DNA-mounted self-assembly: new approaches for genomic analysis and SNP detection.

This article presents an overview of new emerging approaches for nucleic acid detection via hybridization techniques that can potentially be applied to genomic analysis and SNP identification in clinical diagnostics. Despite the availability of a diverse variety of SNP genotyping technologies on the diagnostic market, none has truly succeeded in dominating its competitors thus far. Having been designed for specific diagnostic purposes or clinical applications, each of the existing bio-assay systems (briefly outlined here) is usually limited to a relatively narrow aspect or format of nucleic acid detection, and thus cannot entirely satisfy all the varieties of commercial requirements and clinical demands. This drives the diagnostic sector to pursue novel, cost-effective approaches to ensure rapid and reliable identification of pathogenic or hereditary human diseases. Hence, the purpose of this review is to highlight some new strategic directions in DNA detection technologies in order to inspire development of novel molecular diagnostic tools and bio-assay systems with superior reliability, reproducibility, robustness, accuracy and sensitivity at lower assay cost. One approach to improving the sensitivity of an assay to confidently discriminate between single point mutations is based on the use of target assembled, split-probe systems, which constitutes the main focus of this review.

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

[2]  K. Faulds,et al.  LNA functionalized gold nanoparticles as probes for double stranded DNA through triplex formation. , 2008, Chemical communications.

[3]  D. Whitcombe,et al.  Detection of PCR products using self-probing amplicons and fluorescence , 1999, Nature Biotechnology.

[4]  A. Weller,et al.  Charge‐Transfer Complex and Solvent‐Shared Ion Pair in Fluorescence Quenching , 1967 .

[5]  N. Mataga,et al.  Solvent Effects upon Dynamic Behavior of Intramolecular Heteroexcimers , 1977 .

[6]  Viswanadham Garimella,et al.  Gold nanoparticle-based detection of genomic DNA targets on microarrays using a novel optical detection system. , 2004, Biosensors & bioelectronics.

[7]  John P. Marino,et al.  Fluorescent Nucleotide Base Analogs as Probes of Nucleic Acid Structure, Dynamics and Interactions , 2002 .

[8]  Michael J. Heller,et al.  DNA MICROARRAY TECHNOLOGY: Devices, , 2002 .

[9]  Thomas L Casavant,et al.  Homozygosity mapping with SNP arrays identifies TRIM32, an E3 ubiquitin ligase, as a Bardet-Biedl syndrome gene (BBS11). , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[10]  B. K. Pal,et al.  Allele-specific enzymatic amplification of beta-globin genomic DNA for diagnosis of sickle cell anemia. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[11]  P. Reitsma,et al.  A common genetic variation in the 3'-untranslated region of the prothrombin gene is associated with elevated plasma prothrombin levels and an increase in venous thrombosis. , 1996, Blood.

[12]  C. Mirkin,et al.  Two-color labeling of oligonucleotide arrays via size-selective scattering of nanoparticle probes. , 2001, Journal of the American Chemical Society.

[13]  M. Sudomoina,et al.  Association of SULT1A1 and UGT1A1 polymorphisms with breast cancer risk and phenotypes in Russian women , 2006, Molecular Biology.

[14]  P. Kwok,et al.  Methods for genotyping single nucleotide polymorphisms. , 2003, Annual review of genomics and human genetics.

[15]  L. Drago,et al.  Evaluation of the Abbott LCx HIV-1 RNA Quantitative, a New Assay for Quantitative Determination of Human Immunodeficiency Virus Type 1 RNA , 2000, Journal of Clinical Microbiology.

[16]  Sathyanarayanan V. Puthanveettil,et al.  Pyrene binary probes for unambiguous detection of mRNA using time-resolved fluorescence spectroscopy , 2006, Nucleic acids research.

[17]  F. Lewis,et al.  Solvent-Dependent Behavior of Phenanthrene-Amine Intramolecular Exciplexes , 1994 .

[18]  M. Masuko,et al.  Optimization of excimer-forming two-probe nucleic acid hybridization method with pyrene as a fluorophore. , 1998, Nucleic acids research.

[19]  Chad A Mirkin,et al.  Homogeneous detection of nucleic acids based upon the light scattering properties of silver-coated nanoparticle probes. , 2007, Analytical chemistry.

[20]  L. Morrison 13 – Detection of Energy Transfer and Fluorescence Quenching , 1992 .

[21]  M. Koenig,et al.  Use of SNP array analysis to identify a novel TRIM32 mutation in limb-girdle muscular dystrophy type 2H , 2009, Neuromuscular Disorders.

[22]  C. Cantor,et al.  Pyrene derivatives as fluorescent probes of conformation near the 3′ termini of polyribonucleotides , 1977, Biopolymers.

[23]  T. McCarthy,et al.  A novel process for mutation detection using uracil DNA-glycosylase. , 1998, Nucleic acids research.

[24]  山崎 甞録,et al.  Photochemical Reactions , 1942, Nature.

[25]  A. Krivenko,et al.  The Accurate Detection of One Point Mutations by Ligation of Short Oligonucleotides , 1998 .

[26]  A. Mandal,et al.  ENERGY TRANSFER FROM THIACYANINE TO ACRIDINE ORANGE FACILITATED BY DNA , 1999 .

[27]  Francesco Salvatore,et al.  Genotype-phenotype correlation in cystic fibrosis: the role of modifier genes. , 2002, American journal of medical genetics.

[28]  M Pirmohamed,et al.  Genetic susceptibility to adverse drug reactions. , 2001, Trends in pharmacological sciences.

[29]  B. Nordén,et al.  Peptide nucleic acid (PNA): its medical and biotechnical applications and promise for the future , 2000, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[30]  C. F. Bennett,et al.  Progress in antisense oligonucleotide therapeutics. , 1996, Annual review of pharmacology and toxicology.

[31]  P. Bonnet,et al.  Exciplex fluorescence emission from simple organic intramolecular constructs in non-polar and highly polar media as model systems for DNA-assembled exciplex detectors. , 2006, Organic & biomolecular chemistry.

[32]  J. B. Birks,et al.  Photophysics of aromatic molecules , 1970 .

[33]  J. Papp,et al.  Comparison of Methods for Detection of Chlamydia trachomatis and Neisseria gonorrhoeae Using Commercially Available Nucleic Acid Amplification Tests and a Liquid Pap Smear Medium , 2003, Journal of Clinical Microbiology.

[34]  Jianping Huang,et al.  Primer Design and Marker Clustering for Multiplex SNP-IT Primer Extension Genotyping Assay using Statistical Modeling , 2004, Bioinform..

[35]  M. Rhodes,et al.  Assessment of two flexible and compatible SNP genotyping platforms: TaqMan SNP Genotyping Assays and the SNPlex Genotyping System. , 2005, Mutation research.

[36]  J. Gilbert,et al.  SNPing away at complex diseases: analysis of single-nucleotide polymorphisms around APOE in Alzheimer disease. , 2000, American journal of human genetics.

[37]  N. Gerry,et al.  Universal DNA microarray method for multiplex detection of low abundance point mutations. , 1999, Journal of molecular biology.

[38]  M. Heller,et al.  CHEMILUMINESCENT AND FLUORESCENT PROBES FOR DNA HYBRIDIZATION SYSTEMS , 1985 .

[39]  W. Smith,et al.  Ultrasensitive DNA detection using oligonucleotide-silver nanoparticle conjugates. , 2008, Analytical chemistry.

[40]  M. K. Pal,et al.  Transfer of energy from thiacyanine to acridine orange and formation of exciplex between the two dyes bound to surfactants , 1998 .

[41]  O. Fedorova,et al.  Cooperative interactions of the oligodeoxyribonucleotides on the complementary template. The influence of chemical groups and mismatched nucleotides at the 5'- and 3'-ends of oligonucleotides on the parameters of cooperativity. , 1997, Journal of biomolecular structure & dynamics.

[42]  John B. Shoven,et al.  I , Edinburgh Medical and Surgical Journal.

[43]  A. S. Benight,et al.  The thermodynamic advantage of DNA oligonucleotide 'stacking hybridization' reactions: energetics of a DNA nick. , 1997, Nucleic acids research.

[44]  A. Oser,et al.  Nonradioactive Assay of DNA Hybridization by DNA-Template-Mediated Formation of a Ternary TbIII Complex in Pure Liquid Phase , 1990 .

[45]  J. Todd,et al.  Interaction analysis of the CBLB and CTLA4 genes in type 1 diabetes , 2007, Journal of leukocyte biology.

[46]  D. Stetsenko,et al.  Detection of point mutations using pyrene-labeled DNA probes , 2004 .

[47]  Fuli Yu,et al.  Highly multiplexed molecular inversion probe genotyping: over 10,000 targeted SNPs genotyped in a single tube assay. , 2005, Genome research.

[48]  B. Stevens Some effects of molecular orientation on fluorescence emission and energy transfer in crystalline aromatic hydrocarbons , 1962 .

[49]  N. Kamatani,et al.  Genetic association between the PRKCH gene encoding protein kinase Ceta isozyme and rheumatoid arthritis in the Japanese population. , 2007, Arthritis and rheumatism.

[50]  J. SantaLucia,et al.  Thermodynamics and NMR of internal G.T mismatches in DNA. , 1997, Biochemistry.

[51]  P. Lipsky,et al.  Association of the IL4R single-nucleotide polymorphism I50V with rapidly erosive rheumatoid arthritis. , 2006, Arthritis and rheumatism.

[52]  M. Masuko,et al.  NUCLEIC ACID HYBRIDIZATION ACCOMPANIED WITH EXCIMER FORMATION FROM TWO PYRENE‐LABELED PROBES , 1995, Photochemistry and photobiology.

[53]  P. Kwok,et al.  Overlapping genomic sequences: a treasure trove of single-nucleotide polymorphisms. , 1998, Genome research.

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

[55]  D. Eccles,et al.  Influence of the MDM2 single nucleotide polymorphism SNP309 on tumour development in BRCA1 mutation carriers , 2006, BMC Cancer.

[56]  W. Smith,et al.  Quantitative simultaneous multianalyte detection of DNA by dual-wavelength surface-enhanced resonance Raman scattering. , 2007, Angewandte Chemie.

[57]  Tom Brown,et al.  Fluorescence Based Strategies for Genetic Analysis , 2006 .

[58]  C. Deltas,et al.  Multiplex molecular diagnosis of MEFV mutations in patients with familial Mediterranean fever by LightCycler real-time PCR. , 2005, Clinical chemistry.

[59]  V. Meiner,et al.  Apolipoprotein E genotyping: accurate, simple, high throughput method using ABI Prism SNaPshot Multiplex System. , 2004, Journal of Alzheimer's disease : JAD.

[60]  Fei Wu,et al.  Solvent and solubility effects on exciplex emission of polymer-bound anthryl group and p-N,N-dimethylaminotoluene , 1992 .

[61]  C. Osiowy Sensitive Detection of HBsAg Mutants by a Gap Ligase Chain Reaction Assay , 2002, Journal of Clinical Microbiology.

[62]  Federica Gemignani,et al.  Polymorphisms of the Dopamine Receptor Gene DRD2 and Colorectal Cancer Risk , 2005, Cancer Epidemiology Biomarkers & Prevention.

[63]  Viswanadham Garimella,et al.  Homogeneous detection of unamplified genomic DNA sequences based on colorimetric scatter of gold nanoparticle probes , 2004, Nature Biotechnology.

[64]  M. Drumm,et al.  IL1B polymorphisms modulate cystic fibrosis lung disease , 2009, Pediatric pulmonology.

[65]  Graeme A. Bird,et al.  Chemical Reactions in DSMC , 2011 .

[66]  Duncan Graham,et al.  Quantitative enhanced Raman scattering of labeled DNA from gold and silver nanoparticles. , 2007, Small.

[67]  W. Smith,et al.  Control of enhanced Raman scattering using a DNA-based assembly process of dye-coded nanoparticles. , 2008, Nature nanotechnology.

[68]  D. R. Benson,et al.  Exciplex fluorescence in inclusion complexes of naphthalene derivatives , 1996 .

[69]  Pui-Yan Kwok,et al.  Detection of single nucleotide polymorphisms. , 2003, Current issues in molecular biology.

[70]  I. Sase,et al.  Double-labeled donor probe can enhance the signal of fluorescence resonance energy transfer (FRET) in detection of nucleic acid hybridization. , 2000, Nucleic acids research.

[71]  Anton Simeonov,et al.  Single nucleotide polymorphism genotyping using short, fluorescently labeled locked nucleic acid (LNA) probes and fluorescence polarization detection. , 2002, Nucleic acids research.

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

[73]  Jagotamoy Das,et al.  Nanocatalyst-based assay using DNA-conjugated Au nanoparticles for electrochemical DNA detection. , 2008, Langmuir : the ACS journal of surfaces and colloids.

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

[75]  Weiguo Cao Recent developments in ligase-mediated amplification and detection. , 2004, Trends in biotechnology.

[76]  Sanjay Tyagi,et al.  Real-time assays with molecular beacons and other fluorescent nucleic acid hybridization probes. , 2006, Clinica chimica acta; international journal of clinical chemistry.

[77]  P. Bartlett,et al.  Analysis of short tandem repeats by using SERS monitoring and electrochemical melting. , 2010, Angewandte Chemie.

[78]  D. Turner,et al.  5'-Amino pyrene provides a sensitive, nonperturbing fluorescent probe of RNA secondary and tertiary structure formation , 1993 .

[79]  F. Studier,et al.  DNA sequencing by primer walking with strings of contiguous hexamers. , 1992, Science.

[80]  D. Pyshnyi,et al.  Development of a colorimetric test system for detection of point mutations via ligation of a tandem of short oligonucleotides on methacrylate beads , 2000, Molecular Biology.

[81]  J. Zieleński Genotype and Phenotype in Cystic Fibrosis , 2000, Respiration.

[82]  M. Pirmohamed,et al.  TNFα promoter region gene polymorphisms in carbamazepine-hypersensitive patients , 2001, Neurology.

[83]  Richard M Twyman,et al.  Techniques patents for SNP genotyping. , 2003, Pharmacogenomics.

[84]  B. Valeur,et al.  Molecular Fluorescence: Principles and Applications , 2001 .

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

[86]  18 – Detection of Energy Transfer and Fluorescence Quenching , 1995 .

[87]  J. S. Mann,et al.  Synthesis and properties of an oligodeoxynucleotide modified with a pyrene derivative at the 5'-phosphate. , 1992, Bioconjugate chemistry.

[88]  Detection of nucleic acids in situ: novel oligonucleotide analogues for target-assembled DNA-mounted exciplexes. , 2007, Organic & biomolecular chemistry.

[89]  B. Brenig,et al.  Genotyping of ovine prion protein gene (PRNP) variants by PCR with melting curve analysis. , 2006, Clinical chemistry.

[90]  J. Carrino,et al.  Detection of point mutations with a modified ligase chain reaction (Gap-LCR). , 1995, Nucleic acids research.

[91]  K. Douglas,et al.  DNA mismatch detection by resonance energy transfer between ruthenium(II) and osmium(II) tris(2,2'-bipyridyl) chromophores. , 2005, Inorganic chemistry.

[92]  M. Weiner,et al.  Multiplexed single nucleotide polymorphism genotyping by oligonucleotide ligation and flow cytometry. , 2000, Cytometry.

[93]  G. Aithal,et al.  Association of polymorphisms in the cytochrome P450 CYP2C9 with warfarin dose requirement and risk of bleeding complications , 1999, The Lancet.

[94]  J. Verhoeven,et al.  Solvent effects on the structure of fluorescent 'exciplexes' in rigidly-, flexibly-, and nonbridged donor-acceptor systems , 1993 .

[95]  Hiroshi Miyasaka,et al.  Electron Transfer and Exciplex Chemistry , 2007 .

[96]  Naoshi Kaneko,et al.  Genomewide high-density SNP linkage analysis of 236 Japanese families supports the existence of schizophrenia susceptibility loci on chromosomes 1p, 14q, and 20p. , 2005, American journal of human genetics.

[97]  Duncan Graham,et al.  Selective detection of deoxyribonucleic acid at ultralow concentrations by SERRS , 1997 .

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

[99]  B. Valeur,et al.  Effects of Intermolecular Photophysical Processes on Fluorescence Emission , 2012 .

[100]  M. Komiyama,et al.  Exciplex Formation between Pyrene and N,N-Dimethylaniline in DNA for the Detection of One-base Deletion , 2006 .

[101]  Mary E. Hawkins,et al.  Fluorescent Nucleoside Analogues as DNA Probes , 2003 .

[102]  U Landegren,et al.  A ligase-mediated gene detection technique. , 1988, Science.

[103]  Francis Barany,et al.  Approaching real-time molecular diagnostics: single-pair fluorescence resonance energy transfer (spFRET) detection for the analysis of low abundant point mutations in K-ras oncogenes. , 2003, Journal of the American Chemical Society.

[104]  R. Abramson,et al.  Detection of specific polymerase chain reaction product by utilizing the 5'----3' exonuclease activity of Thermus aquaticus DNA polymerase. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[105]  K. Yamana,et al.  A new method for introduction of a pyrene group into a terminal position of an oligonucleotide , 1994 .

[106]  Matthias W. Hentze,et al.  Increased efficiency of mRNA 3′ end formation: a new genetic mechanism contributing to hereditary thrombophilia , 2001, Nature Genetics.

[107]  G. Marrazza,et al.  Design of an optimal allele-specific oligonucleotide probe for the efficient discrimination of a thermodynamically stable (G x T) mismatch. , 2007, Analytica chimica acta.

[108]  Lysov YuP,et al.  A method for DNA sequencing by hybridization with oligonucleotide matrix. , 1991, DNA sequence : the journal of DNA sequencing and mapping.

[109]  Duncan Graham,et al.  Sequence-specific DNA detection using high-affinity LNA-functionalized gold nanoparticles. , 2007, Small.

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

[111]  H. McLeod,et al.  Disposition of 9-nitrocamptothecin and its 9-aminocamptothecin metabolite in relation to ABC transporter genotypes , 2006, Investigational New Drugs.

[112]  P. Dervan,et al.  Cooperative Triple-Helix Formation at Adjacent DNA Sites: Sequence Composition Dependence at the Junction , 1995 .

[113]  E. Kool,et al.  Fluorescent DNA base replacements: Reporters and sensors for biological systems. , 2006, Organic & biomolecular chemistry.

[114]  L. Brooks,et al.  A DNA polymorphism discovery resource for research on human genetic variation. , 1998, Genome research.

[115]  D. Y. Wu,et al.  The ligation amplification reaction (LAR)--amplification of specific DNA sequences using sequential rounds of template-dependent ligation. , 1989, Genomics.

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

[117]  P. Bartlett,et al.  The Use of an Electroactive Marker as a SERS Label in an E‐melting Mutation Discrimination Assay , 2009 .

[118]  W. Smith,et al.  Detection and identification of labeled DNA by surface enhanced resonance Raman scattering. , 2000, Biopolymers.

[119]  P. Kwok,et al.  Reading bits of genetic information: methods for single-nucleotide polymorphism analysis. , 1998, Genome research.

[120]  T. Spector,et al.  Association between a variation in LRCH1 and knee osteoarthritis: a genome-wide single-nucleotide polymorphism association study using DNA pooling. , 2006, Arthritis and rheumatism.

[121]  K. Douglas,et al.  Target-assembled tandem oligonucleotide systems based on exciplexes for detecting DNA mismatches and single nucleotide polymorphisms. , 2005, Biochemical and biophysical research communications.

[122]  N. A. Lokteva,et al.  Cooperative binding of oligonucleotides to adjacent sites of single-stranded DNA: sequence composition dependence at the junction. , 1999, Journal of biomolecular structure & dynamics.

[123]  Peter E. Nielsen,et al.  PNA hybridizes to complementary oligonucleotides obeying the Watson–Crick hydrogen-bonding rules , 1993, Nature.

[124]  F. Lewis,et al.  Formation and behavior of intramolecular N-(styrylalkyl)aniline exciplexes , 1999 .

[125]  A Rösler,et al.  ROLLING CIRCLE AMPLIFICATION FOR SCORING SINGLE NUCLEOTIDE POLYMORPHISMS , 2001, Nucleosides, nucleotides & nucleic acids.

[126]  A. Ashley-Koch,et al.  Sickle hemoglobin (HbS) allele and sickle cell disease: a HuGE review. , 2000, American journal of epidemiology.

[127]  David L Veenstra,et al.  Association between CYP2C9 genetic variants and anticoagulation-related outcomes during warfarin therapy. , 2002, JAMA.

[128]  D. Persing,et al.  Diagnostic molecular microbiology : principles and applications , 1993 .

[129]  Fei Huang,et al.  Magnetically assisted DNA assays: high selectivity using conjugated polymers for amplified fluorescent transduction , 2005, Nucleic acids research.

[130]  Andrew Gilbert,et al.  Essentials of Molecular Photochemistry , 1991 .

[131]  D. E. Wolf,et al.  Detection of nucleic acid hybridization by nonradiative fluorescence resonance energy transfer. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[132]  M. C. Rogert Bacigalupo,et al.  Target-assembled ExciProbes: Application to DNA Detection at the Level of PCR Product and Plasmid DNA , 2007, Journal of biomolecular structure & dynamics.

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

[134]  Luc J. Smink,et al.  Association of the T-cell regulatory gene CTLA4 with susceptibility to autoimmune disease , 2003, Nature.

[135]  A. Okamoto,et al.  Design of base-discriminating fluorescent nucleosides , 2005 .

[136]  Francis S. Collins,et al.  Variations on a Theme: Cataloging Human DNA Sequence Variation , 1997, Science.

[137]  Jacqueline K. Barton,et al.  Electrochemical DNA sensors , 2003, Nature Biotechnology.

[138]  K. Douglas,et al.  SNP Detection for Cytochrome P450 Alleles by Target-assembled Tandem Oligonucleotide Systems Based on Exciplexes , 2008, Journal of biomolecular structure & dynamics.

[139]  J. K. Ghosh,et al.  Energy transfer and formation of exciplex between thiacyanine and acridine orange facilitated by anionic biopolymers and synthetic polymers , 1994 .

[140]  A Klug,et al.  Mutation in the tau gene in familial multiple system tauopathy with presenile dementia. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[141]  K. Mullis The unusual origin of the polymerase chain reaction. , 1990, Scientific American.

[142]  K. Livak,et al.  A homogeneous, ligase-mediated DNA diagnostic test. , 1998, Genome research.

[143]  Henk Neefs,et al.  High-throughput genotyping of single nucleotide polymorphisms using new biplex invader technology. , 2002, Nucleic acids research.

[144]  J. Wengel,et al.  Sensitive SNP Dual‐Probe Assays Based on Pyrene‐Functionalized 2′‐Amino‐LNA: Lessons To Be Learned , 2007, Chembiochem : a European journal of chemical biology.

[145]  K. Khrapko,et al.  An oligonucleotide hybridization approach to DNA sequencing , 1989, FEBS letters.

[146]  M. Auweraer,et al.  The influence of solvent polarity on the nonradiative decay of exciplexes , 1991 .

[147]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[148]  F. Barany Genetic disease detection and DNA amplification using cloned thermostable ligase. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[149]  D. Pyshnyi,et al.  Detection of Single-Base Substitutions in Amplified Fragments via Ligation of a Tandem of Short Oligonucleotides in Solution and on a Solid Carrier , 2000, Molecular Biology.

[150]  E. Zielińska,et al.  The arylamine N-acetyltransferase (NAT2) polymorphism and the risk of adverse reactions to co-trimoxazole in children , 1998, European Journal of Clinical Pharmacology.

[151]  P. Bartlett,et al.  SERS-melting: a new method for discriminating mutations in DNA sequences. , 2008, Journal of the American Chemical Society.

[152]  J. C. Levy,et al.  Large-scale studies of the association between variation at the TNF/LTA locus and susceptibility to type 2 diabetes , 2005, Diabetologia.

[153]  L. Feuk,et al.  Robust and accurate single nucleotide polymorphism genotyping by dynamic allele-specific hybridization (DASH): design criteria and assay validation. , 2001, Genome research.

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

[155]  N. Candoni,et al.  DNA detection method based on the two-dimensional aggregation and selective desorption of nanoparticle probes. , 2006, The journal of physical chemistry. B.

[156]  L. Kotler,et al.  DNA sequencing: modular primers for automated walking. , 1994, BioTechniques.

[157]  D. Whitcombe,et al.  Target-assembled exciplexes based on Scorpion oligonucleotides. , 2008, Bioscience reports.

[158]  Takashi Asada,et al.  Dynamin-binding protein gene on chromosome 10q is associated with late-onset Alzheimer's disease. , 2006, Human molecular genetics.

[159]  Sharon Marsh,et al.  Association of CYP2C8, CYP3A4, CYP3A5, and ABCB1 Polymorphisms with the Pharmacokinetics of Paclitaxel , 2005, Clinical Cancer Research.

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

[161]  M. Auweraer,et al.  On the electronic structure of exciplexes in α-(1- OR 2-naphthyl)-ω-N,N-dialkylaminoalkanes , 1985 .

[162]  T. Brown,et al.  HyBeacon probes: a new tool for DNA sequence detection and allele discrimination. , 2001, Molecular and cellular probes.

[163]  Duncan Graham,et al.  SERRS as a more sensitive technique for the detection of labelled oligonucleotides compared to fluorescence. , 2004, The Analyst.

[164]  Yusuke Nakamura,et al.  Association of VKORC1 and CYP2C9 polymorphisms with warfarin dose requirements in Japanese patients , 2006, Journal of Human Genetics.

[165]  Tamara Vyshkina,et al.  Haplotypes within genes of β-chemokines in 17q11 are associated with multiple sclerosis: a second phase study , 2005, Human Genetics.

[166]  N. Mataga,et al.  Electronic processes in hetero-excimers and the mechanism of fluorescence quenching , 1967 .

[167]  P. Sham,et al.  Validation of single nucleotide polymorphism quantification in pooled DNA samples with SNaPIT™ , 2002, Molecular biotechnology.

[168]  L. Jorde,et al.  Linkage disequilibrium and the search for complex disease genes. , 2000, Genome research.

[169]  E. Kool,et al.  Probing DNA sequences in solution with a monomer-excimer fluorescence color change. , 1998, Nucleic acids research.

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

[171]  P. Miller,et al.  Use of EDTA derivatization to characterize interactions between oligodeoxyribonucleoside methylphosphonates and nucleic acids. , 1989, Biochemistry.

[172]  D. Marks,et al.  Refined high-field NMR solution structure of a binary-addressed pyrene/perfluoro-azide complementary DNA oligonucleotide system shows extensive distortion in the central nick region. , 1999, Journal of biomolecular structure & dynamics.

[173]  M. Pericak-Vance,et al.  Association between the neuron-specific RNA-binding protein ELAVL4 and Parkinson disease , 2005, Human Genetics.

[174]  M. Masuko,et al.  Fluorescence resonance energy transfer from pyrene to perylene labels for nucleic acid hybridization assays under homogeneous solution conditions. , 2000, Nucleic acids research.

[175]  Functionalized nanoparticles for nucleic acid sequence analysis using optical spectroscopies. , 2009, Biochemical Society transactions.

[176]  Johan Auwerx,et al.  A Pro12Ala substitution in PPARγ2 associated with decreased receptor activity, lower body mass index and improved insulin sensitivity , 1998, Nature Genetics.

[177]  J. Nicklas,et al.  A Real‐Time Multiplex SNP Melting Assay to Discriminate Individuals , 2008, Journal of forensic sciences.

[178]  Ji Hyun Jung,et al.  Interleukin 10 haplotype associated with increased risk of hepatocellular carcinoma. , 2003, Human molecular genetics.

[179]  H. Grönberg,et al.  Comprehensive genetic evaluation of common E-cadherin sequence variants and prostate cancer risk: strong confirmation of functional promoter SNP , 2005, Human Genetics.

[180]  M. Ottolenghi,et al.  Solvent induced changes in the electronic structure of a polar intermolecular exciplex , 1975 .

[181]  Ronald C. Petersen,et al.  Association of missense and 5′-splice-site mutations in tau with the inherited dementia FTDP-17 , 1998, Nature.

[182]  M. Uhlén,et al.  Capture of single-stranded DNA assisted by oligonucleotide modules. , 1998, Analytical biochemistry.

[183]  D. Geschwind,et al.  Pathogenic implications of mutations in the tau gene in pallido-ponto-nigral degeneration and related neurodegenerative disorders linked to chromosome 17. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[184]  D. Kingsbury,et al.  Rapid Detection and Identification of Infectious Agents , 1985 .

[185]  E. Gaidamakova,et al.  Binary Systems of Oligonucleotide Conjugates for Sequence Specific Energy-Transfer Sensitized Photomodification of Nucleic Acids , 1996 .

[186]  Duncan Graham,et al.  Bead-based DNA diagnostic assay for chlamydia using nanoparticle-mediated surface-enhanced resonance Raman scattering detection within a lab-on-a-chip format. , 2007, Analytical chemistry.

[187]  U. Asseline Development and Applications of Fluorescent Oligonucleotides , 2006 .

[188]  F. Lista,et al.  Rapid single tube genotyping of ACP1 by FRET based amplification and dual color melting curve analysis. , 2006, Molecular and cellular probes.

[189]  L. Kricka Nonisotopic DNA probe techniques , 1992 .

[190]  F. Barany,et al.  Ligase detection reaction for identification of low abundance mutations. , 1999, Clinical biochemistry.

[191]  K. Davies,et al.  Human genetic diseases : a practical approach , 1986 .

[192]  K. Douglas,et al.  An exciplex-based, target-assembled fluorescence system with inherently low background to probe for specific nucleic acid sequences. , 2005, Assay and drug development technologies.

[193]  K. Kano,et al.  Three-component complexes of cyclodextrins. Exciplex formation in cyclodextrin cavity , 1984 .

[194]  S. Agrawal,et al.  Design, biochemical, biophysical and biological properties of cooperative antisense oligonucleotides. , 1995, Nucleic acids research.

[195]  J. D. Watson The human genome project: past, present, and future. , 1990, Science.

[196]  D. Marks,et al.  Structural studies by high-field NMR spectroscopy of a binary-addressed complementary oligonucleotide system juxtaposing pyrene and perfluoro-azide units. , 1997, Journal of biomolecular structure & dynamics.