A newly developed optical biochip for bacteria detection based on DNA hybridization

Abstract This paper reports a bacterial optical biochip based on a developed DNA hybridization detection method using an optical measurement. Because the occurrence of bacteremia caused by Acinetobacter baumannii is high in hospitals worldwide, this species was chosen as the source of the DNA samples. Our strategy is based on a developed DNA hybridization detection method which uses probes, PCR-amplified bacterial DNA with biotin labeled primers as well as detection enhancement using gold–streptavidin nanoparticles and an Ag + –hydroquinone solution. Because the gold nanoparticles catalyze silver ions to silver metals by using hydroquinone, the gradually precipitated silver metal causes differences in the optical detection signals, which can be easily observed with the naked eye or with an optical instrument (such as a flatbed scanner). The relationships between sample concentration and detection signal are discussed, and the detection limit for Acinetobacter baumannii genomic DNA is 8.25 ng/mL (1.07 × 10 10  copy/mL). Probe specificity was analyzed by detecting various species of bacteria, various strains of a single species, and various species of a single genus. The DNA hybridization detection method for the bacterial optical biochip presented in this work is easy, rapid, convenient, and promising for detecting bacterial infections and in clinical diagnoses.

[1]  P. de Vos,et al.  Identification of Acinetobacter genomic species by amplified ribosomal DNA restriction analysis , 1995, Journal of clinical microbiology.

[2]  Yu-Cheng Lin,et al.  Using an electro-microchip, a nanogold probe, and silver enhancement in an immunoassay. , 2009, Biosensors & bioelectronics.

[3]  Chia-Hsien Yeh,et al.  An immunoassay using antibody-gold nanoparticle conjugate, silver enhancement and flatbed scanner , 2009 .

[4]  Zheng-ping Li,et al.  Chemiluminescent detection of DNA hybridization using gold nanoparticles as labels , 2007, Analytical and bioanalytical chemistry.

[5]  C. Yeh,et al.  Electro-microchip DNA-biosensor for bacteria detection. , 2010, The Analyst.

[6]  C. Mirkin,et al.  Array-Based Electrical Detection of DNA with Nanoparticle Probes , 2002, Science.

[7]  Kazunori Kataoka,et al.  Quantitative and Reversible Lectin-Induced Association of Gold Nanoparticles Modified with α-Lactosyl-ω-mercapto-poly(ethylene glycol) , 2001 .

[8]  M. Tabrizian,et al.  Biochip functionalization using electrowetting-on-dielectric digital microfluidics for surface plasmon resonance imaging detection of DNA hybridization. , 2009, Biosensors & bioelectronics.

[9]  C. Tseng,et al.  Rapid detection and identification of clinically important bacteria by high-resolution melting analysis after broad-range ribosomal RNA real-time PCR. , 2006, Clinical chemistry.

[10]  Yu-cong Wang,et al.  Silver nanoparticle-based ultrasensitive chemiluminescent detection of DNA hybridization and single-nucleotide polymorphisms. , 2006, Analytical chemistry.

[11]  C. Mirkin,et al.  Scanometric DNA array detection with nanoparticle probes. , 2000, Science.

[12]  Orlin D. Velev,et al.  In situ assembly of colloidal particles into miniaturized biosensors , 1999 .

[13]  Chad A Mirkin,et al.  Multiplexed DNA detection with biobarcoded nanoparticle probes. , 2006, Angewandte Chemie.

[14]  Chad A. Mirkin,et al.  One-Pot Colorimetric Differentiation of Polynucleotides with Single Base Imperfections Using Gold Nanoparticle Probes , 1998 .

[15]  Yoonkey Nam,et al.  Epoxy-silane linking of biomolecules is simple and effective for patterning neuronal cultures. , 2005, Biosensors & bioelectronics.

[16]  J. Storhoff,et al.  Selective colorimetric detection of polynucleotides based on the distance-dependent optical properties of gold nanoparticles. , 1997, Science.

[17]  M. Vaneechoutte,et al.  Species-Level Identification of Isolates of the Acinetobacter calcoaceticus-Acinetobacter baumannii Complex by Sequence Analysis of the 16S-23S rRNA Gene Spacer Region , 2005, Journal of Clinical Microbiology.

[18]  Cui-Yan Tan,et al.  Colorimetric detection of protein microarrays based on nanogold probe coupled with silver enhancement. , 2004, Journal of immunological methods.

[19]  M. Pumera,et al.  Electrochemical genosensors for biomedical applications based on gold nanoparticles. , 2007, Biosensors & bioelectronics.

[20]  Heinrich Neubauer,et al.  Detection of Yersinia pestis using real-time PCR in patients with suspected bubonic plague. , 2011, Molecular and cellular probes.

[21]  Wei Ting Chen,et al.  An immunoassay using an electro-microchip, nanogold probe and silver enhancement , 2009 .

[22]  J. M. Harris,et al.  Characterization of silane-modified immobilized gold colloids as a substrate for surface-enhanced Raman spectroscopy. , 2001, Analytical chemistry.

[23]  J. Luong,et al.  Electrochemical biosensing platforms using platinum nanoparticles and carbon nanotubes. , 2004, Analytical chemistry.

[24]  Chad A Mirkin,et al.  Maximizing DNA loading on a range of gold nanoparticle sizes. , 2006, Analytical chemistry.

[25]  Joseph Wang.  Nanoparticle-Based Electrochemical DNA Detection , 2005 .

[26]  Binh Nguyen,et al.  Biosensor-surface plasmon resonance: quantitative analysis of small molecule-nucleic acid interactions. , 2007, Methods.

[27]  N. Kim,et al.  μAg particle-based molecular sensing/recognition via surface-enhanced Raman spectroscopy , 2007 .

[28]  Ramaier Narayanaswamy,et al.  Analysis of the performance of interferometry, surface plasmon resonance and luminescence as biosensors and chemosensors , 2006 .

[29]  Ningning Zhu,et al.  An electrochemical DNA hybridization detection assay based on a silver nanoparticle label. , 2002, The Analyst.

[30]  J. Storhoff,et al.  A DNA-based method for rationally assembling nanoparticles into macroscopic materials , 1996, Nature.

[31]  P. Lackie,et al.  Immunogold silver staining for light microscopy , 1996, Histochemistry and Cell Biology.