Publications by authors named "Shiping Song"

116 Publications

A nano-integrated microfluidic biochip for enzyme-based point-of-care detection of creatinine.

Chem Commun (Camb) 2021 May;57(38):4726-4729

Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P. R. China. and University of Chinese Academy of Sciences, Beijing 100049, P. R. China and Institute of Molecular Medicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai 200127, P. R. China.

A nano-integrated portable enzymatic microfluidic electrochemical biochip was developed for single-step point-of-care testing of creatinine. The biochip could automatically eliminate a lot of interferences from practical biological samples and enzymatic intermediate products. Gold nanostructure- and carbon nanotube-based screen-printed carbon electrodes were integrated into microfluidic structures to improve the detection performance for creatinine. The microfluidic electrochemical biochip holds promise to become a practical device for medical diagnosis, especially POCT.
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http://dx.doi.org/10.1039/d1cc00825kDOI Listing
May 2021

Multichannel Immunosensor Platform for the Rapid Detection of SARS-CoV-2 and Influenza A(H1N1) Virus.

ACS Appl Mater Interfaces 2021 May 9;13(19):22262-22270. Epub 2021 May 9.

Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, P. R. China.

The coronavirus disease 2019 (COVID-19) can present a similar syndrome to an influenza infection, which may complicate diagnosis and clinical management of these two important respiratory infectious diseases, especially during the peak season of influenza. A rapid and convenient point-of-care test (POCT) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza virus is of great importance for prompt and efficient control of these respiratory epidemics. Herein, a multichannel electrochemical immunoassay (MEIA) platform was developed based on a disposable screen-printed carbon electrode (SPCE) array for the on-site detection of SARS-CoV-2 and A(H1N1). The developed MEIA was constructed with eight channels and allowed rapid detection on a single array. On the SPCE surface, monoclonal antibodies against influenza A(H1N1) hemagglutinin (HA) protein or SARS-CoV-2 spike protein were coated to capture the target antigens, which then interacted with a horseradish peroxidase (HRP)-labeled detection antibody to form an immuno-sandwich complex. The results showed that the MEIA exhibited a broader linear range than ELISA and comparable sensitivity for A(H1N1) HA and SARS-CoV-2 spike protein. The detection results on 79 clinical samples for A(H1N1) suggested that the proposed MEIA platform showed comparable results with ELISA in sensitivity (with a positive rate of 100% for positive samples) but higher specificity, with a false-positive rate of 5.4% for negative samples versus that of 40.5% with ELISA. Thus, it offers great potential for the on-the-spot differential diagnosis of infected patients, which would significantly benefit the efficient control and prevent the spread of these infectious diseases in communities or resource-limited regions in the future.
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http://dx.doi.org/10.1021/acsami.1c05770DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8130191PMC
May 2021

A Carbon-Based Antifouling Nano-Biosensing Interface for Label-Free POCT of HbA1c.

Biosensors (Basel) 2021 Apr 12;11(4). Epub 2021 Apr 12.

Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.

Electrochemical biosensing relies on electron transport on electrode surfaces. However, electrode inactivation and biofouling caused by a complex biological sample severely decrease the efficiency of electron transfer and the specificity of biosensing. Here, we designed a three-dimensional antifouling nano-biosensing interface to improve the efficiency of electron transfer by a layer of bovine serum albumin (BSA) and multi-walled carbon nanotubes (MWCNTs) cross-linked with glutaraldehyde (GA). The electrochemical properties of the BSA/MWCNTs/GA layer were investigated using both cyclic voltammetry and electrochemical impedance to demonstrate its high-efficiency antifouling nano-biosensing interface. The BSA/MWCNTs/GA layer kept 92% of the original signal in 1% BSA and 88% of that in unprocessed human serum after a 1-month exposure, respectively. Importantly, we functionalized the BSA/MWCNTs/GA layer with HbA1c antibody (anti-HbA1c) and 3-aminophenylboronic acid (APBA) for sensitive detection of glycated hemoglobin A (HbA1c). The label-free direct electrocatalytic oxidation of HbA1c was investigated by cyclic voltammetry (CV). The linear dynamic range of 2 to 15% of blood glycated hemoglobin A (HbA1c) in non-glycated hemoglobin (HbAo) was determined. The detection limit was 0.4%. This high degree of differentiation would facilitate a label-free POCT detection of HbA1c.
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http://dx.doi.org/10.3390/bios11040118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8069255PMC
April 2021

Analytical evaluation of Reebio procalcitonin latex-enhanced immunoturbidimetric assay on the HITACHI Labospect 008AS.

Clin Chem Lab Med 2020 Nov 23;59(1):e23-e26. Epub 2020 Nov 23.

Department of Laboratory Medicine, The Fifth Medical Center, Chinese PLA General Hospital (Former 307th hospital of the PLA), Beijing, P.R. China.

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http://dx.doi.org/10.1515/cclm-2020-0796DOI Listing
November 2020

A Carbon-Based DNA Framework Nano-Bio Interface for Biosensing with High Sensitivity and a High Signal-to-Noise Ratio.

ACS Sens 2020 12 23;5(12):3979-3987. Epub 2020 Nov 23.

Shanghai Synchrotron Radiation Facility, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China.

Biosensing interface based on screen-printed carbon electrodes (SPCE) has been widely used for electrochemical biosensors in the field of medical diagnostics, food safety, and environmental monitoring. Nevertheless, SPCE always has a rough surface, which is easy to result in the disorder of nucleic acid capture probes, the nonspecific adsorption of signaling probes, the steric hindrance of target binding, and decrease in the signal-to-noise ratio and sensitivity of biosensors. So far, it still remains extremely challenging to develop high-efficiency carbon-based biosensing interfaces, especially for DNA probe-based assembly and functionalization. In this paper, we first used a specific DNA framework, DNA tetrahedron to solve the defects of the carbon interface, improving the biosensing ability of SPCE. With covalent coupling, the DNA tetrahedron could be immobilized on the carbon surface. Biosensing probe sequences extending from the DNA tetrahedron can be changed for different target molecules. We demonstrated that the improved SPCE could be applied for the detection of a variety of bioactive molecules. Typically, we designed gap hybridization, aptamer "sandwich" and aptamer competition reduction strategy for the detection of miRNA-141, thrombin, and ATP, respectively. High signal-to-noise ratio, sensitivity, and specificity were obtained for all of these kinds. Especially, the DNA tetrahedron-modified SPCE can work well with serum samples. The carbon-based DNA framework nano-bio interface would expand the use of SPCE and make electrochemical biosensors more available and valuable in clinical diagnosis.
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http://dx.doi.org/10.1021/acssensors.0c01745DOI Listing
December 2020

DNA Framework-Supported Electrochemical Analysis of DNA Methylation for Prostate Cancers.

Nano Lett 2020 10 10;20(10):7028-7035. Epub 2020 Sep 10.

School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai 200240, China.

Epigenetic alterations hold great promise as biomarkers for early stage cancer diagnosis. Nevertheless, direct identification of rare methylated DNA in the genome remains challenging. Here, we report an ultrasensitive framework nucleic acid-based electrochemical sensor for quantitative and highly selective analysis of DNA methylation. Notably, we can detect 160 fg of methylated DNA in million-fold unmethylated DNA samples using this electrochemical methylation-specific polymerase chain reaction (E-MSP) method. The high sensitivity of E-MSP enables one-step detection of low-abundance methylation at two different genes in patient serum samples. By using a combination test with two methylation alterations, we achieve high accuracy and sensitivity for reliable differentiation of prostate cancer and benign prostate hypertrophy (BPH). This new method sheds new light on translational use in early cancer diagnosis and in monitoring patients' responses to therapeutic agents.
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http://dx.doi.org/10.1021/acs.nanolett.0c01898DOI Listing
October 2020

Motion State Estimation of Target Vehicle under Unknown Time-Varying Noises Based on Improved Square-Root Cubature Kalman Filter.

Sensors (Basel) 2020 May 4;20(9). Epub 2020 May 4.

State Key Laboratory of Automotive Simulation and Control, Jilin University, Changchun 130022, China.

In the advanced driver assistance system (ADAS), millimeter-wave radar is an important sensor to estimate the motion state of the target-vehicle. In this paper, the estimation of target-vehicle motion state includes two parts: the tracking of the target-vehicle and the identification of the target-vehicle motion state. In the unknown time-varying noise, non-linear target-vehicle tracking faces the problem of low precision. Based on the square-root cubature Kalman filter (SRCKF), the Sage-Husa noise statistic estimator and the fading memory exponential weighting method are combined to derive a time-varying noise statistic estimator for non-linear systems. A method of classifying the motion state of the target vehicle based on the time window is proposed by analyzing the transfer mechanism of the motion state of the target vehicle. The results of the vehicle test show that: (1) Compared with the Sage-Husa extended Kalman filtering (SH-EKF) and SRCKF algorithms, the maximum increase in filtering accuracy of longitudinal distance using the improved square-root cubature Kalman filter (ISRCKF) algorithm is 45.53% and 59.15%, respectively, and the maximum increase in filtering the accuracy of longitudinal speed using the ISRCKF algorithm is 23.53% and 29.09%, respectively. (2) The classification and recognition results of the target-vehicle motion state are consistent with the target-vehicle motion state.
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http://dx.doi.org/10.3390/s20092620DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7248912PMC
May 2020

DNA Origami-Enabled Engineering of Ligand-Drug Conjugates for Targeted Drug Delivery.

Small 2020 04 19;16(16):e1904857. Epub 2020 Mar 19.

School of Chemistry and Chemical Engineering and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China.

Effective drug delivery systems that can systematically and selectively transport payloads to disease cells remain a challenge. Here, a targeting ligand-modified DNA origami nanostructure (DON) as an antibody-drug conjugate (ADC)-like carrier for targeted prostate cancer therapy is reported. Specifically, DON of six helical bundles is modified with a ligand 2-[3-(1,3-dicarboxy propyl)-ureido] pentanedioic acid (DUPA) against prostate-specific membrane antigen (PSMA), to serve as the antibody for drug conjugation in ADC. Doxorubicin (Dox) is then loaded to DON through intercalation to dsDNA. This platform features in spatially controllable organization of targeting ligands and high drug loading capacity. With this nanocomposite, selective delivery of Dox to the PSMA+ cancer cell line LNCaP is readily achieved. The consequent therapeutic efficacy is critically dependent on the numbers of targeting ligand assembled on DON. This target-specific and biocompatible drug delivery platform with high maximum tolerated doses shows immense potential for developing novel nanomedicine.
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http://dx.doi.org/10.1002/smll.201904857DOI Listing
April 2020

Serum soluble VSIG4 as a surrogate marker for the diagnosis of lymphoma-associated hemophagocytic lymphohistiocytosis.

Br J Haematol 2020 04 21;189(1):72-83. Epub 2020 Jan 21.

Department of Laboratory Medicine, The Fifth Medical Center, Chinese PLA General Hospital (Former 307th hospital of the PLA), Beijing, China.

Lymphoma-associated haemophagocytic lymphohistiocytosis (L-HLH) is characterized by excessively activated macrophages and cytotoxic T lymphocytes, but few reliable markers for activated macrophages are available clinically. This study, designed to discover novel biomarkers for the diagnosis of lymphoma patients with L-HLH, was initiated between 2016 and 2018. Fifty-seven adult lymphoma patients were enrolled - 39 without HLH and 18 with HLH. The differential serum protein expression profile was first screened between lymphoma patients with and without L-HLH by a quantitative mass spectrometric approach. Soluble V-set and immunoglobulin domain-containing 4 (sVSIG4), specifically expressed by macrophages, was significantly upregulated in the L-HLH group. Subsequently, sVSIG4 concentration was confirmed by enzyme-linked immunosorbent assay to be significantly increased in lymphoma patients with L-HLH. When it was exploited for the diagnosis of lymphoma patients with L-HLH, the area under a receiver operating characteristic curve was 0·98 with an optimal cut-off point of 2195 pg/ml and the corresponding sensitivity and specificity were 94·44% and 94·87% respectively. In addition, the one-year overall survival was significantly worse in patients with a sVSIG4 concentration above 2195 pg/ml compared with those below 2195 pg/ml (5·3% vs. 72·2%, P < 0·0001). sVSIG4 may be a surrogate marker of activated macrophages for the diagnosis of lymphoma patients with L-HLH.
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http://dx.doi.org/10.1111/bjh.16299DOI Listing
April 2020

Sample dilution for soluble interleukin-2 receptor α measurement: comparison of two different matrices.

Clin Chem Lab Med 2020 01;58(2):e47-e50

Department of Laboratory Medicine, The Fifth Medical Center, Chinese PLA General Hospital (Former 307th Hospital of the PLA), Beijing, P.R. China.

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http://dx.doi.org/10.1515/cclm-2019-0430DOI Listing
January 2020

Cancer-Specific MicroRNA Analysis with a Nonenzymatic Nucleic Acid Circuit.

ACS Appl Mater Interfaces 2019 Mar 14;11(12):11220-11226. Epub 2019 Mar 14.

Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM) , Nanjing University of Posts and Telecommunications , Nanjing 210023 , China.

Sensitive detection of gastric cancer-related biomarkers in human serum provides a promising means for early cancer diagnosis. Herein, we report the design of a nucleic acid circuit for gastric cancer-related microRNA-27a (miRNA-27a) detection based on dual toehold-mediated circular strand displacement amplification (CSDA). In the presence of miRNA-27a, the hybridization between miRNA-27a and probe DNA on magnetic beads through toehold 1 leads to the release of fluorescent DNA and the exposure of a new toehold 2 on linker DNA. After hybridization with catalytic DNA, CSDA is initiated and target miRNA-27a is released to participate in the next cyclic reaction; therefore, a greatly enhanced fluorescence signal is produced. The efficient magnetic separation makes the sensitive detection of miRNA-27a be accomplished within 45 min. With the efficient CSDA, the detection limit of the system (0.8 pM) is ∼100 folds lower than that of the system based on strand displacement without CSDA (79.3 pM). Furthermore, the system also showed good stability and sensitivity to discriminate single-base mismatch, which allows the detection of miRNA-27a in human serum samples. This study provides a novel platform and approach for the rapid quantitative determination of miRNA, which has great potential in clinical diagnosis and disease treatment.
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http://dx.doi.org/10.1021/acsami.9b01653DOI Listing
March 2019

Highly Stable Graphene-Based Nanocomposite (GO-PEI-Ag) with Broad-Spectrum, Long-Term Antimicrobial Activity and Antibiofilm Effects.

ACS Appl Mater Interfaces 2018 May 16;10(21):17617-17629. Epub 2018 May 16.

Institute of Disease Control and Prevention, PLA , Beijing 100071 , P. R. China.

Various silver nanoparticle (AgNP)-decorated graphene oxide (GO) nanocomposites (GO-Ag) have received increasing attention owing to their antimicrobial activity and biocompatibility; however, their aggregation in physiological solutions and the generally complex synthesis methods warrant improvement. This study aimed to synthesize a polyethyleneimine (PEI)-modified and AgNP-decorated GO nanocomposite (GO-PEI-Ag) through a facile approach through microwave irradiation without any extra reductants and surfactants; its antimicrobial activity was investigated on Gram-negative/-positive bacteria (including drug-resistant bacteria) and fungi. Compared with GO-Ag, GO-PEI-Ag acquired excellent stability in physiological solutions and electropositivity, showing substantially higher antimicrobial efficacy. Moreover, GO-PEI-Ag exhibited particularly excellent long-term effects, presenting no obvious decline in antimicrobial activity after 1 week storage in physiological saline and repeated use for three times and the lasting inhibition of bacterial growth in nutrient-rich culture medium. In contrast, GO-Ag exhibited a >60% decline in antimicrobial activity after storage. Importantly, GO-PEI-Ag effectively eliminated adhered bacteria, thereby preventing biofilm formation. The primary antimicrobial mechanisms of GO-PEI-Ag were evidenced as physical damage to the pathogen structure, causing cytoplasmic leakage. Hence, stable GO-PEI-Ag with robust, long-term antimicrobial activity holds promise in combating public-health threats posed by drug-resistant bacteria and biofilms.
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http://dx.doi.org/10.1021/acsami.8b03185DOI Listing
May 2018

Logic Catalytic Interconversion of G-Molecular Hydrogel.

ACS Appl Mater Interfaces 2018 Feb 26;10(5):4512-4518. Epub 2018 Jan 26.

Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University , 500 Dongchuan Road, Shanghai 200241, P. R. China.

By incorporating hemin into G-quadruplex (G) during cation-templated self-assembly between guanosine and KB(OH), we have constructed an artificial enzyme hydrogel (AEH)-based system for the highly sensitive and selective detection of Pb. The sensing strategy is based on a Pb-induced decrease in AEH activity. Because of the higher efficiency of Pb for stabilizing G compared with K, the Pb ions substitute K and trigger hemin release from G, thus giving rise to a conformational interconversion accompanied by the loss of enzyme activity. The Pb-induced catalytic interconversion endows the AEH-based system with high sensitivity and selectivity for detecting Pb. As a result, the AEH-based system shows an excellent response for Pb in the range from 1 pM to 50 nM with a limit of detection of ∼0.32 pM, which is much lower than that of the previously reported G-DNAzyme. We also demonstrate that this AEH-based system exhibits high selectivity toward Pb over other metal ions. Furthermore, two two-input INHIBIT logic gates have been constructed via switching of the catalytic interconversion induced by K and Pb or K and pH. Given its versatility, this AEH-based system provides a novel platform for sensing and biomolecular computation.
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http://dx.doi.org/10.1021/acsami.7b17926DOI Listing
February 2018

Identifying the Genotypes of Hepatitis B Virus (HBV) with DNA Origami Label.

Small 2018 02 28;14(6). Epub 2017 Dec 28.

Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, 200030, China.

The hepatitis B virus (HBV) genotyping may profoundly affect the accurate diagnosis and antiviral treatment of viral hepatitis. Existing genotyping methods such as serological, immunological, or molecular testing are still suffered from substandard specificity and low sensitivity in laboratory or clinical application. In a previous study, a set of high-efficiency hybridizable DNA origami-based shape ID probes to target the templates through which genetic variation could be determined in an ultrahigh resolution of atomic force microscopy (AFM) nanomechanical imaging are established. Here, as a further confirmatory research to explore the sensitivity and applicability of this assay, differentially predesigned DNA origami shape ID probes are also developed for precisely HBV genotyping. Through the specific identification of visualized DNA origami nanostructure with clinical HBV DNA samples, the genetic variation information of genotypes can be directly identified under AFM. As a proof-of-concept, five genotype B and six genotype C are detected in 11 HBV-infected patients' blood DNA samples of Han Chinese population in the single-blinded test. The AFM image-based DNA origami shape ID genotyping approach shows high specificity and sensitivity, which could be promising for virus infection diagnosis and precision medicine in the future.
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http://dx.doi.org/10.1002/smll.201701718DOI Listing
February 2018

Epitope Binning Assay Using an Electron Transfer-Modulated Aptamer Sensor.

ACS Appl Mater Interfaces 2018 Jan 26;10(1):341-349. Epub 2017 Dec 26.

Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China.

Surface plasmon resonance and quartz crystal microbalance are workhorses of protein-DNA interaction research for over 20 years, providing ways to quantitatively determine the protein-DNA binding. However, the cost, necessary technical expertise, and severe nonspecific adsorption poses barriers to their use. Convenient and effective techniques for the measurement of protein-DNA binding affinity and the epitope binning between DNA and proteins for developing highly sensitive detection platform remain challenging. Here, we develop a binding-induced alteration in electron transfer kinetics of the redox reporter labeled (methylene blue) on DNA aptamer to measure the binding affinity between prostate-specific antigen (PSA) and aptamer. We demonstrate that the binding of PSA to aptamer decreases the electron transfer rate of methylene blue for ∼45%. Further, we identify the best pairwise selection of aptamers for developing sandwich assay by sorting from 10 pairwise modes with the PSA detection limit of 500 ng/mL. Our study provides promising ways to analyze the binding affinity between ligand and receptor and to sort pairwise between aptamers or antibodies for the development of highly sensitive sandwich immunoassays.
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http://dx.doi.org/10.1021/acsami.7b17324DOI Listing
January 2018

Organelle-Specific Triggered Release of Immunostimulatory Oligonucleotides from Intrinsically Coordinated DNA-Metal-Organic Frameworks with Soluble Exoskeleton.

J Am Chem Soc 2017 11 26;139(44):15784-15791. Epub 2017 Oct 26.

Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences , Shanghai 201800, People's Republic of China.

DNA has proven of high utility to modulate the surface functionality of metal-organic frameworks (MOFs) for various biomedical applications. Nevertheless, current methods for preparing DNA-MOF nanoparticles rely on either inefficient covalent conjugation or specific modification of oligonucleotides. In this work, we report that unmodified oligonucleotides can be loaded on MOFs with high density (∼2500 strands/particle) via intrinsic, multivalent coordination between DNA backbone phosphate and unsaturated zirconium sites on MOFs. More significantly, surface-bound DNA can be efficiently released in either bulk solution or specific organelles in live cells when free phosphate ions are present. As a proof-of-concept for using this novel type of DNA-MOFs in immunotherapy, we prepared a construct of immunostimulatory DNA-MOFs (isMOFs) by intrinsically coordinating cytosine-phosphate-guanosine (CpG) oligonucleotides on biocompatible zirconium MOF nanoparticles, which was further armed by a protection shell of calcium phosphate (CaP) exoskeleton. We demonstrated that isMOFs exhibited high cellular uptake, organelle specificity, and spatiotemporal control of Toll-like receptors (TLR)-triggered immune responses. When isMOF reached endolysosomes via microtubule-mediated trafficking, the CaP exoskeleton dissolved in the acidic environment and in situ generated free phosphate ions. As a result, CpG was released from isMOFs and stimulated potent immunostimulation in living macrophage cells. Compared with naked CpG-MOF, isMOFs exhibited 83-fold up-regulation in stimulated secretion of cytokines. We thus expect this isMOF design with soluble CaP exoskeleton and an embedded sequential "protect-release" program provides a highly generic approach for intracellular delivery of therapeutic nucleic acids.
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http://dx.doi.org/10.1021/jacs.7b07895DOI Listing
November 2017

Single copy-sensitive electrochemical assay for circulating methylated DNA in clinical samples with ultrahigh specificity based on a sequential discrimination-amplification strategy.

Chem Sci 2017 Jul 18;8(7):4764-4770. Epub 2017 May 18.

Key Laboratory of Biomedical Information Engineering of Education Ministry , School of Life Science and Technology , Xi'an Jiaotong University , Xianning West Road , Xi'an , Shaanxi 710049 , P. R. China . Email:

Tumor-related circulating methylated DNA represents only a small fraction of the total DNA in clinical samples ( plasma), challenging the accurate analysis of specific DNA methylation patterns. Yet conventional assays based on the real-time quantitative methylation-specific PCR (qMSP) are generally limited in detection sensitivity and specificity due to its non-specific amplification interference including primer dimers and off-target amplification. Here we propose a single copy-sensitive electrochemical assay for circulating methylated DNA with ultrahigh specificity on the basis of a sequential discrimination-amplification strategy. Methylated DNA rather than unmethylated DNA in a bisulfite-modified sample is identified and amplified by the asymmetric MSP to generate abundant biotin-labeled single-stranded amplicons with reduced primer-dimer artifacts. Self-assembled tetrahedral DNA probes, which are readily decorated on an electrode surface as nanostructured probes with ordered orientation and well controlled spacing, enable the highly efficient hybridization of the specific single-stranded amplicons due to greatly increased target accessibility and significantly decreased noise. The interfacial hybridization event is quantitatively translated into electrochemical signals utilizing an enzymatic amplification. The proposed assay integrates dual sequence discrimination processes and cascade signal amplification processes, achieving the identification of as few as one methylated DNA molecule in the presence of a 1000-fold excess of unmethylated alleles. Furthermore, the excellent assay performance enables tumor related methylation detection in lung cancer patients with 200 microlitre plasma samples. The results are in good consistency with those of clinical diagnosis, whereas the conventional qMSP failed to detect the corresponding methylation pattern of these clinically confirmed positive patients in such trace amounts of samples.
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http://dx.doi.org/10.1039/c7sc01035dDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5603958PMC
July 2017

PD-1 mRNA expression in peripheral blood cells and its modulation characteristics in cancer patients.

Oncotarget 2017 Aug 2;8(31):50782-50791. Epub 2017 Feb 2.

Cancer Therapy Center, Affiliated Hospital of The Academy of Military Medical Sciences, Beijing 100071, China.

Immune checkpoint inhibitors that block the PD-1/PD-L1 signaling pathway have been used to treat a wide variety of cancers. Although results have been promising, significant inter-individual and inter-tumor variability has been observed. It is believed that better clinical outcome could be achieved if the treatment was individually designed based on the functional status of the PD-1/PD-L1 signaling and the cellular immunity. In this study, we analyzed the mRNA expression of PD-1 and other immunomodulatory genes in peripheral blood from cancer patients, and immunomodulatory gene expression during radiotherapy and immunomodulation therapy with cytokines. Our results show that the PD-1 mRNA expression is significantly increased in peripheral blood in cancer patients. Anti-cancer treatments can significantly modulate the PD-1 expression, but this is largely dependent on the initial immune status. Moreover, the PD-1 expression on peripheral lymphocytes can be immunoactivation-derived. These results suggest that the regulation and expression pattern of PD-1/PD-L1 signal is complicated which will influence the effect of blockade of the PD-1/PD-L1 signaling pathway for cancer treatment. Through combined analysis of PD-1, CTLA-4, and other immune markers in peripheral blood, we may accurately evaluate the functional status of PD-1/PD-L1 signaling and cellular immunity, thereby providing clues for guiding anti-PD-1 or anti-PD-L1 treatment.
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http://dx.doi.org/10.18632/oncotarget.15006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5584204PMC
August 2017

DNA-Encoded Raman-Active Anisotropic Nanoparticles for microRNA Detection.

Anal Chem 2017 09 29;89(18):9850-9856. Epub 2017 Aug 29.

Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University , 500 Dongchuan Road, Shanghai 200241, P. R. China.

The development of highly sensitive and selective methods for the detection of microRNA (miRNA) has attracted tremendous attention because of its importance in fundamental biological studies and diagnostic applications. In this work, we develop DNA-encoded Raman-active anisotropic nanoparticles modified origami paper analytical devices (oPADs) for rapid, highly sensitive, and specific miRNA detection. The Raman-active anisotropic nanoparticles were prepared using 10-mer oligo-A, -T, -C, and -G to mediate the growth of Ag cubic seeds into Ag nanoparticles (AgNPs) with different morphologies. The resulting AgNPs were further encoded with DNA probes to serve as effective surface-enhanced Raman scattering (SERS) probes. The analytical device was then fabricated on a single piece of SERS probes loaded paper-based substrate and assembled based on the principles of origami. The addition of the target analyte amplifies the Raman signals on DNA-encoded AgNPs through a target-dependent, sequence specific DNA hybridization assembly. This simple and low-cost analytical device is generic and applicable to a variety of miRNAs, allowing detection sensitivity down to 1 pM and assay time within 15 min, and therefore holds promising applications in point-of-care diagnostics.
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http://dx.doi.org/10.1021/acs.analchem.7b01861DOI Listing
September 2017

Multifunctional Yolk-Shell Nanostructure as a Superquencher for Fluorescent Analysis of Potassium Ion Using Guanine-Rich Oligonucleotides.

ACS Appl Mater Interfaces 2017 Sep 29;9(36):30406-30413. Epub 2017 Aug 29.

College of Chemistry and Chemical Engineering, Shanghai University of Engineering Science , Shanghai 201620, China.

The excellent performance of a biosensor generally depends on the high signal-to-noise ratio, and the superquencher plays a dominant role in fluorescent sensors. Novel nanoquenchers exhibited high quenching efficiency in various fluorescent assays of biological/chemical molecules. Here, we developed a novel nano-biosensor using [email protected] yolk-shell nanoparticles (YSNPs) and studied their quenching effect. We found [email protected] YSNP was a superquencher and exhibited an ultrastrong quenching ability, up to almost 100% quenching efficiency, toward fluorophores. Also, [email protected] YSNPs possessed the most superior fluorescence restoration efficiency, due to biomolecular recognition event, compared to the other nanoquenchers, including bare FeO NPs, graphene oxide (GO), and single-wall carbon nanotubes (SWCNTs). On the basis of that, a fluorescent sensing platform for potassium-ion (K) analysis with guanine (G)-rich oligonucleotides was designed. As a result, [email protected] YSNP-based fluorescent sensors demonstrated excellent performance, with an ultrahigh sensitivity of a detection limit as low as 1.3 μM, as well as a wide dynamic range from 50 μM to 10 mM. The proposed method is fast, simple, and cost-effective, suggesting the great potential for practical applications in biomedical detection and clinical diagnosis.
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http://dx.doi.org/10.1021/acsami.7b08732DOI Listing
September 2017

Programming Cell Adhesion for On-Chip Sequential Boolean Logic Functions.

J Am Chem Soc 2017 08 19;139(30):10176-10179. Epub 2017 Jul 19.

Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, P. R. China.

Programmable remodelling of cell surfaces enables high-precision regulation of cell behavior. In this work, we developed in vitro constructed DNA-based chemical reaction networks (CRNs) to program on-chip cell adhesion. We found that the RGD-functionalized DNA CRNs are entirely noninvasive when interfaced with the fluidic mosaic membrane of living cells. DNA toehold with different lengths could tunably alter the release kinetics of cells, which shows rapid release in minutes with the use of a 6-base toehold. We further demonstrated the realization of Boolean logic functions by using DNA strand displacement reactions, which include multi-input and sequential cell logic gates (AND, OR, XOR, and AND-OR). This study provides a highly generic tool for self-organization of biological systems.
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http://dx.doi.org/10.1021/jacs.7b04040DOI Listing
August 2017

Cavity-Type DNA Origami-Based Plasmonic Nanostructures for Raman Enhancement.

ACS Appl Mater Interfaces 2017 Jul 23;9(26):21942-21948. Epub 2017 Jun 23.

Key Laboratory for Organic Electronics & Information Displays (KLOEID), Institute of Advanced Materials (IAM), National Syngerstic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications , 9 Wenyuan Road, Nanjing 210023, China.

DNA origami has been established as addressable templates for site-specific anchoring of gold nanoparticles (AuNPs). Given that AuNPs are assembled by charged DNA oligonucleotides, it is important to reduce the charge repulsion between AuNPs-DNA and the template to realize high yields. Herein, we developed a cavity-type DNA origami as templates to organize 30 nm AuNPs, which formed dimer and tetramer plasmonic nanostructures. Transmission electron microscopy images showed that high yields of dimer and tetramer plasmonic nanostructures were obtained by using the cavity-type DNA origami as the template. More importantly, we observed significant Raman signal enhancement from molecules covalently attached to the plasmonic nanostructures, which provides a new way to high-sensitivity Raman sensing.
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http://dx.doi.org/10.1021/acsami.7b05959DOI Listing
July 2017

Size-Dependent Regulation of Intracellular Trafficking of Polystyrene Nanoparticle-Based Drug-Delivery Systems.

ACS Appl Mater Interfaces 2017 Jun 24;9(22):18619-18625. Epub 2017 May 24.

Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China.

Nanoparticles (NPs) have shown great promise as intracellular imaging probes or nanocarriers and are increasingly being used in biomedical applications. A detailed understanding of how NPs get "in and out" of cells is important for developing new nanomaterials with improved selectivity and less cytotoxicity. Both physical and chemical characteristics have been proven to regulate the cellular uptake of NPs. However, the exocytosis process and its regulation are less explored. Herein, we investigated the size-regulated endocytosis and exocytosis of carboxylated polystyrene (PS) NPs. PS NPs with a smaller size were endocytosed mainly through the clathrin-dependent pathway, whereas PS NPs with a larger size preferred caveolae-mediated endocytosis. Furthermore, our results revealed exocytosis of larger PS NPs and tracked the dynamic process at the single-particle level. These results indicate that particle size is a key factor for the regulation of intracellular trafficking of NPs and provide new insight into the development of more effective cellular nanocarriers.
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http://dx.doi.org/10.1021/acsami.7b05383DOI Listing
June 2017

Bubble-Mediated Ultrasensitive Multiplex Detection of Metal Ions in Three-Dimensional DNA Nanostructure-Encoded Microchannels.

ACS Appl Mater Interfaces 2017 May 4;9(19):16026-16034. Epub 2017 May 4.

Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University , 500 Dongchuan Road, Shanghai 200241, P. R. China.

The development of rapid and sensitive point-of-test devices for on-site monitoring of heavy-metal contamination has great scientific and technological importance. However, developing fast, inexpensive, and sensitive microarray sensors to achieve such a goal remains challenging. In this work, we present a DNA-nanostructured microarray (DNM) with a tubular three-dimensional sensing surface and an ordered nanotopography. This microarray enables enhanced molecular interaction toward the rapid and sensitive multiplex detection of heavy-metal ions. In our design, the use of DNA tetrahedral-structured probes engineers the sensing interface with spatially resolved and density-tunable sensing spots that improve the microconfined molecular recognition. A bubble-mediated shuttle reaction was used inside the DNM-functionalized microchannel to improve the target-capturing efficiency. Using this novel DNM biosensor, the sensitive and selective detection of multiple heavy-metal ions (i.e., Hg, Ag, and Pb) was achieved within 5 min, the detection limit was down to 10, 10, and 20 nM for Hg, Ag, and Pb, respectively. The feasibility of our DNM sensor was further demonstrated by probing heavy-metal ions in real water samples with a direct optical readout. Beyond metal ions, this unique DNM sensor can easily be extended to in vitro bioassays and clinical diagnostics.
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http://dx.doi.org/10.1021/acsami.7b03645DOI Listing
May 2017

Stable Nanocomposite Based on PEGylated and Silver Nanoparticles Loaded Graphene Oxide for Long-Term Antibacterial Activity.

ACS Appl Mater Interfaces 2017 May 28;9(18):15328-15341. Epub 2017 Apr 28.

Institute of Disease Control and Prevention, AMMS , Beijing 100071, P. R. China.

The increasing occurrence of antibiotic-resistant pathogens, especially superbugs, is compromising the efficacy of traditional antibiotics. Silver nanoparticles (AgNPs) loaded graphene oxide (GO) nanocomposite (GO-Ag) has drawn great interest as a promising alternative antibacterial material. However, GO-Ag nanocomposite often irreversibly aggregates in physiological solutions, severely influencing its antibacterial capacity and practical application. Herein, a PEGylated and AgNPs loaded GO nanocomposite (GO-PEG-Ag) is synthesized through a facile approach utilizing microwave irradiation, while avoiding extra reducing agents. Through PEGylation, the synthesized GO-PEG-Ag nanocomposite dispersed stably over one month in a series of media and resisted centrifugation at 10 000×g for 5 min, which would benefit effective contact between the nanocomposite and the bacteria. In contrast, GO-Ag aggregated within 1 h of dispersion in physiological solutions. In comparison with GO-Ag, GO-PEG-Ag showed stronger bactericidal capability toward not only normal Gram-negative/positive bacteria such as E. coli and S. aureus (∼100% of E. coli and ∼95.3% of S. aureus reduction by 10 μg/mL nanocomposite for 2.5 h), but also superbugs. Moreover, GO-PEG-Ag showed lower cytotoxicity toward HeLa cells. Importantly, GO-PEG-Ag presented long-term antibacterial effectiveness, remaining ∼95% antibacterial activity after one-week storage in saline solution versus <35% for GO-Ag. The antibacterial mechanisms of GO-PEG-Ag were evidenced as damage to the bacterial structure and production of reactive oxygen species, causing cytoplasm leakage and metabolism decrease. The stable GO-PEG-Ag nanocomposite with powerful and long-term antibacterial capability provides a more practical and effective strategy for fighting superbugs-including pathogen threats in biomedicine and public health.
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http://dx.doi.org/10.1021/acsami.7b03987DOI Listing
May 2017

Graphene Nanoprobes for Real-Time Monitoring of Isothermal Nucleic Acid Amplification.

ACS Appl Mater Interfaces 2017 May 25;9(18):15245-15253. Epub 2017 Apr 25.

Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China.

Isothermal amplification is an efficient way to amplify DNA with high accuracy; however, the real-time monitoring for quantification analysis mostly relied on expensive and precisely designed probes. In the present study, a graphene oxide (GO)-based nanoprobe was used to real-time monitor the isothermal amplification process. The interaction between GO and different DNA structures was systematically investigated, including single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), DNA 3-helix, and long rolling circle amplification (RCA) and hybridization chain reaction (HCR) products, which existed in one-, two-, and three-dimensional structures. It was found that the high rigid structures exhibited much lower affinity with GO than soft ssDNA, and generally the rigidity was dependent on the length of targets and the hybridization position with probe DNA. On the basis of these results, we successfully monitored HCR amplification process, RCA process, and the enzyme restriction of RCA products with GO nanoprobe; other applications including the detection of the assembly/disassembly of DNA 3-helix structures were also performed. Compared to the widely used end-point detection methods, the GO-based sensing platform is simple, sensitive, cost-effective, and especially in a real-time monitoring mode. We believe such studies can provide comprehensive understandings and evocation on design of GO-based biosensors for broad application in various fields.
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http://dx.doi.org/10.1021/acsami.7b01134DOI Listing
May 2017

Nuclease-free target recycling signal amplification for ultrasensitive multiplexing DNA biosensing.

Biosens Bioelectron 2017 Aug 25;94:605-608. Epub 2017 Mar 25.

Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, 2019 Jialuo Road, Shanghai 201800, China. Electronic address:

Ultrasensitive biosensing technologies without gene amplification held great promise for direct detection of DNA. Herein we report a novel biosensing method, combining target recycling signal-amplification strategy and a homemade electrochemical device. Especially, the target recycling was achieved by a strand displacement process, no needing the help of any nucleases. In the presence of target DNA, the recycling system could be activated to generate a cascade of assembly steps with three hairpin DNA segments. Each recycling process were accompanied by a disassembly step that the last hairpin DNA segment displaces target DNA from the complex at the end of each circulation, freeing targets to activate the self-assembly of more trefoil DNA structures. This biosensing method could detect target DNA at aM level and can distinguish target DNA from interfering DNAs, demonstrating its high sensitivity and high selectivity. Importantly, the biosensing method could work well with serum samples.
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http://dx.doi.org/10.1016/j.bios.2017.03.051DOI Listing
August 2017

Facile Synthesis of a MoS-Prussian Blue Nanocube Nanohybrid-Based Electrochemical Sensing Platform for Hydrogen Peroxide and Carcinoembryonic Antigen Detection.

ACS Appl Mater Interfaces 2017 Apr 30;9(14):12773-12781. Epub 2017 Mar 30.

Division of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China.

Herein, an electrochemical detection platform was designed based on a Prussian blue nanocube-decorated molybdenum disulfide (MoS-PBNCs) nanocomposite. Shape-controlled and high-dispersion PBNCs were supported on the MoS nanosheet surface, which would be simply controlled by varying the experimental conditions. Expectedly, such obtained MoS-based nanocomposites possessed excellent electrocatalytic ability, which could be employed to construct an electrochemical sensor for nonenzymatic hydrogen peroxide (HO) detection. More interestingly, MoS-PBNCs nanocomposites could be utilized to construct a sensor for label-free detection of carcinoembryonic antigen (CEA). The electrochemical response of the MoS-based immunosensor was linear with the CEA concentration ranging from 0.005 to 10 ng mL. Moreover, the detection limit was calculated to be 0.54 pg mL. The acceptable selectivity and high stability made such immunosensors detect CEA in human serum with satisfactory results. All data indicated that this MoS-PBNCs nanocomposite may be a promising electrochemical sensing platform for the detection of chemical and biological molecules.
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http://dx.doi.org/10.1021/acsami.7b01141DOI Listing
April 2017

Yolk-shell nanostructured [email protected] magnetic nanoparticles with enhanced peroxidase-like activity for label-free colorimetric detection of HO and glucose.

Nanoscale 2017 Mar;9(13):4508-4515

Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.

Herein, we have developed a simple and facile method to synthesize yolk-shell nanostructured [email protected] nanoparticles (NPs) as a multifunctional biosensing platform for the label-free colorimetric detection of HO and glucose. It was demonstrated that [email protected] yolk-shell nanostructures (YSNs) retained the magnetic properties that can be used for separation and concentration. Also importantly, the [email protected] YSNs exhibited an intrinsic peroxidase-like activity that could quickly catalyze the enzyme substrate in the presence of HO and produce a blue color. Compared to other similar ferric oxide-based NPs with different structures, [email protected] YSNs exhibited greatly enhanced catalytic activities due to their unique structural features. Moreover, steady-state kinetics indicated the catalytic behaviors in agreement with the classic Michaelis-Menten models. Taking advantage of the high catalytic activity, [email protected] YSNs were employed as novel peroxidase mimetics for label-free, rapid, sensitive, and specific colorimetric sensing of HO and glucose, suggesting that [email protected] YSNs have the potential for construction of portable sensors in the application of point-of-care (POC) diagnosis and on-site tests.
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http://dx.doi.org/10.1039/c7nr00819hDOI Listing
March 2017

Multicolor Gold-Silver Nano-Mushrooms as Ready-to-Use SERS Probes for Ultrasensitive and Multiplex DNA/miRNA Detection.

Anal Chem 2017 02 9;89(4):2531-2538. Epub 2017 Feb 9.

Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China.

Uniform silver-containing metal nanostructures with strong and stable surface-enhanced Raman scattering (SERS) signals hold great promise for developing ultrasensitive probes for biodetection. Nevertheless, the direct synthesis of such ready-to-use nanoprobes remains extremely challenging. Herein we report a DNA-mediated gold-silver nanomushroom with interior nanogaps directly synthesized and used for multiplex and simultaneous SERS detection of various DNA and RNA targets. The DNA involved in the nanostructures can act as not only gap DNA (mediated DNA) but also probe DNA (hybridized DNA), and DNA's involvement enables the nanostructures to have the inherent ability to recognize DNA and RNA targets. Importantly, we were the first to establish a new method for the generation of multicolor SERS probes using two different strategies. First Raman-labeled alkanethiol probe DNA was assembled on gold nanoparticles, and second, thiol-containing Raman reporters were coassembled with the probe DNA. The ready-to-use probes also give great potential to develop ultrasensitive detection methods for various biological molecules.
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http://dx.doi.org/10.1021/acs.analchem.6b04729DOI Listing
February 2017