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Feng C, Liu X, Sun YF, Ren CL. Double-Stranded DNA Immobilized in Lying-Flat and Upright Orientation on a PNIPAm-Coated Surface: A Theoretical Study. ACS Macro Lett 2024:105-111. [PMID: 38190547 DOI: 10.1021/acsmacrolett.3c00647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Surface-immobilized double-stranded DNA (dsDNA) in upright orientation plays an important role in optimizing and understanding DNA-based nanosensors and nanodevices. However, it is difficult to regulate the surface density of upright DNA due to the fact that DNA usually stands vertically at a high packing density but may lie down at a low packing density. We herein report dsDNA immobilized in upright orientation on a poly(N-isopropylacrylamide) (PNIPAm)-coated surface in theory. The theoretical results reveal that the angle of upright DNA relative to the surface is larger than that of DNA immobilized on the bare surface caused by the lying-flat DNA under proper PNIPAm surface coverage at 45 °C. The surface density of upright DNA is significantly influenced by DNA concentration and DNA length. It is envisioned that the density-regulated DNA molecules immobilized in upright orientation in the present work are well suited to bottom-up construction of complex DNA-based nanostructures and nanodevices.
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Affiliation(s)
- Chao Feng
- State Key Laboratory of Metastable Materials Science & Technology and Hebei Key Laboratory of Microstructural Material Physics, School of Science, Yanshan University, Qinhuangdao 066004, China
| | - Xiao Liu
- State Key Laboratory of Metastable Materials Science & Technology and Hebei Key Laboratory of Microstructural Material Physics, School of Science, Yanshan University, Qinhuangdao 066004, China
| | - Yang-Feng Sun
- Industrial Technology Center, Chengde Petroleum College, Chengde 067000, China
| | - Chun-Lai Ren
- National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, China
- Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
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2
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Bi S, Hang C, Qi J, Zhang W, Jiang X. Green Synthesis of Liquid Metal-Doped Carbon Dots for Treating Multidrug-Resistant Gram-Negative Bacteria. Adv Biol (Weinh) 2023; 7:e2200297. [PMID: 36650944 DOI: 10.1002/adbi.202200297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/26/2022] [Indexed: 01/19/2023]
Abstract
Global emergence of multidrug-resistant (MDR) gram-negative bacteria triggers severe infections that result in an epidemic. It is urgent to discover novel classes of antibacterial agents. Here, a green route for synthesizing polyethylene glycol-based carbon dots (PEG-CDs) doped with liquid metal (LM-Cdots) via a solvent-free system is presented. LM-Cdots synthesized via ultrasound exhibit great antibacterial activity against gram-negative bacteria (E. coli, P. aeruginosa, K. pneumoniae, and A. baumannii) and their multidrug-resistant (MDR) clinical isolates. In the in vitro antibacterial test with MDR K. pneumoniae, LM-Cdots show an extremely low minimum inhibition concentration (MIC) of 0.63 µg mL-1 . Compared to naked PEG-CDs, the MIC is improved by 1000 times. In vivo results reveal that LM-Cdots can accelerate wound healing with low biotoxicity and inflammation.
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Affiliation(s)
- Shunchao Bi
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, No. 11 Zhongguancun Beiyitiao, 100190, Beijing, P. R. China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, 100049, Beijing, P. R. China
| | - Chen Hang
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, No. 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen, Guangdong, 518055, P. R. China
| | - Jie Qi
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, No. 11 Zhongguancun Beiyitiao, 100190, Beijing, P. R. China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, 100049, Beijing, P. R. China
| | - Wei Zhang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for NanoScience and Technology, No. 11 Zhongguancun Beiyitiao, 100190, Beijing, P. R. China
| | - Xingyu Jiang
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, No. 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen, Guangdong, 518055, P. R. China
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Temperature–regulated non-monotonic behavior of DNA immobilization on poly(N–isopropylacrylamide) (PNIPAm)–grafted surface. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.128507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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4
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Hinson CM, Bardo AM, Shannon CE, Rivera S, Swaminathan J, Marcotte EM, Anslyn EV. Studies of Surface Preparation for the Fluorosequencing of Peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:14856-14865. [PMID: 34904833 PMCID: PMC8982273 DOI: 10.1021/acs.langmuir.1c02644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Silica passivating agents have shown great success in minimizing nonspecific protein binding to glass surfaces for imaging and microscopy applications. Amine-derivatized surfaces are commonly used in conjugation with amide coupling agents to immobilize peptides/proteins through C-terminal or side-chain carboxylic acids. In the case of the single-molecule fluorosequencing of peptides, attachment occurs via the C-terminus and nonspecific surface binding has previously been a source of error in peptide identification. Here, we employ fluorosequencing as a high-throughput, single-molecule sensitivity assay to identify and quantify the extent of nonspecific binding of peptides to amine-derivatized surfaces. We show that there is little improvement when using common passivating agents in combination with the surface derivatizing agent 3-aminopropyl-triethoxysilane (APTES) to couple the peptides to the modified surface. Furthermore, many xanthene fluorophores have carboxylic acids in the appended phenyl ring at positions ortho and meta or ortho and para, and the literature shows that conjugation through the ortho position is not favored. Because xanthene-derived fluorophores are commonly used for single-molecule applications, we devised a novel assay to probe the conjugation of peptides via their fluorophores relative to their C-termini on silane-derivatized surfaces. We find significant attachment to the ortho position, which is a warning to those attempting to immobilize fluorophore-labeled peptides to silica surfaces via amide coupling agents. However, eliminating all amines on the surface by switching to 3-azidopropyl-triethoxysilane (AzTES) for coupling via copper-catalyzed azide-alkyne cycloaddition (CuAAC) and omitting additional passivation agents allowed us to achieve a high level of C-terminally bound peptides relative to nonspecifically or ortho-phenyl-bound, fluorophore-labeled peptides. This strategy substantially improves the specificity of peptide immobilization for single-molecule fluorosequencing experiments.
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Feng C, Mu JX, Ren CL. Regulation of oligonucleotide adsorption by a thermo and pH dual-responsive copolymer layer. Phys Chem Chem Phys 2021; 23:14296-14307. [PMID: 34160496 DOI: 10.1039/d1cp01644j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Oligonucleotides hold great promise as therapeutic agents to specifically and selectively inhibit gene expression. In order to achieve better targeting efficiency and treatment efficacy, nanocarriers that are dual-responsive to both temperature and pH are more attractive and suitable due to the fact that certain malignancies can cause a slight increase of local temperature and a minor decrease in extracellular pH around the tumor site at the same time. Here, we systematically study oligonucleotide adsorption on the poly(ethyleneimine)-b-poly(N-isopropylacrylamide) (PEI-b-PNIPAm) copolymer layer grafted on a planar surface and nanoparticles with various radii, where the single effect of temperature or pH alone on oligonucleotide adsorption has been extensively investigated, but the combined effect of temperature and pH is less discussed. The theoretical results show that the surface density of the adsorbed oligonucleotides exhibits thermo and pH dual-responsive behavior, in which temperature and pH exhibit a combined effect on the loading capacity of the oligonucleotides. The underlying molecular mechanism of the dual-responsive behavior is revealed. Besides, the effect of important but coupled parameters in nanocarrier design such as polymer surface coverage and length, salt concentration as well as surface curvature (inverse nanoparticle radius) that may influence the dual-responsive behavior of oligonucleotide adsorption is further discussed, which is of great significance to direct the optimal design of PNIPAm/PEI-based nanocarriers to improve the transfection efficiency by achieving the maximal loading capacity of oligonucleotides at different temperatures and pH values.
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Affiliation(s)
- Chao Feng
- State Key Laboratory of Metastable Materials Science & Technology and Hebei Key Laboratory of Microstructural Material Physics, School of Science, Yanshan University, Qinhuangdao, 066004, China.
| | - Jiang-Xue Mu
- State Key Laboratory of Metastable Materials Science & Technology and Hebei Key Laboratory of Microstructural Material Physics, School of Science, Yanshan University, Qinhuangdao, 066004, China.
| | - Chun-Lai Ren
- National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing, 210093, China. and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing, 210093, China
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Stereochemistry of the α-carbon in the benzylic modifying moiety attached at the C-5 end of thymidine affects the potency of a newly identified anti-cancer lead nucleoside. Tetrahedron 2020. [DOI: 10.1016/j.tet.2020.131705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Fabrication, Characterization and Application of Biomolecule Micropatterns on Cyclic Olefin Polymer (COP) Surfaces with Adjustable Contrast. BIOSENSORS-BASEL 2019; 10:bios10010003. [PMID: 31905666 PMCID: PMC7168193 DOI: 10.3390/bios10010003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/19/2019] [Accepted: 12/25/2019] [Indexed: 01/08/2023]
Abstract
Peptide and protein micropatterns are powerful tools for the investigation of various cellular processes, including protein–protein interactions (PPIs). Within recent years, various approaches for the production of functional surfaces have been developed. Most of these systems use glass as a substrate, which has several drawbacks, including high fragility and costs, especially if implemented for fluorescence microscopy. In addition, conventional fabrication technologies such as microcontact printing (µCP) are frequently used for the transfer of biomolecules to the glass surface. In this case, it is challenging to adjust the biomolecule density. Here, we show that cyclic olefin polymer (COP) foils, with their encouraging properties, including the ease of manufacturing, chemical resistance, biocompatibility, low water absorption, and optical clarity, are a promising alternative to glass substrates for the fabrication of micropatterns. Using a photolithography-based approach, we generated streptavidin/biotinylated antibody patterns on COPs with the possibility of adjusting the pattern contrast by varying plasma activation parameters. Our experimental setup was finally successfully implemented for the analysis of PPIs in the membranes of live cells via total internal reflection fluorescence (TIRF) microscopy.
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Traeger JC, Lamberty Z, Schwartz DK. Influence of Oligonucleotide Grafting Density on Surface-Mediated DNA Transport and Hybridization. ACS NANO 2019; 13:7850-7859. [PMID: 31244029 DOI: 10.1021/acsnano.9b02157] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Adsorption of soluble DNA to surfaces decorated with complementary DNA plays an important role in many bionanotechnology applications, and previous studies have reported complex dependencies of the surface density of immobilized DNA on hybridization. While these effects have been speculatively ascribed to steric or electrostatic effects, the influence of surface-mediated molecular transport (i.e., intermittent "hopping diffusion") has not been fully appreciated. Here, single-molecule tracking and Förster resonance energy transfer (FRET) were employed to characterize the mobility and the hybridization efficiency of adsorbed ssDNA oligonucleotides ("target") at solid-liquid interfaces exhibiting surface-immobilized ssDNA ("probe") over a wide range of surface grafting densities. Two distinct regimes were observed, with qualitatively different transport and hybridization behaviors. At dilute grafting density, only 1-3% of target molecules were observed to associate with probes (i.e., to hybridize). Adsorbing target molecules often searched unsuccessfully and "flew", via desorption-mediated diffusion, to secondary locations before hybridizing. In contrast, at high probe grafting density, approximately 20% of target DNA hybridized to immobilized probes, and almost always in the vicinity of initial adsorption. Moreover, following a dehybridization event, target molecules rehybridized at high probe density, but rehybridization was infrequent in the dilute density regime. Interestingly, the intermittent interfacial transport of mobile target molecules was suppressed by the presence of immobilized probe DNA, presumably due to an increased probability of readsorption following each "hop". Together, these findings suggested that many salient effects of grafting density on surface-mediated DNA hybridization can be directly related to the mechanisms of surface-mediated intermittent diffusion.
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Affiliation(s)
- Jeremiah C Traeger
- Department of Chemical and Biological Engineering , University of Colorado Boulder , Boulder , Colorado 80309 , United States
| | - Zachary Lamberty
- Department of Chemical and Biological Engineering , University of Colorado Boulder , Boulder , Colorado 80309 , United States
| | - Daniel K Schwartz
- Department of Chemical and Biological Engineering , University of Colorado Boulder , Boulder , Colorado 80309 , United States
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Vacuum induced dehydration of swollen poly(methoxy diethylene glycol acrylate) and polystyrene-block-poly(methoxy diethylene glycol acrylate)-block-polystyrene films probed by in-situ neutron reflectivity. POLYMER 2017. [DOI: 10.1016/j.polymer.2017.07.066] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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10
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Antibody-free detection of infectious bacteria using quantum dots-based barcode assay. J Pharm Biomed Anal 2016; 134:325-332. [PMID: 27894780 DOI: 10.1016/j.jpba.2016.10.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/26/2016] [Accepted: 10/30/2016] [Indexed: 01/18/2023]
Abstract
Staphylococcus aureus, methicillin-resistant Staphylococcus aureus and Klebsiella pneumoniae are the most representative bacteria causing infectious diseases. Due to the increased application of antibiotics, the bacterial resistance is growing causing severe complications. Therefore, a sensitive determination of these pathogens is crucial for effective treatment. The aim of this study was to design an effective method for multiplex detection of Staphylococcus aureus, methicillin-resistant Staphylococcus aureus and Klebsiella pneumoniae taking advantage from properties of magnetic particles as well as fluorescent nanoparticles (quantum dots). The method was able to detect as low concentrations of bacteria as 102 CFU/mL using the bacteria-specific genes (fnbA, mecA and wcaG).
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Lee BS, Kim H, Choi IS, Cho WK. Formation of activation-free, selectively bioconjugatable poly(N-acryloxysuccinimide-co-oligoethylene glycol methyl ether methacrylate) films by surface-initiated ARGET ATRP. ACTA ACUST UNITED AC 2016. [DOI: 10.1002/pola.28390] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Bong Soo Lee
- Department of Chemistry, KAIST; Center for Cell-Encapsulation Research; Daejeon 34141 Korea
| | - Hyunsuk Kim
- Department of Chemistry, KAIST; Center for Cell-Encapsulation Research; Daejeon 34141 Korea
| | - Insung S. Choi
- Department of Chemistry, KAIST; Center for Cell-Encapsulation Research; Daejeon 34141 Korea
| | - Woo Kyung Cho
- Department of Chemistry; Chungnam National University; Daejeon 34134 Korea
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Hager R, Burns JR, Grydlik MJ, Halilovic A, Haselgrübler T, Schäffler F, Howorka S. Co-Immobilization of Proteins and DNA Origami Nanoplates to Produce High-Contrast Biomolecular Nanoarrays. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:2877-2884. [PMID: 27062557 DOI: 10.1002/smll.201600311] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 02/18/2016] [Indexed: 06/05/2023]
Abstract
The biofunctionalization of nanopatterned surfaces with DNA origami nanostructures is an important topic in nanobiotechnology. An unexplored challenge is, however, to co-immobilize proteins with DNA origami at pre-determined substrate sites in high contrast relative to the nontarget areas. The immobilization should, in addition, preferably be achieved on a transparent substrate to allow ultrasensitive optical detection. If successful, specific co-binding would be a step towards stoichiometrically defined arrays with few to individual protein molecules per site. Here, we successfully immobilize with high specificity positively charged avidin proteins and negatively charged DNA origami nanoplates on 100 nm-wide carbon nanoislands while suppressing undesired adsorption to surrounding nontarget areas. The arrays on glass slides achieve unprecedented selectivity factors of up to 4000 and allow ultrasensitive fluorescence read-out. The co-immobilization onto the nanoislands leads to layered biomolecular architectures, which are functional because bound DNA origami influences the number of capturing sites on the nanopatches for other proteins. The novel hybrid DNA origami-protein nanoarrays allow the fabrication of versatile research platforms for applications in biosensing, biophysics, and cell biology, and, in addition, represent an important step towards single-molecule protein arrays.
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Affiliation(s)
- Roland Hager
- Center for Advanced Bioanalysis GmbH, 4020, Linz, Austria
| | - Jonathan R Burns
- Department of Chemistry, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Martyna J Grydlik
- Institute for Semiconductor and Solid State Physics, Johannes Kepler University, 4040, Linz, Austria
| | - Alma Halilovic
- Institute for Semiconductor and Solid State Physics, Johannes Kepler University, 4040, Linz, Austria
| | | | - Friedrich Schäffler
- Institute for Semiconductor and Solid State Physics, Johannes Kepler University, 4040, Linz, Austria
| | - Stefan Howorka
- Center for Advanced Bioanalysis GmbH, 4020, Linz, Austria
- Department of Chemistry, Institute of Structural and Molecular Biology, University College London, London, UK
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