An Efficient DNA‐Fueled Molecular Machine for the Discrimination of Single‐Base Changes

A new strategy for single-base polymorphism (SNP) detection based on the assembly of DNA-AuNPs (gold nanoparticles) driven by a DNA-fueled molecular machine, is established and optimized. It is highly efficient, works at room temperature, and is easy to handle. A single-base change on an oligonucleotide strand is unambiguously discriminated for either SNPs or insertions and deletions (indels). The strategy is demonstrated to detect a mutation in the breast cancer gene BRCA1 in homogeneous solution at room temperature.

[1]  Sudhakar S. Marla,et al.  SNP identification in unamplified human genomic DNA with gold nanoparticle probes , 2005, Nucleic acids research.

[2]  D. Tong,et al.  BRCA1 gene mutations in sporadic ovarian carcinomas: detection by PCR and reverse allele-specific oligonucleotide hybridization. , 1999, Clinical Chemistry.

[3]  Ryan E. Mills,et al.  An initial map of insertion and deletion (INDEL) variation in the human genome. , 2006, Genome research.

[4]  Z. Tian,et al.  What molecular assembly can learn from catalytic chemistry. , 2014, Chemical Society reviews.

[5]  Haojun Liang,et al.  Synchronized assembly of gold nanoparticles driven by a dynamic DNA-fueled molecular machine. , 2012, Journal of the American Chemical Society.

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

[7]  C. Mirkin,et al.  Nanoparticles with Raman spectroscopic fingerprints for DNA and RNA detection. , 2002, Science.

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

[9]  P. Schultz,et al.  Organization of 'nanocrystal molecules' using DNA , 1996, Nature.

[10]  Sanjay Tyagi,et al.  Molecular Beacons: Probes that Fluoresce upon Hybridization , 1996, Nature Biotechnology.

[11]  Itamar Willner,et al.  Powering the programmed nanostructure and function of gold nanoparticles with catenated DNA machines , 2013, Nature Communications.

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

[13]  K. Saitoh,et al.  Application of single nucleotide polymorphisms to non‐model species: a technical review , 2010, Molecular ecology resources.

[14]  Evanthia Papadopoulou,et al.  Label-Free Detection of Single-Base Mismatches in DNA by Surface-Enhanced Raman Spectroscopy , 2011, Angewandte Chemie.

[15]  Longhua Guo,et al.  Oriented gold nanoparticle aggregation for colorimetric sensors with surprisingly high analytical figures of merit. , 2013, Journal of the American Chemical Society.

[16]  Erik Winfree,et al.  Integrating DNA strand-displacement circuitry with DNA tile self-assembly , 2013, Nature Communications.

[17]  A. Turberfield,et al.  A DNA-fuelled molecular machine made of DNA , 2022 .

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

[19]  Chengde Mao,et al.  Reversibly switching the surface porosity of a DNA tetrahedron. , 2012, Journal of the American Chemical Society.

[20]  Kevin W Plaxco,et al.  Fluorescence detection of single-nucleotide polymorphisms with a single, self-complementary, triple-stem DNA probe. , 2009, Angewandte Chemie.

[21]  Chad A. Mirkin,et al.  Oligonucleotide-Modified Gold Nanoparticles for Intracellular Gene Regulation , 2006, Science.

[22]  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.

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

[24]  K. Douglas,et al.  DNA-mounted self-assembly: new approaches for genomic analysis and SNP detection. , 2011, Biochimica et biophysica acta.

[25]  Russell P. Goodman,et al.  Reconfigurable, braced, three-dimensional DNA nanostructures. , 2008, Nature nanotechnology.

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

[27]  D. Cooper,et al.  Meta‐analysis of indels causing human genetic disease: mechanisms of mutagenesis and the role of local DNA sequence complexity , 2003, Human mutation.

[28]  Timothy B. Stockwell,et al.  The Sequence of the Human Genome , 2001, Science.

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

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

[31]  D. Y. Zhang,et al.  Engineering Entropy-Driven Reactions and Networks Catalyzed by DNA , 2007, Science.

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

[33]  N. Seeman,et al.  A robust DNA mechanical device controlled by hybridization topology , 2002, Nature.

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

[35]  Giuseppe Spoto,et al.  Functionalized gold nanoparticles for ultrasensitive DNA detection , 2012, Analytical and Bioanalytical Chemistry.

[36]  J. E. Mattson,et al.  A Group-IV Ferromagnetic Semiconductor: MnxGe1−x , 2002, Science.

[37]  Kevin W Plaxco,et al.  Polarity-switching electrochemical sensor for specific detection of single-nucleotide mismatches. , 2011, Angewandte Chemie.

[38]  D. Kolpashchikov,et al.  Real-time SNP analysis in secondary-structure-folded nucleic acids. , 2010, Angewandte Chemie.

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

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

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

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

[43]  Hari K. K. Subramanian,et al.  The label-free unambiguous detection and symbolic display of single nucleotide polymorphisms on DNA origami. , 2011, Nano letters.

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

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

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

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

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

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