Enzyme-free and label-free ultrasensitive electrochemical detection of human immunodeficiency virus DNA in biological samples based on long-range self-assembled DNA nanostructures.

Biosensors based on nanomaterials have been used for detection of various biological molecules with high sensitivity and selectivity. Herein, we developed a simple and ultrasensitive electrochemical DNA biosensor using long-range self-assembled DNA nanostructures as carriers for signal amplification, which can achieve an impressive detection limit of 5 aM human immunodeficiency virus (HIV) DNA even in complex biological samples. In this study, we designed two auxiliary probes. A cascade of hybridization events between the two auxiliary probes can lead to long-range self-assembly and form micrometer-long one-dimensional DNA nanostructures. In the presence of target DNA, each copy of the target can act as a trigger to connect a DNA nanostructure to a capture probe on the electrode surface. Then, a great amount of redox indicator [Ru(NH(3))(6)](3+) can be electrostatically bound to the DNA nanostructures and eventually result in significantly amplified electrochemical signals.

[1]  H. Soh,et al.  An electrochemical sensor for single nucleotide polymorphism detection in serum based on a triple-stem DNA probe. , 2009, Journal of the American Chemical Society.

[2]  Guonan Chen,et al.  Efficient detection of secondary structure folded nucleic acids related to Alzheimer's disease based on junction probes. , 2012, Biosensors & bioelectronics.

[3]  B. Ye,et al.  An ultrasensitive electrochemical DNA sensor based on the ssDNA-assisted cascade of hybridization reaction. , 2012, Chemical communications.

[4]  Hao Yan,et al.  A DNA Nanostructure‐based Biomolecular Probe Carrier Platform for Electrochemical Biosensing , 2010, Advanced materials.

[5]  Guonan Chen,et al.  An ultrahighly sensitive and selective electrochemical DNA sensor via nicking endonuclease assisted current change amplification. , 2010, Chemical communications.

[6]  Juan Li,et al.  General approach for monitoring peptide-protein interactions based on graphene-peptide complex. , 2011, Analytical chemistry.

[7]  Friedrich C Simmel,et al.  Periodic DNA nanotemplates synthesized by rolling circle amplification. , 2005, Nano letters.

[8]  Ronghua Yang,et al.  Rolling circle amplification combined with gold nanoparticle aggregates for highly sensitive identification of single-nucleotide polymorphisms. , 2010, Analytical chemistry.

[9]  Ashok Mulchandani,et al.  Nanowire‐Based Electrochemical Biosensors , 2006 .

[10]  Hao Yan,et al.  Challenges and opportunities for structural DNA nanotechnology. , 2011, Nature nanotechnology.

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

[12]  Itamar Willner,et al.  Organizing protein-DNA hybrids as nanostructures with programmed functionalities. , 2010, Trends in biotechnology.

[13]  M. Bergeron,et al.  Amplification strategy using aggregates of ferrocene-containing cationic polythiophene for sensitive and specific electrochemical detection of DNA. , 2011, Analytical chemistry.

[14]  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.

[15]  Jian-hui Jiang,et al.  Electrochemical DNA biosensor based on the proximity-dependent surface hybridization assay. , 2009, Analytical chemistry.

[16]  Ryan J. White,et al.  An electrochemical supersandwich assay for sensitive and selective DNA detection in complex matrices. , 2010, Journal of the American Chemical Society.

[17]  Hui Li,et al.  Ultrasensitive electrochemical detection for DNA arrays based on silver nanoparticle aggregates. , 2010, Analytical chemistry.

[18]  Kevin W Plaxco,et al.  Preparation of electrode-immobilized, redox-modified oligonucleotides for electrochemical DNA and aptamer-based sensing , 2007, Nature Protocols.

[19]  Chunhai Fan,et al.  Sequence-specific detection of femtomolar DNA via a chronocoulometric DNA sensor (CDS): effects of nanoparticle-mediated amplification and nanoscale control of DNA assembly at electrodes. , 2006, Journal of the American Chemical Society.

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

[21]  B. Ye,et al.  Sensitive DNA-based electrochemical strategy for trace bleomycin detection. , 2010, Analytical chemistry.

[22]  Zhiqiang Gao,et al.  Amplified detection of microRNA based on ruthenium oxide nanoparticle-initiated deposition of an insulating film. , 2011, Analytical chemistry.

[23]  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.

[24]  J. Tucker,et al.  Detection of DNA point mutations and mRNA expression levels by rolling circle amplification in individual cells , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[25]  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.

[26]  Yingfu Li,et al.  DNA polymerization on gold nanoparticles through rolling circle amplification: towards novel scaffolds for three-dimensional periodic nanoassemblies. , 2006, Angewandte Chemie.

[27]  K. Mullis,et al.  Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. , 1988, Science.

[28]  Zhengping Li,et al.  Highly sensitive determination of microRNA using target-primed and branched rolling-circle amplification. , 2009, Angewandte Chemie.

[29]  Susana Campuzano,et al.  Ternary surface monolayers for ultrasensitive (zeptomole) amperometric detection of nucleic acid hybridization without signal amplification. , 2010, Analytical chemistry.

[30]  N. Seeman From genes to machines: DNA nanomechanical devices. , 2005, Trends in biochemical sciences.

[31]  Dongsheng Liu,et al.  DNA-based switchable devices and materials , 2011 .

[32]  F. Crick,et al.  Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid , 1953, Nature.

[33]  A. Steel,et al.  Electrochemical quantitation of DNA immobilized on gold. , 1998, Analytical chemistry.

[34]  Itamar Willner,et al.  DNAzyme-Functionalized Au Nanoparticles for the Amplified Detection of DNA or Telomerase Activity , 2004 .

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

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

[37]  Chunhai Fan,et al.  A gold nanoparticle-based chronocoulometric DNA sensor for amplified detection of DNA , 2007, Nature Protocols.

[38]  J. Compton,et al.  Nucleic acid sequence-based amplification , 1991, Nature.

[39]  Huang-Hao Yang,et al.  A simple and ultrasensitive electrochemical DNA biosensor based on DNA concatamers. , 2011, Chemical communications.

[40]  Shusheng Zhang,et al.  Electrochemical DNA biosensor based on nanoporous gold electrode and multifunctional encoded DNA-Au bio bar codes. , 2008, Analytical chemistry.

[41]  Ming Zhou,et al.  Bioelectrochemical interface engineering: toward the fabrication of electrochemical biosensors, biofuel cells, and self-powered logic biosensors. , 2011, Accounts of chemical research.

[42]  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.

[43]  Jian-hui Jiang,et al.  Highly specific and sensitive electrochemical genotyping via gap ligation reaction and surface hybridization detection. , 2009, Journal of the American Chemical Society.

[44]  C. Fan,et al.  Electrochemical interrogation of DNA monolayers on gold surfaces. , 2005, Analytical chemistry.

[45]  Feng Gao,et al.  Self-assembly of quantum dots and carbon nanotubes for ultrasensitive DNA and antigen detection. , 2008, Analytical chemistry.

[46]  N. Seeman Nucleic acid junctions and lattices. , 1982, Journal of theoretical biology.