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Hierarchical DNA branch assembly-encoded fluorescent nanoladders for single-cell transcripts imaging SCIE
期刊论文 | 2022 | NUCLEIC ACIDS RESEARCH
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Abstract :

Spatial visualization of single-cell transcripts is limited by signal specificity and multiplexing. Here, we report hierarchical DNA branch assembly-encoded fluorescent nanoladders, which achieve denoised and highly multiplexed signal amplification for single-molecule transcript imaging. This method first offers independent RNA-primed rolling circle amplification without nonspecific amplification based on circular DNAzyme. It then executes programmable DNA branch assembly on these amplicons to encode virtual signals for visualizing numbers of targets by FISH. In theory, more virtual signals can be encoded via the increase of detection spectral channels and repeats of the same sequences on barcode. Our method almost eliminates nonspecific amplification in fixed cells (reducing nonspecific spots of single cells from 16 to nearly zero), and achieves simultaneous quantitation of nine transcripts by using only two detection spectral channels. We demonstrate accurate RNA profiling in different cancer cells, and reveal diverse localization patterns for spatial regulation of transcripts.

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GB/T 7714 Cao, Xiaowen , Chen, Feng , Xue, Jing et al. Hierarchical DNA branch assembly-encoded fluorescent nanoladders for single-cell transcripts imaging [J]. | NUCLEIC ACIDS RESEARCH , 2022 .
MLA Cao, Xiaowen et al. "Hierarchical DNA branch assembly-encoded fluorescent nanoladders for single-cell transcripts imaging" . | NUCLEIC ACIDS RESEARCH (2022) .
APA Cao, Xiaowen , Chen, Feng , Xue, Jing , Zhao, Yue , Bai, Min , Zhao, Yongxi . Hierarchical DNA branch assembly-encoded fluorescent nanoladders for single-cell transcripts imaging . | NUCLEIC ACIDS RESEARCH , 2022 .
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Nucleic Acids-encoded Amplification for Single-cell Imaging SCIE Scopus
期刊论文 | 2022 , 43 (12) | CHEMICAL JOURNAL OF CHINESE UNIVERSITIES-CHINESE
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Abstract :

Single-cell imaging is of great significance in the field of life science and clinical medicine for its application on visualizing and quantifying of targets in single cells. Nucleic acids-encoded amplification converts targets to nucleic acids barcodes through specific molecular reactions,which is easy to achieve signal amplification. Due to its variety of probes,ease of programming,mild reaction conditions and high amplification efficiency,nucleic acids -encoded amplification emerges outstanding performance on sensitive and multiplexed imaging of various targets with low abundance in single cells,emerging as a new strategy for understanding cell state and exploring life process. This paper reviews the research progress of nucleic acids-encoded amplification in the field of single-cell fluorescence imaging on the basis of the encoding methods,which systematically clarifies the characteristics of encoding and amplification methods for living cell imaging and in situ cell imaging. Finally,the challenges of multiplex detection in living cells and future perspectives of nucleic acids-encoded amplification are summarized and discussed.

Keyword :

Fluorescence imaging Nucleic acids amplification Nucleic acids encoding Single-cell analysis

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GB/T 7714 Zhao, Xueqi , Zhao, Yue , Xue, Jing et al. Nucleic Acids-encoded Amplification for Single-cell Imaging [J]. | CHEMICAL JOURNAL OF CHINESE UNIVERSITIES-CHINESE , 2022 , 43 (12) .
MLA Zhao, Xueqi et al. "Nucleic Acids-encoded Amplification for Single-cell Imaging" . | CHEMICAL JOURNAL OF CHINESE UNIVERSITIES-CHINESE 43 . 12 (2022) .
APA Zhao, Xueqi , Zhao, Yue , Xue, Jing , Bai, Min , Chen, Feng , Sun, Ying et al. Nucleic Acids-encoded Amplification for Single-cell Imaging . | CHEMICAL JOURNAL OF CHINESE UNIVERSITIES-CHINESE , 2022 , 43 (12) .
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Universal Exponential Amplification Confers Multilocus Detection of Mutation-Prone Virus EI SCIE Scopus
期刊论文 | 2022 , 94 (2) , 927-933 | ANALYTICAL CHEMISTRY
SCOPUS Cited Count: 4
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The recent outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19) has spread rapidly around the world. Accurate and scalable diagnostics are essential for immediate intervention and control of viral transmission. Currently reported diagnostics are rapid and sensitive, yet most are limited by their principle of single-locus identification and suffer from falsenegative results because of the mutation-prone nature of RNA viruses. Here, we propose a multilocus detection method for SARS-CoV-2 based on a modified loop-mediated isothermal amplification with a pair of universal primers. The sequencespecific probes are designed to recognize the sequence of nucleocapsid protein (N) and the open reading frame 1ab (Orf1ab) gene from the SARS-CoV-2 genome. In the presence of a target locus, separated probes are ligated to be an intact template, the bipartite ends of which are repetitive sequences for the sequential binding of universal primers to initiate strand displacement. A kind of flap structure-dependent endonuclease is involved in cleaving multicolor TaqMan probes during multiplex amplification, realizing a real-time and multiplex analysis. We evaluated the quantitative performance of the developed method with spiked samples using synthetic target RNA, resulting in a limit of detection as low as 250 aM. Furthermore, the feasibility of multilocus detection was validated using various mutation-prone genes, demonstrating a significant potential for accurate analysis of SARS-CoV-2 and holding great promise for the clinical diagnosis of other infectious diseases.

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GB/T 7714 Zhao, Yue , Fang, Xiaoxing , Yu, Huahang et al. Universal Exponential Amplification Confers Multilocus Detection of Mutation-Prone Virus [J]. | ANALYTICAL CHEMISTRY , 2022 , 94 (2) : 927-933 .
MLA Zhao, Yue et al. "Universal Exponential Amplification Confers Multilocus Detection of Mutation-Prone Virus" . | ANALYTICAL CHEMISTRY 94 . 2 (2022) : 927-933 .
APA Zhao, Yue , Fang, Xiaoxing , Yu, Huahang , Fu, Youlan , Zhao, Yongxi . Universal Exponential Amplification Confers Multilocus Detection of Mutation-Prone Virus . | ANALYTICAL CHEMISTRY , 2022 , 94 (2) , 927-933 .
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A microfluidic surface-enhanced Raman scattering (SERS) sensor for microRNA in extracellular vesicles with nucleic acid-tyramine cascade amplification SCIE Scopus
期刊论文 | 2022 , 33 (4) , 2101-2104 | CHINESE CHEMICAL LETTERS
SCOPUS Cited Count: 39
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Abstract :

Exosomal microRNA (miRNA) is an ideal candidate of noninvasive biomarker for the early diagnosis of cancer. Sensitive and accurate sensing of abnormal exosomal miRNA plays essential role for clinical promotion due to its close correlation with tumor proliferation and progression. Herein, a microfluidic surface-enhanced Raman scattering (SERS) sensor was proposed for an on-line detection of exosomal miRNA based on rolling circle amplification (RCA) and tyramine signal amplification (TSA) strategy. The microfluidic chip consists of a magnetic enrichment chamber, a serpentine fluidic mixer and a plasmonic SERS substrate functionalized with capture probes. The released miRNA activates the capture probe, triggers RCA reaction, and generates a large number of single-stranded DNA products to drive the catalysis of nanotags deposition via TSA, producing numerous "hot spots" to enhance the SERS signals. In merit of the microfluidics chip and nucleic acid-tyramine cascade amplification, the developed SERS sensor significantly improves the sensitivity for the exosomal miRNA assay, resulting in a limit of detection (LOD) as low as 1 pmol/L and can be successfully applied in the analysis of exosomes secreted from breast tumor cells, which demonstrates the potential utility in practical applications. (c) 2021 Published by Elsevier B.V. on behalf of Chinese Chemical Society and Institute of Materia Medica, Chinese Academy of Medical Sciences.

Keyword :

Exosome Microfluidic chips Nucleic acid amplification Surface-enhanced Raman scattering (SERS) Tyramide signal amplification

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GB/T 7714 Zhao, Yue , Fang, Xiaoxing , Bai, Min et al. A microfluidic surface-enhanced Raman scattering (SERS) sensor for microRNA in extracellular vesicles with nucleic acid-tyramine cascade amplification [J]. | CHINESE CHEMICAL LETTERS , 2022 , 33 (4) : 2101-2104 .
MLA Zhao, Yue et al. "A microfluidic surface-enhanced Raman scattering (SERS) sensor for microRNA in extracellular vesicles with nucleic acid-tyramine cascade amplification" . | CHINESE CHEMICAL LETTERS 33 . 4 (2022) : 2101-2104 .
APA Zhao, Yue , Fang, Xiaoxing , Bai, Min , Zhang, Jin , Yu, Huahang , Chen, Feng et al. A microfluidic surface-enhanced Raman scattering (SERS) sensor for microRNA in extracellular vesicles with nucleic acid-tyramine cascade amplification . | CHINESE CHEMICAL LETTERS , 2022 , 33 (4) , 2101-2104 .
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Bioorthogonal Chemical Signature Enabling Amplified Visualization of Cellular Oxidative Thymines EI SCIE PubMed
期刊论文 | 2021 , 93 (30) , 10495-10501 | ANALYTICAL CHEMISTRY
WoS CC Cited Count: 1
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Abstract :

Cellular oxidative thymines, 5-hydroxymethyluracil (5hmU) and 5-formyluracil (5fU), are found in the genomes of a diverse range of organisms, the distribution of which profoundly influence biological processes and living systems. However, the distribution of cellular oxidative thymines has not been explored because of lacking both specific bioorthogonal labeling and sensitivity methods for single-cell analysis. Herein, we report a bioorthogonal chemical signature enabling amplified visualization of cellular oxidative thymines in single cells. The synthesized ATP-gamma-alkyne, an ATP analogue with bioorthogonal tag modified on gamma-phosphate can be specifically linked to cellular 5hmU by chemoenzymatic labeling. DNA with 5-alkynephosphomethyluracil were then clicked with azide (N-3)-modified 5hmU-primer. Identification of 5fU is based on selective reduction from 5fU to 5hmU, subsequent chemoenzymatic labeling of the newly generated 5hmU, and cross-linking with N-3-modified 5fU-primer via click chemistry. Then, all of the 5hmU and 5fU sites are encoded with respective circularized barcodes. These barcodes are simultaneously amplified for multiplexed single-molecule imaging. The above two kinds of barcodes can be simultaneously amplified for differentiated visualization of 5hmU and 5fU in single cells. We find these two kinds of cellular oxidative thymines are spatially organized in a cell-type-dependent style with cell-to-cell heterogeneity. We also investigate their multilevel subcellular information and explore their dynamic changes during cell cycles. Further, using DNA sequencing instead of fluorescence imaging, our proposed bioorthogonal chemical signature holds great potential to offer the sequence information of these oxidative thymines in cells and may provide a reliable chemical biology approach for studying the whole-genome oxidative thymines profiles and insights into their functional role and dynamics in biology.

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GB/T 7714 Bai, Min , Cao, Xiaowen , Chen, Feng et al. Bioorthogonal Chemical Signature Enabling Amplified Visualization of Cellular Oxidative Thymines [J]. | ANALYTICAL CHEMISTRY , 2021 , 93 (30) : 10495-10501 .
MLA Bai, Min et al. "Bioorthogonal Chemical Signature Enabling Amplified Visualization of Cellular Oxidative Thymines" . | ANALYTICAL CHEMISTRY 93 . 30 (2021) : 10495-10501 .
APA Bai, Min , Cao, Xiaowen , Chen, Feng , Xue, Jing , Zhao, Yue , Zhao, Yongxi . Bioorthogonal Chemical Signature Enabling Amplified Visualization of Cellular Oxidative Thymines . | ANALYTICAL CHEMISTRY , 2021 , 93 (30) , 10495-10501 .
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Addition-Elimination Mechanism-Activated Nucleotide Transition Sequencing for RNA Dynamics Profiling EI SCIE PubMed
期刊论文 | 2021 , 93 (41) , 13974-13980 | ANALYTICAL CHEMISTRY
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Dynamic information of intracellular transcripts is essential to understand their functional roles. Routine RNA-sequencing (RNA-seq) methods only measure RNA species at a steady state and do not provide RNA dynamic information. Here, we develop addition-elimination mechanism-activated nucleotide transition sequencing (AENT-seq) for transcriptome-wide profiling of RNA dynamics. In AENT-seq, nascent transcripts are metabolically labeled with 4-thiouridine (4sU). The total RNA is treated with N2H4 center dot H2O under aqueous conditions. N2H4 center dot H2O is demonstrated to convert 4sU to 4-hydrazino cytosine (C*) based on an addition-elimination chemistry. C* is regarded as cytosine (C) during the DNA extension process. This 4sU-to-C transition marks nascent transcripts, so it enables sequencing analysis of RNA dynamics. We apply our AENT-seq to investigate transcript dynamic information of several genes involved in cancer progression and metastasis. This method uses a simple chemical reaction in aqueous solutions and will be rapidly disseminated with extensive applications.

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GB/T 7714 Su, Li , Chen, Feng , Yu, Huahang et al. Addition-Elimination Mechanism-Activated Nucleotide Transition Sequencing for RNA Dynamics Profiling [J]. | ANALYTICAL CHEMISTRY , 2021 , 93 (41) : 13974-13980 .
MLA Su, Li et al. "Addition-Elimination Mechanism-Activated Nucleotide Transition Sequencing for RNA Dynamics Profiling" . | ANALYTICAL CHEMISTRY 93 . 41 (2021) : 13974-13980 .
APA Su, Li , Chen, Feng , Yu, Huahang , Yan, Hao , Zhao, Fengjiao , Fan, Chunhai et al. Addition-Elimination Mechanism-Activated Nucleotide Transition Sequencing for RNA Dynamics Profiling . | ANALYTICAL CHEMISTRY , 2021 , 93 (41) , 13974-13980 .
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Cellular macromolecules-tethered DNA walking indexing to explore nanoenvironments of chromatin modifications SCIE PubMed
期刊论文 | 2021 , 12 (1) | NATURE COMMUNICATIONS
WoS CC Cited Count: 1
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Exploring spatial organization and relationship of diverse biomolecules within cellular nanoenvironments is important to elucidate the fundamental processes of life. However, it remains methodologically challenging. Herein, we report a molecular recognition mechanism cellular macromolecules-tethered DNA walking indexing (Cell-TALKING) to probe the nanoenvironments containing diverse chromatin modifications. As an example, we characterize the nanoenvironments of three DNA modifications around one histone posttranslational modification (PTM). These DNA modifications in fixed cells are labeled with respective DNA barcoding probes, and then the PTM site is tethered with a DNA walking probe. Cell-TALKING can continuously produce cleavage records of any barcoding probes nearby the walking probe. New 3'-OH ends are generated on the cleaved barcoding probes to induce DNA amplification for downstream detections. Combining fluorescence imaging, we identify various combinatorial chromatin modifications and investigate their dynamic changes during cell cycles. We also explore the nanoenvironments in different cancer cell lines and clinical specimens. In principle, using high-throughput sequencing instead of fluorescence imaging may allow the detection of complex cellular nanoenvironments containing tens of biomolecules such as transcription factors. Investigation of spatial organization and relationships of biomolecules in cellular nanoenvironments is necessary to understand essential biological processes, but methodologically challenging. Here, the authors report cellular macromolecules-tethered DNA walking indexing (Cell-TALKING) to probe the nanoenvironments of DNA modifications around histone post-translational modifications, and explore the nanoenvironments in different cancer cell lines and clinical specimens.

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GB/T 7714 Chen, Feng , Bai, Min , Cao, Xiaowen et al. Cellular macromolecules-tethered DNA walking indexing to explore nanoenvironments of chromatin modifications [J]. | NATURE COMMUNICATIONS , 2021 , 12 (1) .
MLA Chen, Feng et al. "Cellular macromolecules-tethered DNA walking indexing to explore nanoenvironments of chromatin modifications" . | NATURE COMMUNICATIONS 12 . 1 (2021) .
APA Chen, Feng , Bai, Min , Cao, Xiaowen , Xue, Jing , Zhao, Yue , Wu, Na et al. Cellular macromolecules-tethered DNA walking indexing to explore nanoenvironments of chromatin modifications . | NATURE COMMUNICATIONS , 2021 , 12 (1) .
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Controllable synthesis of iron-polyphenol colloidal nanoparticles with composition-dependent photothermal performance EI SCIE PubMed
期刊论文 | 2021 , 593 , 172-181 | Journal of Colloid and Interface Science
WoS CC Cited Count: 5
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Abstract :

Iron-polyphenol nanoparticles are usually prepared with nontoxic plant polyphenols as a main building block, which are an emerging photothermal agent for photothermal therapy. However, till now, few works have been made on the controllable synthesis of iron-polyphenol nanoparticles with tunable composition, as well as investigation of the relationship between material composition and photothermal property. In the present study, iron-polyphenol colloidal nanoparticles with tunable diameter (21–303 nm) and ion content (9.2–97.6 mg/g), as well as high colloidal stability are successfully synthesized using different polyphenols (such as tannic acid, epigallocatechin gallate, gallic acid, epicatechin and proanthocyanidin) as a ligand. In addition, photothermal performance is highly dependent on the organic ligand, iron content and particle size. Higher iron content and smaller diameter can contribute to higher photothermal performance. The iron-polyphenol nanoparticles with the optimal iron content and particle size are selected as a photothermal agent. They can effectively inhibit the tumour growth in vivo. The current work demonstrates a general synthesis strategy for iron-polyphenol colloidal nanoparticles with tailorable composition and clarifies the relationship between material composition and photothermal performance. Moreover, it is conductive to the rational design of polyphenol-based photothermal agents for theranostic applications. © 2021 Elsevier Inc.

Keyword :

Flavonoids Iron Ligands Nanoparticles Particle size Synthesis (chemical) Theranostics

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GB/T 7714 Qin, Jing , Liang, Guohai , Cheng, Dong et al. Controllable synthesis of iron-polyphenol colloidal nanoparticles with composition-dependent photothermal performance [J]. | Journal of Colloid and Interface Science , 2021 , 593 : 172-181 .
MLA Qin, Jing et al. "Controllable synthesis of iron-polyphenol colloidal nanoparticles with composition-dependent photothermal performance" . | Journal of Colloid and Interface Science 593 (2021) : 172-181 .
APA Qin, Jing , Liang, Guohai , Cheng, Dong , Liu, Yining , Cheng, Xiaoran , Yang, Pengkun et al. Controllable synthesis of iron-polyphenol colloidal nanoparticles with composition-dependent photothermal performance . | Journal of Colloid and Interface Science , 2021 , 593 , 172-181 .
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Development of pH-responsive nanocomposites with remarkably synergistic antibiofilm activities based on ultrasmall silver nanoparticles in combination with aminoglycoside antibiotics EI SCIE PubMed
期刊论文 | 2021 , 208 | COLLOIDS AND SURFACES B-BIOINTERFACES
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Bacterial biofilms are responsible for many chronic infections because antibacterial agents exhibit poor penetration into the dense matrix barrier and cannot easily reach the internal bacteria. Herein, we reported pHresponsive nanocomposites (PDA@Kana-AgNPs) that could penetrate and disperse biofilms, which were synthesized by the combination of ultrasmall silver nanoparticles (AgNPs) and kanamycin, and then coating with polydopamine. Confocal fluorescence imaging indicated that PDA@Kana-AgNPs could respond to the acidic microenvironment of biofilms, leading to biofilm-triggered on- demand drug release in situ. The zone of inhibition test and Resazurin assay showed that the combination of kanamycin and AgNPs had greater antimicrobial activity against test strains (Staphylococcus aureus, Streptococcus pneumoniae, Pseudomonas aeruginosa, and Escherichia coli BL21) than when applied separately. The crystal violet staining test demonstrated that biofilms were effectively dispersed by the proposed nanocomposites. Biocompatibility was also evaluated, which showed that PDA@Kana-AgNPs were non-toxic to mammalian cells. Therefore, the proposed pH-responsive nanocomposites held great potential for efficient antibiotics delivery and showed synergistic antibacterial and antibiofilm activities. This strategy could also be used to encapsulate a variety of antibiotics in combination with other drugs or materials, thereby showing therapeutic potential in preventing biofilm-related infections and realizing fluorescence imaging in situ.

Keyword :

Aminoglycoside antibiotics Antibacterial activity Biofilms dispersion pH-responsive

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GB/T 7714 Li, Xizhe , Li, Bingyu , Liu, Ruirui et al. Development of pH-responsive nanocomposites with remarkably synergistic antibiofilm activities based on ultrasmall silver nanoparticles in combination with aminoglycoside antibiotics [J]. | COLLOIDS AND SURFACES B-BIOINTERFACES , 2021 , 208 .
MLA Li, Xizhe et al. "Development of pH-responsive nanocomposites with remarkably synergistic antibiofilm activities based on ultrasmall silver nanoparticles in combination with aminoglycoside antibiotics" . | COLLOIDS AND SURFACES B-BIOINTERFACES 208 (2021) .
APA Li, Xizhe , Li, Bingyu , Liu, Ruirui , Dong, Yanhua , Zhao, Yongxi , Wu, Yayan . Development of pH-responsive nanocomposites with remarkably synergistic antibiofilm activities based on ultrasmall silver nanoparticles in combination with aminoglycoside antibiotics . | COLLOIDS AND SURFACES B-BIOINTERFACES , 2021 , 208 .
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Facile synthesis of metal-polyphenol-formaldehyde coordination polymer colloidal nanoparticles with sub-50 nm for T-1-weighted magnetic resonance imaging SCIE CSCD
期刊论文 | 2021 , 32 (2) , 842-848 | CHINESE CHEMICAL LETTERS
WoS CC Cited Count: 10
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Plant polyphenol-based coordination polymers (CPs) with ultra-small particle size and tailorable compositions are highly desired in biomedical applications, but their synthesis is still challenging due to the sophisticated coordination assembly process and unavoidable self-oxidation polymerization of polyphenol. Herein, a general ligand covalent-modification mediated coordination assembly strategy is proposed for the synthesis of water-dispersible CPs with tunable metal species (e.g., Gd, Cu, Ni, Zn, Fe) and ultra-small diameter (8.6-37.8 nm) using nontoxic plant polyphenol (e.g., tannic acid, gallic acid) as a polymerizable ligand. Polyphenol molecules react with formaldehyde firstly, which can effectively retard the oxidation induced self-polymerization of polyphenol and lead to the formation of metal ions containing CPs colloidal nanoparticles. These ultrafine nanoparticles with stably chelated metal ions are highly water dispersible and thus advantageous for bioimaging. As an example, ultra-small Gd contained CPs exhibit higher longitudinal relaxivity (r(1) = 25.5 L mmol(-1) s(-1)) value with low r(2)/r(1) (1.19) than clinically used Magnevist (Gd-DTPA, r(1) = 3.7 L mmol(-1) s(-1)). Due to the enhanced permeability and retention effect, they can be further used as a positive contrast agent for T-1-weighted MR imaging of tumour. (C) 2020 Chinese Chemical Society and Institute of Materia Medica, Chinese Academy of Medical Sciences. Published by Elsevier B.V. All rights reserved.

Keyword :

Contrast agent Coordination polymer Nanoparticle Plant polyphenol Self-assembly

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GB/T 7714 Qin, Jing , Liang, Guohai , Feng, Bingxi et al. Facile synthesis of metal-polyphenol-formaldehyde coordination polymer colloidal nanoparticles with sub-50 nm for T-1-weighted magnetic resonance imaging [J]. | CHINESE CHEMICAL LETTERS , 2021 , 32 (2) : 842-848 .
MLA Qin, Jing et al. "Facile synthesis of metal-polyphenol-formaldehyde coordination polymer colloidal nanoparticles with sub-50 nm for T-1-weighted magnetic resonance imaging" . | CHINESE CHEMICAL LETTERS 32 . 2 (2021) : 842-848 .
APA Qin, Jing , Liang, Guohai , Feng, Bingxi , Wang, Gen , Wu, Na , Deng, Yonghui et al. Facile synthesis of metal-polyphenol-formaldehyde coordination polymer colloidal nanoparticles with sub-50 nm for T-1-weighted magnetic resonance imaging . | CHINESE CHEMICAL LETTERS , 2021 , 32 (2) , 842-848 .
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