| | - Yi-Zu Liu
- Department of Materials Science and Engineering, National Taiwan University of Science and Technology, 43, Sec 4, Keelung Rd, Taipei 106, Taiwan
| | - Po-Li Wei
- Cancer Center, Division of General Surgery, Department of Surgery, Taipei Medical University Hospital, Department of Surgery, College of Medicine, Graduate Institute of Cancer Biology and Drug Discovery, Taipei Medical University, Taipei, Taiwan
| | - Jem-Kun Chen
- Department of Materials Science and Engineering, National Taiwan University of Science and Technology, 43, Sec 4, Keelung Rd, Taipei 106, Taiwan.
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28
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Ghobadi AF, Jayaraman A. Effects of Polymer Conjugation on Hybridization Thermodynamics of Oligonucleic Acids. J Phys Chem B 2016; 120:9788-99. [DOI: 10.1021/acs.jpcb.6b06970] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Ahmadreza F. Ghobadi
- Department
of Chemical and Biomolecular Engineering, Colburn Laboratory, University of Delaware, 150 Academy Street, Newark, Delaware 19711, United States
| | - Arthi Jayaraman
- Department
of Chemical and Biomolecular Engineering, Colburn Laboratory, University of Delaware, 150 Academy Street, Newark, Delaware 19711, United States
- Department
of Material Science and Engineering, University of Delaware, Newark, Delaware 19711, United States
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29
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Trinh T, Chidchob P, Bazzi HS, Sleiman HF. DNA micelles as nanoreactors: efficient DNA functionalization with hydrophobic organic molecules. Chem Commun (Camb) 2016; 52:10914-7. [PMID: 27533528 DOI: 10.1039/c6cc04970b] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We report a micelle-templated method to enhance the reactivity of DNA with highly hydrophobic molecules. Lipids, chromophores and polymers can be conjugated to DNA in high yield and under mild conditions. This method expands the range of DNA-templated reactions for DNA-encoded libraries, oligonucleotide and drug delivery, nanopore mimetics and DNA nanotechnology.
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Affiliation(s)
- Tuan Trinh
- Department of Chemistry and Center for Self-Assembled Chemical Structures, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8.
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30
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Design of polyelectrolyte core-shells with DNA to control TMPyP binding. Colloids Surf B Biointerfaces 2016; 146:127-35. [PMID: 27285535 DOI: 10.1016/j.colsurfb.2016.05.047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 04/19/2016] [Accepted: 05/16/2016] [Indexed: 11/23/2022]
Abstract
The interaction of DNA with 5,10,15,20-tetrakis(4-N-methylpyridiniumyl)porphyrin (TMPyP) in polyelectrolyte core-shells obtained via layer by layer adsorption of poly(sodium 4-styrenesulfonate), PSS, and poly(allylamine hydrochloride), PAH, polyelectrolytes was followed by steady state, time resolved fluorescence and by Fluorescence Lifetime Imaging Microscopy (FLIM). Our results show that DNA adsorption onto polyelectrolyte core-shell changes the TMPyP interaction within PSS/PAH core-shells structure and increase significantly the TMPyP uptake. Specific DNA/TMPyP interactions are also altered by DNA adsorption favouring porphyrin intercalation onto GC pair rich regions. Circular dichroism (CD) spectra reveal that DNA undergoes important conformational changes upon adsorption onto the core-shell surface, which are reverted upon TMPyP encapsulation.
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31
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Kumari R, Singh S, Monisha M, Bhowmick S, Roy A, Das N, Das P. Hierarchical coassembly of DNA-triptycene hybrid molecular building blocks and zinc protoporphyrin IX. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2016; 7:697-707. [PMID: 27335759 PMCID: PMC4901925 DOI: 10.3762/bjnano.7.62] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 04/29/2016] [Indexed: 05/06/2023]
Abstract
Herein, we describe the successful construction of composite DNA nanostructures by the self-assembly of complementary symmetrical 2,6,14-triptycenetripropiolic acid (TPA)-DNA building blocks and zinc protoporphyrin IX (Zn PpIX). DNA-organic molecule scaffolds for the composite DNA nanostructure were constructed through covalent conjugation of TPA with 5'-C12-amine-terminated modified single strand DNA (ssDNA) and its complementary strand. The repeated covalent conjugation of TPA with DNA was confirmed by using denaturing polyacrylamide gel electrophoresis (PAGE), reverse-phase high-performance liquid chromatography (RP-HPLC) and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF). The biologically relevant photosensitizer Zn PpIX was used to direct the hybridization-mediated self-assembly of DNA-TPA molecular building blocks as well as a model guest molecule within the DNA-TPA supramolecular self-assembly. The formation of fiber-like composite DNA nanostructures was observed. Native PAGE, circular dichroism (CD) and atomic force microscopy (AFM) have been utilized for analyzing the formation of DNA nanofibers after the coassembly. Computational methods were applied to discern the theoretical dimension of the DNA-TPA molecular building block of the nanofibers. A notable change in photocatalytic efficiency of Zn PpIX was observed when it was inside the TPA-DNA scaffold. The significant increase in ROS generation by Zn PpIX when trapped in this biocompatible DNA-TPA hybrid nanofiber may be an effective tool to explore photodynamic therapy (PDT) applications as well as photocatalytic reactions.
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Affiliation(s)
- Rina Kumari
- Department of Chemistry, IIT Patna, Bihata 801118, India
| | - Sumit Singh
- Department of Chemistry, IIT Patna, Bihata 801118, India
| | - Mohan Monisha
- Department of Biotechnology, IIT Hyderabad, Hyderabad, 502205, India
| | | | - Anindya Roy
- Department of Biotechnology, IIT Hyderabad, Hyderabad, 502205, India
| | - Neeladri Das
- Department of Chemistry, IIT Patna, Bihata 801118, India
| | - Prolay Das
- Department of Chemistry, IIT Patna, Bihata 801118, India
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32
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Vyborna Y, Vybornyi M, Häner R. From Ribbons to Networks: Hierarchical Organization of DNA-Grafted Supramolecular Polymers. J Am Chem Soc 2015; 137:14051-4. [DOI: 10.1021/jacs.5b09889] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Yuliia Vyborna
- Department of Chemistry and
Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Mykhailo Vybornyi
- Department of Chemistry and
Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Robert Häner
- Department of Chemistry and
Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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33
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Hong BJ, Cho VY, Bleher R, Schatz GC, Nguyen ST. Enhancing DNA-Mediated Assemblies of Supramolecular Cage Dimers through Tuning Core Flexibility and DNA Length—A Combined Experimental–Modeling Study. J Am Chem Soc 2015; 137:13381-8. [DOI: 10.1021/jacs.5b08678] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Bong Jin Hong
- Department
of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Vincent Y. Cho
- Department
of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Reiner Bleher
- NUANCE
Center and Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208-3108, United States
| | - George C. Schatz
- Department
of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - SonBinh T. Nguyen
- Department
of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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34
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Chinen AB, Guan CM, Ferrer JR, Barnaby SN, Merkel TJ, Mirkin CA. Nanoparticle Probes for the Detection of Cancer Biomarkers, Cells, and Tissues by Fluorescence. Chem Rev 2015; 115:10530-74. [PMID: 26313138 DOI: 10.1021/acs.chemrev.5b00321] [Citation(s) in RCA: 621] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Alyssa B Chinen
- Department of Chemistry, ‡Department of Chemical Engineering, §Department of Interdepartmental Biological Sciences, and ∥International Institute for Nanotechnology, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Chenxia M Guan
- Department of Chemistry, ‡Department of Chemical Engineering, §Department of Interdepartmental Biological Sciences, and ∥International Institute for Nanotechnology, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Jennifer R Ferrer
- Department of Chemistry, ‡Department of Chemical Engineering, §Department of Interdepartmental Biological Sciences, and ∥International Institute for Nanotechnology, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Stacey N Barnaby
- Department of Chemistry, ‡Department of Chemical Engineering, §Department of Interdepartmental Biological Sciences, and ∥International Institute for Nanotechnology, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Timothy J Merkel
- Department of Chemistry, ‡Department of Chemical Engineering, §Department of Interdepartmental Biological Sciences, and ∥International Institute for Nanotechnology, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Chad A Mirkin
- Department of Chemistry, ‡Department of Chemical Engineering, §Department of Interdepartmental Biological Sciences, and ∥International Institute for Nanotechnology, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208, United States
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35
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Vyborna Y, Vybornyi M, Rudnev AV, Häner R. DNA-Grafted Supramolecular Polymers: Helical Ribbon Structures Formed by Self-Assembly of Pyrene-DNA Chimeric Oligomers. Angew Chem Int Ed Engl 2015; 54:7934-8. [DOI: 10.1002/anie.201502066] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 03/31/2015] [Indexed: 12/31/2022]
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36
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Vyborna Y, Vybornyi M, Rudnev AV, Häner R. DNA-Grafted Supramolecular Polymers: Helical Ribbon Structures Formed by Self-Assembly of Pyrene-DNA Chimeric Oligomers. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502066] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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37
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Wu C, Cheng Q, Wu K. Electrochemical Functionalization of N-Methyl-2-pyrrolidone-Exfoliated Graphene Nanosheets as Highly Sensitive Analytical Platform for Phenols. Anal Chem 2015; 87:3294-9. [DOI: 10.1021/ac504309j] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Can Wu
- Key Laboratory for Large-Format
Battery Materials and
System, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Qin Cheng
- Key Laboratory for Large-Format
Battery Materials and
System, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Kangbing Wu
- Key Laboratory for Large-Format
Battery Materials and
System, Ministry of Education, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
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38
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Marciel AB, Mai DJ, Schroeder CM. Template-Directed Synthesis of Structurally Defined Branched Polymers. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b00219] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Amanda B. Marciel
- Center for Biophysics and Quantitative
Biology, ‡Department of Chemical and Biomolecular
Engineering, §Department of Chemistry, and ∥Department of Materials Science and Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Danielle J. Mai
- Center for Biophysics and Quantitative
Biology, ‡Department of Chemical and Biomolecular
Engineering, §Department of Chemistry, and ∥Department of Materials Science and Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Charles M. Schroeder
- Center for Biophysics and Quantitative
Biology, ‡Department of Chemical and Biomolecular
Engineering, §Department of Chemistry, and ∥Department of Materials Science and Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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39
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Jia F, Lu X, Tan X, Zhang K. Facile synthesis of nucleic acid–polymer amphiphiles and their self-assembly. Chem Commun (Camb) 2015; 51:7843-6. [DOI: 10.1039/c5cc01934f] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Facile synthesis of nucleic acid–polymer amphiphiles (NAPAs) is developed and the self-assembly behavior of the NAPAs is studied.
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Affiliation(s)
- Fei Jia
- Department of Chemistry and Chemical Biology
- Northeastern University
- Boston
- USA
| | - Xueguang Lu
- Department of Chemistry and Chemical Biology
- Northeastern University
- Boston
- USA
| | - Xuyu Tan
- Department of Chemistry and Chemical Biology
- Northeastern University
- Boston
- USA
| | - Ke Zhang
- Department of Chemistry and Chemical Biology
- Northeastern University
- Boston
- USA
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40
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Peterson AM, Heemstra JM. Controlling self‐assembly of
DNA
‐polymer conjugates for applications in imaging and drug delivery. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2014; 7:282-97. [DOI: 10.1002/wnan.1309] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 08/18/2014] [Accepted: 09/16/2014] [Indexed: 01/01/2023]
Affiliation(s)
- Amberlyn M. Peterson
- Department of Chemistry and the Center for Cell and Genome ScienceUniversity of UtahSalt Lake CityUTUSA
| | - Jennifer M. Heemstra
- Department of Chemistry and the Center for Cell and Genome ScienceUniversity of UtahSalt Lake CityUTUSA
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41
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Liu K, Zheng L, Liu Q, de Vries JW, Gerasimov JY, Herrmann A. Nucleic acid chemistry in the organic phase: from functionalized oligonucleotides to DNA side chain polymers. J Am Chem Soc 2014; 136:14255-62. [PMID: 25265497 DOI: 10.1021/ja5080486] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
DNA-incorporating hydrophobic moieties can be synthesized by either solid-phase or solution-phase coupling. On a solid support the DNA is protected, and hydrophobic units are usually attached employing phosphoramidite chemistry involving a DNA synthesizer. On the other hand, solution coupling in aqueous medium results in low yields due to the solvent incompatibility of DNA and hydrophobic compounds. Hence, the development of a general coupling method for producing amphiphilic DNA conjugates with high yield in solution remains a major challenge. Here, we report an organic-phase coupling strategy for nucleic acid modification and polymerization by introducing a hydrophobic DNA-surfactant complex as a reactive scaffold. A remarkable range of amphiphile-DNA structures (DNA-pyrene, DNA-triphenylphosphine, DNA-hydrocarbon, and DNA block copolymers) and a series of new brush-type DNA side-chain homopolymers with high DNA grafting density are produced efficiently. We believe that this method is an important breakthrough in developing a generalized approach to synthesizing functional DNA molecules for self-assembly and related technological applications.
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Affiliation(s)
- Kai Liu
- Zernike Institute for Advanced Materials , Nijenborgh 4, 9747 AG Groningen, The Netherlands
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42
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Cho BS, Kim JS, Lee JM, Kweon JO, Noh ST. Synthesis and characterization of poly(ferrocenyl glycidyl ether)-1,2-butylene oxide copolymers. Macromol Res 2014. [DOI: 10.1007/s13233-014-2115-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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43
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James C, Rush AM, Insley T, Vuković L, Adamiak L, Král P, Gianneschi NC. Poly(oligonucleotide). J Am Chem Soc 2014; 136:11216-9. [PMID: 25077676 PMCID: PMC4140503 DOI: 10.1021/ja503142s] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Indexed: 01/01/2023]
Abstract
Here we report the preparation of poly(oligonucleotide) brush polymers and amphiphilic brush copolymers from nucleic acid monomers via graft-through polymerization. We describe the polymerization of PNA-norbornyl monomers to yield poly-PNA (poly(peptide nucleic acid)) via ring-opening metathesis polymerization (ROMP) with the initiator, (IMesH2)(C5H5N)2(Cl)2RuCHPh.1 In addition, we present the preparation of poly-PNA nanoparticles from amphiphilic block copolymers and describe their hybridization to a complementary single-stranded DNA (ssDNA) oligonucleotide.
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Affiliation(s)
- Carrie
R. James
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Anthony M. Rush
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Thomas Insley
- Department of Chemistry, Department of Physics University
of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Lela Vuković
- Department of Chemistry, Department of Physics University
of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Lisa Adamiak
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Petr Král
- Department of Chemistry, Department of Physics University
of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Nathan C. Gianneschi
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
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44
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Gu H, Rapakousiou A, Castel P, Guidolin N, Pinaud N, Ruiz J, Astruc D. Living Ring-Opening Metathesis–Polymerization Synthesis and Redox-Sensing Properties of Norbornene Polymers and Copolymers Containing Ferrocenyl and Tetraethylene Glycol Groups. Organometallics 2014. [DOI: 10.1021/om5006897] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Haibin Gu
- ISM,
UMR CNRS No. 5255, University of Bordeaux, 33405 Talence Cedex, France
| | - Amalia Rapakousiou
- ISM,
UMR CNRS No. 5255, University of Bordeaux, 33405 Talence Cedex, France
| | - Patricia Castel
- ISM,
UMR CNRS No. 5255, University of Bordeaux, 33405 Talence Cedex, France
| | - Nicolas Guidolin
- LCPO,
UMR CNRS No. 5629, University of Bordeaux, 33607 Pessac Cedex, France
| | - Nöel Pinaud
- ISM,
UMR CNRS No. 5255, University of Bordeaux, 33405 Talence Cedex, France
| | - Jaime Ruiz
- ISM,
UMR CNRS No. 5255, University of Bordeaux, 33405 Talence Cedex, France
| | - Didier Astruc
- ISM,
UMR CNRS No. 5255, University of Bordeaux, 33405 Talence Cedex, France
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45
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Lu X, Watts E, Jia F, Tan X, Zhang K. Polycondensation of Polymer Brushes via DNA Hybridization. J Am Chem Soc 2014; 136:10214-7. [DOI: 10.1021/ja504790r] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Xueguang Lu
- Department of Chemistry and
Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Eleanor Watts
- Department of Chemistry and
Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Fei Jia
- Department of Chemistry and
Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Xuyu Tan
- Department of Chemistry and
Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Ke Zhang
- Department of Chemistry and
Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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46
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Yildirim I, Eryazici I, Nguyen ST, Schatz GC. Hydrophobic organic linkers in the self-assembly of small molecule-DNA hybrid dimers: a computational-experimental study of the role of linkage direction in product distributions and stabilities. J Phys Chem B 2014; 118:2366-76. [PMID: 24494718 PMCID: PMC3954456 DOI: 10.1021/jp501041m] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Detailed computational and experimental studies reveal the crucial role that hydrophobic interactions play in the self-assembly of small molecule-DNA hybrids (SMDHs) into cyclic nanostructures. In aqueous environments, the distribution of the cyclic structures (dimers or higher-order structures) greatly depends on how well the hydrophobic surfaces of the organic cores in these nanostructures are minimized. Specifically, when the cores are attached to the 3'-ends of the DNA component strands, they can insert into the minor groove of the duplex that forms upon self-assembly, favoring the formation of cyclic dimers. However, when the cores are attached to the 5'-ends of the DNA component strands, such insertion is hindered, leading to the formation of higher-order cyclic structures. These computational insights are supported by experimental results that show clear differences in product distributions and stabilities for a broad range of organic core-linked DNA hybrids with different linkage directions and flexibilities.
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Affiliation(s)
- Ilyas Yildirim
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208
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47
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Abd-El-Aziz AS, Agatemor C, Etkin N. Sandwich complex-containing macromolecules: property tunability through versatile synthesis. Macromol Rapid Commun 2014; 35:513-59. [PMID: 24474608 DOI: 10.1002/marc.201300826] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 12/03/2013] [Indexed: 12/17/2022]
Abstract
Sandwich complexes feature unique properties as the physical and electronic properties of a hydrocarbon ligand or its derivative are integrated into the physical, electronic, magnetic, and optical properties of a metal. Incorporation of these complexes into macromolecules results in intriguing physical, electrical, and optical properties that were hitherto unknown in organic-based macromolecules. These properties are tunable through well-designed synthetic strategies. This review surveys many of the synthetic approaches that have resulted in tuning the properties of sandwich complex-containing macromolecules. While the past two decades have seen an ever-growing number of research publications in this field, gaps remain to be filled. Thus, we expect this review to stimulate research interest towards bridging these gaps, which include the insolubility of some of these macromolecules as well as expanding the scope of the sandwich complexes.
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Affiliation(s)
- Alaa S Abd-El-Aziz
- Department of Chemistry, University of Prince Edward Island, 550 University Avenue, Charlottetown, Prince Edward Island, C1A 4P3, Canada
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48
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Thaner RV, Eryazici I, Farha OK, Mirkin CA, Nguyen ST. Facile one-step solid-phase synthesis of multitopic organic–DNA hybrids via “click” chemistry. Chem Sci 2014. [DOI: 10.1039/c3sc53206b] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Small molecule–DNA hybrids can be synthesized in a one-pot fashion and in good yields by coupling multiazide cores to alkyne-modified DNAs on a solid support using click chemistry.
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Affiliation(s)
- Ryan V. Thaner
- Department of Chemistry and the International Institute for Nanotechnology
- Northwestern University
- Evanston, USA
| | - Ibrahim Eryazici
- Department of Chemistry and the International Institute for Nanotechnology
- Northwestern University
- Evanston, USA
| | - Omar K. Farha
- Department of Chemistry and the International Institute for Nanotechnology
- Northwestern University
- Evanston, USA
| | - Chad A. Mirkin
- Department of Chemistry and the International Institute for Nanotechnology
- Northwestern University
- Evanston, USA
| | - SonBinh T. Nguyen
- Department of Chemistry and the International Institute for Nanotechnology
- Northwestern University
- Evanston, USA
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49
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Wilks TR, Pitto-Barry A, Kirby N, Stulz E, O'Reilly RK. Construction of DNA–polymer hybrids using intercalation interactions. Chem Commun (Camb) 2014; 50:1338-40. [DOI: 10.1039/c3cc48726a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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50
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Latorre A, Lorca R, Zamora F, Somoza Á. Enhanced fluorescence of silver nanoclusters stabilized with branched oligonucleotides. Chem Commun (Camb) 2013; 49:4950-2. [PMID: 23609158 DOI: 10.1039/c3cc40446c] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
DNA stabilized silver nanoclusters (AgNCs) are promising optical materials, whose fluorescence properties can be tuned by the selection of the DNA sequence employed. In this work we have used modified oligonucleotides in the preparation of AgNCs. The fluorescent intensity obtained was 60 times higher than that achieved with standard oligonucleotides.
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Affiliation(s)
- Alfonso Latorre
- Instituto Madrileño de Estudios Avanzados en Nanociencia & CNB-CSIC-IMDEA Nanociencia Associated Unit Unidad de Nanobiotecnología Cantoblanco, 28049 Madrid, Spain
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