Fe₃O₄@Ag magnetic nanoparticles for microRNA capture and duplex-specific nuclease signal amplification based SERS detection in cancer cells.

A functionalized Fe3O4@Ag magnetic nanoparticle (NP) biosensor for microRNA (miRNA) capture and ultrasensitive detection in total RNA extract from cancer cells was reported in this paper. Herein, Raman tags-DNA probes modified Fe3O4@Ag NPs were designed both as surface-enhanced Raman scattering (SERS) SERS and duplex-specific nuclease signal amplification (DSNSA) platform. Firstly, target miRNAs were captured to the surface of Fe3O4@Ag NPs through DNA/RNA hybridization. In the presence of endonuclease duplex specific nuclease (DSN), one target miRNA molecule could rehybrid thousands of DNA probes to trigger the signal-amplifying recycling. Base on the superparamagnetic of Fe3O4@Ag NPs, target miRNA let-7b can be captured, concentrated and direct quantified within a PE tube without any PCR preamplification treatment. The detection limit was 0.3fM (15 zeptomole, 50μL), nearly 3 orders of magnitude lower than conventional fluorescence based DSN biosensors for miRNA(∼100fM), even single-base difference between the let-7 family members can be discriminated. The result provides a novel proposal to combine the perfect single-base recognition and signal-amplifying ability of the endonuclease DSN with cost-effective SERS strategy for miRNA point-of-care (POC) clinical diagnostics.

[1]  Chad A Mirkin,et al.  Polyvalent DNA nanoparticle conjugates stabilize nucleic acids. , 2020, Nano letters.

[2]  K. Livak,et al.  Real-time quantification of microRNAs by stem–loop RT–PCR , 2005, Nucleic acids research.

[3]  Duncan Graham,et al.  Silver and magnetic nanoparticles for sensitive DNA detection by SERS. , 2014, Chemical communications.

[4]  Shengqi Wang,et al.  A fluorescent aptasensor for H5N1 influenza virus detection based-on the core-shell nanoparticles metal-enhanced fluorescence (MEF). , 2015, Biosensors & bioelectronics.

[5]  C. Perou,et al.  A custom microarray platform for analysis of microRNA gene expression , 2004, Nature Methods.

[6]  Vahid Sandoghdar,et al.  Enhancement of single-molecule fluorescence using a gold nanoparticle as an optical nanoantenna. , 2006, Physical review letters.

[7]  B. Ye,et al.  Attomolar ultrasensitive microRNA detection by DNA-scaffolded silver-nanocluster probe based on isothermal amplification. , 2012, Analytical chemistry.

[8]  T. Gao,et al.  Magnetic-based silver composite microspheres with nanosheet-assembled shell for effective SERS substrate , 2013 .

[9]  Tierui Zhang,et al.  Core-satellite nanocomposite catalysts protected by a porous silica shell: controllable reactivity, high stability, and magnetic recyclability. , 2008, Angewandte Chemie.

[10]  Lin He,et al.  MicroRNAs: small RNAs with a big role in gene regulation , 2004, Nature reviews genetics.

[11]  Qian Wang,et al.  High specific and ultrasensitive isothermal detection of microRNA by padlock probe-based exponential rolling circle amplification. , 2013, Analytical chemistry.

[12]  Pier Paolo Pompa,et al.  Absolute and direct microRNA quantification using DNA-gold nanoparticle probes. , 2014, Journal of the American Chemical Society.

[13]  Zhiqiang Gao,et al.  A highly sensitive and selective electrochemical biosensor for direct detection of microRNAs in serum. , 2013, Analytical chemistry.

[14]  S. Lukyanov,et al.  A novel method for SNP detection using a new duplex-specific nuclease from crab hepatopancreas. , 2002, Genome research.

[15]  Zhiqiang Gao,et al.  A label-free biosensor for electrochemical detection of femtomolar microRNAs. , 2013, Analytical chemistry.

[16]  S. Campuzano,et al.  Magnetobiosensors based on viral protein p19 for microRNA determination in cancer cells and tissues. , 2014, Angewandte Chemie.

[17]  C. Mirkin,et al.  Selective enhancement of nucleases by polyvalent DNA-functionalized gold nanoparticles. , 2011, Journal of the American Chemical Society.

[18]  A. Mehta,et al.  Biomechanics, One Molecule at a Time* , 1999, The Journal of Biological Chemistry.

[19]  Chun-yang Zhang,et al.  Sensitive detection of microRNA with isothermal amplification and a single-quantum-dot-based nanosensor. , 2012, Analytical chemistry.

[20]  R. Stephens,et al.  Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. , 2006, Cancer cell.

[21]  Nianqiang Wu,et al.  Detection of adenosine triphosphate with an aptamer biosensor based on surface-enhanced Raman scattering. , 2012, Analytical chemistry.

[22]  Phillip A. Sharp,et al.  The RNAi revolution , 2004, Nature.

[23]  Yongqiang Cheng,et al.  Ultrasensitive detection of microRNAs by exponential isothermal amplification. , 2010, Angewandte Chemie.

[24]  Thomas Tuschl,et al.  miRNAs in human cancer , 2011, The Journal of pathology.

[25]  P. Stomper,et al.  Breast stereotactic core biopsy washings: abundant cell samples from clinically occult lesions for flow cytometric DNA analysis. , 1998, Investigative radiology.

[26]  Jun Hu,et al.  A Simple and Highly Sensitive Electrochemical Biosensor for microRNA Detection Using Target-Assisted Isothermal Exponential Amplification Reaction , 2013 .

[27]  Andrew Ustianowski,et al.  Tropical infectious diseases: Diagnostics for the developing world , 2004, Nature Reviews Microbiology.

[28]  T. Tuschl,et al.  Identification of Novel Genes Coding for Small Expressed RNAs , 2001, Science.

[29]  Zissimos Mourelatos,et al.  Microarray-based, high-throughput gene expression profiling of microRNAs , 2004, Nature Methods.

[30]  Label-free detection of microRNA: two-step signal enhancement with a hairpin-probe-based graphene fluorescence switch and isothermal amplification. , 2013, Chemistry.

[31]  Tugba Kilic,et al.  Electrochemical based detection of microRNA, mir21 in breast cancer cells. , 2012, Biosensors & bioelectronics.

[32]  Mehmet Ozsoz,et al.  SERS-based direct and sandwich assay methods for mir-21 detection. , 2014, The Analyst.

[33]  Hsien-Da Huang,et al.  Let-7b is a novel regulator of hepatitis C virus replication , 2012, Cellular and Molecular Life Sciences.

[34]  Yu-Qiang Liu,et al.  One-step, multiplexed fluorescence detection of microRNAs based on duplex-specific nuclease signal amplification. , 2012, Journal of the American Chemical Society.

[35]  Ru-Qin Yu,et al.  Highly sensitive and selective strategy for microRNA detection based on WS2 nanosheet mediated fluorescence quenching and duplex-specific nuclease signal amplification. , 2014, Analytical chemistry.

[36]  Jia Guo,et al.  Highly sensitive detection of target ssDNA based on SERS liquid chip using suspended magnetic nanospheres as capturing substrates. , 2013, Langmuir : the ACS journal of surfaces and colloids.