Enhanced DNA toehold exchange reaction on a chip surface to discriminate single-base changes.

In this study, a single-base change discrimination strategy was developed through enhanced DNA toehold exchange reaction on a chip surface. A DNA strand with single-base change (SNPs, insertion or deletion) at an arbitrary position was clearly discriminated with nucleic acid concentrations from 0.8 nM to 1 μM through this method.

[1]  Kemin Wang,et al.  Combination of DNA ligase reaction and gold nanoparticle-quenched fluorescent oligonucleotides: a simple and efficient approach for fluorescent assaying of single-nucleotide polymorphisms. , 2010, Analytical chemistry.

[2]  Na Li,et al.  Highly selective detection of single-nucleotide polymorphisms using a quartz crystal microbalance biosensor based on the toehold-mediated strand displacement reaction. , 2012, Analytical chemistry.

[3]  Weihong Tan,et al.  DNA branch migration reactions through photocontrollable toehold formation. , 2013, Journal of the American Chemical Society.

[4]  Na Li,et al.  A reusable quartz crystal microbalance biosensor for highly specific detection of single-base DNA mutation. , 2013, Biosensors & bioelectronics.

[5]  Rolf Hilfiker,et al.  The use of single-nucleotide polymorphism maps in pharmacogenomics , 2000, Nature Biotechnology.

[6]  Patricio Yankilevich,et al.  Evaluating HapMap SNP data transferability in a large-scale genotyping project involving 175 cancer-associated genes , 2006, Human Genetics.

[7]  Deborah A Nickerson,et al.  Comprehensive identification and characterization of diallelic insertion-deletion polymorphisms in 330 human candidate genes. , 2005, Human molecular genetics.

[8]  M. Heller.  DNA microarray technology: devices, systems, and applications. , 2002, Annual review of biomedical engineering.

[9]  M. Relling,et al.  Pharmacogenomics: translating functional genomics into rational therapeutics. , 1999, Science.

[10]  Andrew J Turberfield,et al.  DNA hairpins: fuel for autonomous DNA devices. , 2006, Biophysical journal.

[11]  E. Kool,et al.  Nonenzymatic autoligation in direct three-color detection of RNA and DNA point mutations , 2001, Nature Biotechnology.

[12]  James J. Russo,et al.  Combinatorial fluorescence energy transfer tags for multiplex biological assays , 2001, Nature Biotechnology.

[13]  K. Gunderson,et al.  A genome-wide scalable SNP genotyping assay using microarray technology , 2005, Nature Genetics.

[14]  Magnus Jobs,et al.  Dynamic allele-specific hybridization , 1999, Nature Biotechnology.

[15]  G. Seelig,et al.  Dynamic DNA nanotechnology using strand-displacement reactions. , 2011, Nature chemistry.

[16]  Georg Seelig,et al.  Conditionally fluorescent molecular probes for detecting single base changes in double-stranded DNA. , 2013, Nature chemistry.

[17]  H. Allawi,et al.  Sensitive detection of DNA polymorphisms by the serial invasive signal amplification reaction. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[18]  Peng Yin,et al.  Optimizing the specificity of nucleic acid hybridization. , 2012, Nature chemistry.

[19]  A. Syvänen.  Accessing genetic variation: genotyping single nucleotide polymorphisms , 2001, Nature Reviews Genetics.

[20]  D. Y. Zhang,et al.  Control of DNA strand displacement kinetics using toehold exchange. , 2009, Journal of the American Chemical Society.

[21]  Sung Jin Kim,et al.  Washing-free electrochemical DNA detection using double-stranded probes and competitive hybridization reaction. , 2004, Chemical communications.

[22]  Haojun Liang,et al.  Using dual-polarization interferometry to study surface-initiated DNA hybridization chain reactions in real time. , 2014, Biosensors & bioelectronics.

[23]  Jeremy Heil,et al.  Human diallelic insertion/deletion polymorphisms. , 2002, American journal of human genetics.

[24]  Yuqian Ren,et al.  Gold nanoparticle enhanced fluorescence anisotropy for the assay of single nucleotide polymorphisms (SNPs) based on toehold-mediated strand-displacement reaction. , 2013, Biosensors & bioelectronics.

[25]  O. Seitz,et al.  Nucleic acid templated reactions: consequences of probe reactivity and readout strategy for amplified signaling and sequence selectivity. , 2009, Chemistry.

[26]  Z. Gao,et al.  Detection of single-nucleotide polymorphisms using an ON-OFF switching of regenerated biosensor based on a locked nucleic acid-integrated and toehold-mediated strand displacement reaction. , 2014, Analytical chemistry.

[27]  Wei Xu,et al.  Multiplex single-nucleotide polymorphism typing by nanoparticle-coupled DNA-templated reactions. , 2009, Journal of the American Chemical Society.

[28]  Adrian Linacre,et al.  Toehold-mediated nonenzymatic DNA strand displacement as a platform for DNA genotyping. , 2013, Journal of the American Chemical Society.

[29]  N. McGranahan,et al.  The causes and consequences of genetic heterogeneity in cancer evolution , 2013, Nature.

[30]  A. Misra,et al.  SNP genotyping: technologies and biomedical applications. , 2007, Annual review of biomedical engineering.

[31]  Chunhai Fan,et al.  A DNA-Origami chip platform for label-free SNP genotyping using toehold-mediated strand displacement. , 2010, Small.

[32]  M. Daly,et al.  A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms , 2001, Nature.

[33]  Haojun Liang,et al.  Real-time study of a DNA strand displacement reaction using dual polarization interferometry. , 2013, Biosensors & bioelectronics.

[34]  Haojun Liang,et al.  Capability of DNA-fueled molecular machine in tuning association rate of DNA-functionalized gold nanoparticles , 2013, Chinese Journal of Polymer Science.

[35]  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.

[36]  Detection of single-nucleotide polymorphisms based on the formation of an electron-transfer impeding layer on an electrode surface. , 2013, Chemical communications.

[37]  Yudong D. He,et al.  Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer , 2001, Nature Biotechnology.