Enzyme-free colorimetric detection of DNA by using gold nanoparticles and hybridization chain reaction amplification.

A novel, high sensitive, and specific DNA assay based on gold nanoparticle (AuNP) colorimetric detection and hybridization chain reaction (HCR) amplification has been demonstrated in this article. Two hairpin auxiliary probes were designed with single-stranded DNA (ssDNA) sticky ends which stabilize AuNPs and effectively prevent them from salt-induced aggregation. The target DNA hybridized with the hairpin auxiliary probes and triggered the formation of extended double-stranded DNA (dsDNA) polymers through HCR. As a result, the formed dsDNA polymers provide less stabilization without ssDNA sticky ends, and AuNPs undergo aggregation when salt concentration is increased. Subsequently, a pale purple-to-blue color variation is observed in the colloid solution. The system is simple in design and convenient in operation. The novel strategy eliminates the need for enzymatic reactions, separation processes, chemical modifications, and sophisticated instrumentation. The detection and discrimination process can be seen with the naked eye. The detection limit of this method is lower than or at least comparable to previous AuNP-based methods. Importantly, the protocol offers high selectivity for the determination between perfectly matched target oligonucleotides and targets with single base-pair mismatches.

[1]  Itamar Willner,et al.  Amplified electrochemical detection of DNA through the aggregation of Au nanoparticles on electrodes and the incorporation of methylene blue into the DNA-crosslinked structure. , 2007, Chemical communications.

[2]  Huixiang Li,et al.  Label-free colorimetric detection of specific sequences in genomic DNA amplified by the polymerase chain reaction. , 2004, Journal of the American Chemical Society.

[3]  K. Plaxco,et al.  Folding-based electrochemical biosensors: the case for responsive nucleic acid architectures. , 2010, Accounts of chemical research.

[4]  Huang-Hao Yang,et al.  A graphene platform for sensing biomolecules. , 2009, Angewandte Chemie.

[5]  Miroslav Fojta,et al.  Electrochemical detection of DNA triplet repeat expansion. , 2004, Journal of the American Chemical Society.

[6]  Juan Li,et al.  General colorimetric detection of proteins and small molecules based on cyclic enzymatic signal amplification and hairpin aptamer probe. , 2012, Analytical chemistry.

[7]  Itamar Willner,et al.  Amplified analysis of DNA by the autonomous assembly of polymers consisting of DNAzyme wires. , 2011, Journal of the American Chemical Society.

[8]  Chaoyong James Yang,et al.  A universal platform for sensitive and selective colorimetric DNA detection based on Exo III assisted signal amplification. , 2011, Biosensors & bioelectronics.

[9]  Genxi Li,et al.  A new strategy for a DNA assay based on a target-triggered isothermal exponential degradation reaction. , 2011, Chemical communications.

[10]  T. G. Drummond,et al.  Electrochemical DNA sensors , 2003, Nature Biotechnology.

[11]  Chad A Mirkin,et al.  Nanostructures in biodiagnostics. , 2005, Chemical reviews.

[12]  Kemin Wang,et al.  Pyrene-excimer probes based on the hybridization chain reaction for the detection of nucleic acids in complex biological fluids. , 2011, Angewandte Chemie.

[13]  Xiaodi Su,et al.  Colorimetric detection of DNA using unmodified metallic nanoparticles and peptide nucleic acid probes. , 2009, Analytical chemistry.

[14]  Robert M. Dirks,et al.  Triggered amplification by hybridization chain reaction. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

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

[16]  Harry M. T. Choi,et al.  Programming biomolecular self-assembly pathways , 2008, Nature.

[17]  X. Qu,et al.  Colorimetric Biosensing Using Smart Materials , 2011, Advanced materials.

[18]  Zhaoxin Li,et al.  Simple colorimetric DNA detection based on hairpin assembly reaction and target-catalytic circuits for signal amplification. , 2012, Analytical biochemistry.

[19]  L. Blum,et al.  DNA biosensors and microarrays. , 2008, Chemical reviews.

[20]  Robert M. Dirks,et al.  An autonomous polymerization motor powered by DNA hybridization , 2007, Nature Nanotechnology.

[21]  Huixiang Li,et al.  Detection of specific sequences in RNA using differential adsorption of single-stranded oligonucleotides on gold nanoparticles. , 2005, Analytical chemistry.

[22]  Lianghai Hu,et al.  Aptamer in bioanalytical applications. , 2011, Analytical chemistry.

[23]  Xinrui Duan,et al.  Cationic conjugated polymers for optical detection of DNA methylation, lesions, and single nucleotide polymorphisms. , 2010, Accounts of chemical research.

[24]  Le A. Trinh,et al.  Programmable in situ amplification for multiplexed imaging of mRNA expression , 2010, Nature Biotechnology.

[25]  I. Willner,et al.  Amplified detection of DNA and analysis of single-base mismatches by the catalyzed deposition of gold on Au-nanoparticles. , 2001, The Analyst.

[26]  Huixiang Li,et al.  Colorimetric detection of DNA sequences based on electrostatic interactions with unmodified gold nanoparticles. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[27]  Chunhai Fan,et al.  Target-responsive structural switching for nucleic acid-based sensors. , 2010, Accounts of chemical research.

[28]  Guodong Liu,et al.  Electrochemical coding technology for simultaneous detection of multiple DNA targets. , 2003, Journal of the American Chemical Society.

[29]  Michael A. Brook,et al.  Design of Gold Nanoparticle‐Based Colorimetric Biosensing Assays , 2008, Chembiochem : a European journal of chemical biology.

[30]  Itamar Willner,et al.  Amplified detection of DNA through the enzyme-free autonomous assembly of hemin/G-quadruplex DNAzyme nanowires. , 2012, Analytical chemistry.

[31]  Chunhai Fan,et al.  Visual cocaine detection with gold nanoparticles and rationally engineered aptamer structures. , 2008, Small.

[32]  Anil Kumar,et al.  Long genomic DNA amplicons adsorption onto unmodified gold nanoparticles for colorimetric detection of Bacillus anthracis. , 2013, Chemical communications.

[33]  Angelika Niemz,et al.  Isothermal DNA amplification coupled with DNA nanosphere-based colorimetric detection. , 2005, Analytical chemistry.

[34]  Mario Leclerc,et al.  Optical detection of DNA and proteins with cationic polythiophenes. , 2008, Accounts of chemical research.

[35]  Y. Chai,et al.  In situ hybridization chain reaction amplification for universal and highly sensitive electrochemiluminescent detection of DNA. , 2012, Analytical chemistry.

[36]  Juewen Liu,et al.  Functional nucleic acid sensors. , 2009, Chemical reviews.

[37]  Chunhai Fan,et al.  Electrochemical interrogation of conformational changes as a reagentless method for the sequence-specific detection of DNA , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[38]  Giovanna Marrazza,et al.  Electrochemical and piezoelectric DNA biosensors for hybridisation detection. , 2008, Analytica chimica acta.

[39]  Wei Xu,et al.  Ultrasensitive and selective colorimetric DNA detection by nicking endonuclease assisted nanoparticle amplification. , 2009, Angewandte Chemie.

[40]  Wei Xu,et al.  Ultrasensitive colorimetric DNA detection using a combination of rolling circle amplification and nicking endonuclease-assisted nanoparticle amplification (NEANA). , 2012, Small.

[41]  Sarit S. Agasti,et al.  Gold nanoparticles in chemical and biological sensing. , 2012, Chemical reviews.