Design of 2′-phenylethynylpyrene excimer forming DNA/RNA probes for homogeneous SNP detection: The attachment manner matters

[1]  A. Venyaminova,et al.  5′-Bispyrene molecular beacons for RNA detection , 2017, Russian Journal of Bioorganic Chemistry.

[2]  A. Venyaminova,et al.  Rational design and studies of excimer forming novel dual probes to target RNA. , 2017, Bioorganic & medicinal chemistry.

[3]  S. Andreescu,et al.  Biomolecular detection at ssDNA-conjugated nanoparticles by nano-impact electrochemistry. , 2017, Biosensors & bioelectronics.

[4]  Michael Mertig,et al.  Methods to Characterize the Oligonucleotide Functionalization of Quantum Dots. , 2016, Small.

[5]  S. Ladame,et al.  Amplification-Free Detection of Circulating microRNA Biomarkers from Body Fluids Based on Fluorogenic Oligonucleotide-Templated Reaction between Engineered Peptide Nucleic Acid Probes: Application to Prostate Cancer Diagnosis. , 2016, Analytical chemistry.

[6]  R. Manderville,et al.  A Simple Molecular Rotor for Defining Nucleoside Environment within a DNA Aptamer-Protein Complex. , 2016, ACS chemical biology.

[7]  Jacob Kongsted,et al.  Revealing Nucleic Acid Mutations Using Förster Resonance Energy Transfer-Based Probes , 2016, Sensors.

[8]  P. Derrick,et al.  G-Quadruplex Supramolecular Assemblies in Photochemical Upconversion. , 2016, Chemistry.

[9]  Mitsunobu Nakamura,et al.  Helically Assembled Pyrene Arrays on an RNA Duplex That Exhibit Circularly Polarized Luminescence with Excimer Formation. , 2016, Chemistry.

[10]  R. Pohl,et al.  Solvatochromic fluorene-linked nucleoside and DNA as color-changing fluorescent probes for sensing interactions , 2016, Chemical science.

[11]  L. Zhang,et al.  Microenvironmental Effect of 2'-O-(1-Pyrenylmethyl)uridine Modified Fluorescent Oligonucleotide Probes on Sensitive and Selective Detection of Target RNA. , 2016, Analytical chemistry.

[12]  M. Sekine,et al.  7-(Benzofuran-2-yl)-7-deazadeoxyguanosine as a fluorescence turn-ON probe for single-strand DNA binding protein. , 2016, Chemical communications.

[13]  T. Zatsepin,et al.  1-Phenylethynylpyrene (PEPy) as a novel blue-emitting dye for qPCR assay. , 2016, The Analyst.

[14]  K. E. Lundin,et al.  Next-generation bis-locked nucleic acids with stacking linker and 2′-glycylamino-LNA show enhanced DNA invasion into supercoiled duplexes , 2016, Nucleic acids research.

[15]  E. V. Kostina,et al.  Synthesis of TaqMan probes using bisphosphoramidite of cyanine dye Cy3 , 2016, Russian Journal of Bioorganic Chemistry.

[16]  Michal Hocek,et al.  Inhibition of non-templated nucleotide addition by DNA polymerases in primer extension using twisted intercalating nucleic acid modified templates. , 2016, Bioorganic & medicinal chemistry letters.

[17]  B. Teo Synthesis and Applications of Luminescent Nucleic Acid-Based Silver Nanoclusters , 2015 .

[18]  P. Jurkiewicz,et al.  A Rotational BODIPY Nucleotide: An Environment-Sensitive Fluorescence-Lifetime Probe for DNA Interactions and Applications in Live-Cell Microscopy. , 2015, Angewandte Chemie.

[19]  P. Derrick,et al.  DNA-Based Assemblies for Photochemical Upconversion. , 2015, The journal of physical chemistry. B.

[20]  T. Zatsepin,et al.  Solid- and solution-phase synthesis and application of R6G dual-labeled oligonucleotide probes. , 2015, Bioorganic & medicinal chemistry.

[21]  P. Hrdlicka,et al.  Bulged Invader probes: activated duplexes for mixed-sequence dsDNA recognition with improved thermodynamic and kinetic profiles. , 2015, Chemical communications.

[22]  H. Wagenknecht,et al.  One-Dimensional Multichromophor Arrays Based on DNA: From Self-Assembly to Light-Harvesting. , 2015, Accounts of chemical research.

[23]  Jong-Wha Jung,et al.  In Vitro Fluorogenic Real‐Time Assay of the Repair of Oxidative DNA Damage , 2015, Chembiochem : a European journal of chemical biology.

[24]  V. Korshun,et al.  Recent advances in self-assembled fluorescent DNA structures and probes. , 2015, Current topics in medicinal chemistry.

[25]  P. Hrdlicka,et al.  Invader probes: harnessing the energy of intercalation to facilitate recognition of chromosomal DNA for diagnostic applications , 2015, Chemical science.

[26]  Carlos González,et al.  Interdependence of pyrene interactions and tetramolecular G4-DNA assembly. , 2015, Organic & biomolecular chemistry.

[27]  Yong You,et al.  Cy3 and Cy5 dyes attached to oligonucleotide terminus stabilize DNA duplexes: predictive thermodynamic model. , 2015, Biophysical chemistry.

[28]  R. Pohl,et al.  Bodipy-labeled nucleoside triphosphates for polymerase synthesis of fluorescent DNA. , 2014, Bioconjugate chemistry.

[29]  A. Madsen,et al.  Recognition of double-stranded DNA using energetically activated duplexes with interstrand zippers of 1-, 2- or 4-pyrenyl-functionalized O2'-alkylated RNA monomers. , 2014, Organic & biomolecular chemistry.

[30]  P. Derrick,et al.  DNA duplex as a scaffold for a ground state complex formation between a zinc cationic porphyrin and phenylethynylpyren-1-yl , 2014 .

[31]  Monika A. Ciuba,et al.  Photophysical processes in single molecule organic fluorescent probes. , 2014, Chemical Society reviews.

[32]  C. Fan,et al.  DNA-conjugated quantum dot nanoprobe for high-sensitivity fluorescent detection of DNA and micro-RNA. , 2014, ACS applied materials & interfaces.

[33]  V. Filichev,et al.  Assembly Dependent Fluorescence Enhancing Nucleic Acids in Sequence-Specific Detection of Double-Stranded DNA. , 2014, ChemPlusChem.

[34]  Alya G. Venyaminova,et al.  Fluorescent Probes for Nucleic Acid Visualization in Fixed and Live Cells , 2013, Molecules.

[35]  H. Asanuma,et al.  Evaluation of intrinsic spectroscopic properties of chromophore assemblies by shielding with cyclohexyl base pairs within a DNA duplex. , 2013, Bioorganic & medicinal chemistry.

[36]  S. Sau,et al.  Invaders: Recognition of Double‐Stranded DNA by Using Duplexes Modified with Interstrand Zippers of 2′‐O‐(Pyren‐1‐yl)methyl‐ribonucleotides , 2013, Chembiochem : a European journal of chemical biology.

[37]  Hiroshi Ito,et al.  Selective labeling of mature RISC using a siRNA carrying fluorophore–quencher pair , 2013 .

[38]  H. Yeh,et al.  Fluorescent silver nanoclusters as DNA probes. , 2013, Nanoscale.

[39]  P. Hrdlicka,et al.  DNA strands with alternating incorporations of LNA and 2'-O-(pyren-1-yl)methyluridine: SNP-discriminating RNA detection probes. , 2013, Chemical science.

[40]  Lik Hang Yuen,et al.  DNA-polyfluorophore Chemosensors for Environmental Remediation: Vapor-phase Identification of Petroleum Products in Contaminated Soil. , 2013, Chemical science.

[41]  Huabing Sun,et al.  Template-directed fluorogenic oligonucleotide ligation using "click" chemistry: detection of single nucleotide polymorphism in the human p53 tumor suppressor gene. , 2013, Bioconjugate chemistry.

[42]  Peter M. Kasson,et al.  GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit , 2013, Bioinform..

[43]  S. Zorzet,et al.  MAZ-binding G4-decoy with locked nucleic acid and twisted intercalating nucleic acid modifications suppresses KRAS in pancreatic cancer cells and delays tumor growth in mice , 2013, Nucleic acids research.

[44]  V. Filichev,et al.  Molecular engineering of guanine-rich sequences: Z-DNA, DNA triplexes, and G-quadruplexes. , 2013, Chemical reviews.

[45]  B. Kim,et al.  A fluorescent probe for the 3'-overhang of telomeric DNA based on competition between two interstrand G-quadruplexes. , 2013, Chemical communications.

[46]  J. Wengel,et al.  Interfacing click chemistry with automated oligonucleotide synthesis for the preparation of fluorescent DNA probes containing internal xanthene and cyanine dyes. , 2013, Chemistry.

[47]  Kemin Wang,et al.  Recent advances in fluorescent nucleic acid probes for living cell studies. , 2013, The Analyst.

[48]  A. El-Sayed,et al.  Studying the Influence of the Pyrene Intercalator TINA on the Stability of DNA i-Motifs , 2012, Nucleosides, nucleotides & nucleic acids.

[49]  Mitsunobu Nakamura,et al.  Highly ordered pyrene π-stacks on an RNA duplex display static excimer fluorescence. , 2012, Organic & biomolecular chemistry.

[50]  Meiping Zhao,et al.  Nucleic Acid Fluorescent Probes for Biological Sensing , 2012, Applied spectroscopy.

[51]  H. Yoshida,et al.  RNA-based diagnosis in a multicellular specimen by whole mount in situ hybridization using an RNA-specific probe. , 2012, Bioorganic & medicinal chemistry.

[52]  Hao Yan,et al.  Robust DNA-functionalized core/shell quantum dots with fluorescent emission spanning from UV-vis to near-IR and compatible with DNA-directed self-assembly. , 2012, Journal of the American Chemical Society.

[53]  Jong Seung Kim,et al.  Enhanced electrogenerated chemiluminescence of phenylethynylpyrene derivatives: use of weakly electron-donating group as a substituent. , 2012, The Journal of organic chemistry.

[54]  Wim F Vranken,et al.  ACPYPE - AnteChamber PYthon Parser interfacE , 2012, BMC Research Notes.

[55]  E. Kool,et al.  DNA polyfluorophores for real-time multicolor tracking of dynamic biological systems. , 2012, Angewandte Chemie.

[56]  E. Kool,et al.  DNA-multichromophore systems. , 2012, Chemical reviews.

[57]  J. Wengel,et al.  Novel (Phenylethynyl)pyrene–LNA Constructs for Fluorescence SNP Sensing in Polymorphic Nucleic Acid Targets , 2012, Chembiochem : a European journal of chemical biology.

[58]  Alfonso Latorre,et al.  DNA‐Mediated Silver Nanoclusters: Synthesis, Properties and Applications , 2012, Chembiochem : a European journal of chemical biology.

[59]  X. Piao,et al.  Effect of LNA- and OMeN-modified oligonucleotide probes on the stability and discrimination of mismatched base pairs of duplexes , 2012, Journal of Biosciences.

[60]  H. Asanuma,et al.  Preparation of supramolecular chromophoric assemblies using a DNA duplex. , 2012, Physical chemistry chemical physics : PCCP.

[61]  T. Brown,et al.  A highly fluorescent DNA toolkit: synthesis and properties of oligonucleotides containing new Cy3, Cy5 and Cy3B monomers , 2012, Nucleic acids research.

[62]  Jingyue Ju,et al.  Fluorescent hybridization probes for nucleic acid detection , 2012, Analytical and Bioanalytical Chemistry.

[63]  G. Mayer,et al.  Chemical Maturation of a Bivalent Aptamer by Single Domain Variation , 2012, Chembiochem : a European journal of chemical biology.

[64]  T. Brown,et al.  Efficient reverse click labeling of azide oligonucleotides with multiple alkynyl Cy-Dyes applied to the synthesis of HyBeacon probes for genetic analysis , 2012 .

[65]  V. Korshun,et al.  4',5'-Dichloro-2',7'-dimethoxy-5(6)-carboxyfluorescein (JOE): synthesis and spectral properties of oligonucleotide conjugates. , 2012, The Journal of organic chemistry.

[66]  D. Itkis,et al.  Modification of quantum dots with nucleic acids , 2011 .

[67]  Y. Wang,et al.  Fluorescence Detection of Single‐Nucleotide Polymorphism with Single‐Strand Triplex‐Forming DNA Probes , 2011, Chembiochem : a European journal of chemical biology.

[68]  P. Hrdlicka,et al.  Pyrene-functionalized oligonucleotides and locked nucleic acids (LNAs): tools for fundamental research, diagnostics, and nanotechnology. , 2011, Chemical Society reviews.

[69]  A. Boutorine,et al.  Triplex‐Forming Twisted Intercalating Nucleic Acids (TINAs): Design Rules, Stabilization of Antiparallel DNA Triplexes and Inhibition of G‐Quartet‐Dependent Self‐Association , 2011, Chembiochem : a European journal of chemical biology.

[70]  P. Nielsen,et al.  High-affinity DNA targeting using readily accessible mimics of N2'-functionalized 2'-amino-α-L-LNA. , 2011, The Journal of organic chemistry.

[71]  G. Lisby,et al.  Increasing the Analytical Sensitivity by Oligonucleotides Modified with Para- and Ortho-Twisted Intercalating Nucleic Acids – TINA , 2011, PloS one.

[72]  T. Brown,et al.  Ultrasensitive fluorescence-based methods for nucleic acid detection: towards amplification-free genetic analysis. , 2011, Chemical communications.

[73]  I. V. Astakhova,et al.  LNA for optimization of fluorescent oligonucleotide probes: improved spectral properties and target binding. , 2011, Bioconjugate chemistry.

[74]  H. Wagenknecht,et al.  4,4-Difluoro-4-bora-3a,4a-diaza-s-indacene as a bright fluorescent label for DNA. , 2011, The Journal of organic chemistry.

[75]  Cong Yu,et al.  Label-free detection of polynucleotide single-base mismatch via pyrene probe excimer emission. , 2011, Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy.

[76]  W. Tan,et al.  Pyrene Excimer for DNA Sensors , 2011 .

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

[78]  E. Pedersen,et al.  Enhanced anti-HIV-1 activity of G-quadruplexes comprising locked nucleic acids and intercalating nucleic acids , 2010, Nucleic acids research.

[79]  I. V. Astakhova,et al.  Novel interstrand communication systems within DNA duplexes based on 1-, 2- and 4-(phenylethynyl)pyrenes attached to 2'-amino-LNA: high-affinity hybridization and fluorescence sensing. , 2010, Chemical communications.

[80]  K. Shinozuka,et al.  Modified OligoDNA Having Two Consecutive Silylated-pyrene Moieties in Minor Groove Exhibiting an Excimer Fluorescent Signal upon Binding to Fully Complementary DNA Strand , 2010 .

[81]  Bernard Juskowiak,et al.  Nucleic acid-based fluorescent probes and their analytical potential , 2010, Analytical and bioanalytical chemistry.

[82]  Piotr Cieplak,et al.  The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building. , 2010, Physical chemistry chemical physics : PCCP.

[83]  H. Griesser,et al.  Synthesis of 3′‐BODIPY‐Labeled Active Esters of Nucleotides and a Chemical Primer Extension Assay on Beads , 2010 .

[84]  Y. Tor,et al.  Fluorescent analogs of biomolecular building blocks: design, properties, and applications. , 2010, Chemical reviews.

[85]  S. Sau,et al.  Invader LNA: efficient targeting of short double stranded DNA. , 2010, Organic & biomolecular chemistry.

[86]  K. Fujimoto,et al.  Specific induced circular dichroism and enhanced B to z transitions of duplexes stabilized by chromophore-linked alkynylnucleoside residues. , 2010, Chemistry.

[87]  R. Häner,et al.  Nucleic acid-guided assembly of aromatic chromophores. , 2010, Chemical Society reviews.

[88]  T. Maier,et al.  Nucleotides. Part LXXV: New Types of Fluorescence Labeling of 2â²-Deoxycytidine , 2009 .

[89]  C. Yang,et al.  Pyrene excimer nucleic acid probes for biomolecule signaling. , 2009, Journal of biomedical nanotechnology.

[90]  Mitsunobu Nakamura,et al.  RNA-mediated electron transfer: double exponential distance dependence. , 2009, Journal of the American Chemical Society.

[91]  V. Korshun,et al.  Practical synthesis of isomerically pure 5- and 6-carboxytetramethylrhodamines, useful dyes for DNA probes. , 2009, Bioconjugate chemistry.

[92]  Mitsunobu Nakamura,et al.  Fluorescence quenching properties of multiple pyrene-modified RNAs. , 2009, Bioorganic & medicinal chemistry.

[93]  Gang Bao,et al.  Fluorescent probes for live-cell RNA detection. , 2009, Annual review of biomedical engineering.

[94]  H. Asanuma,et al.  Rational Design of Functional DNA with a Non-Ribose Acyclic Scaffold , 2009 .

[95]  P. Herdewijn,et al.  Detection of RNA Hybridization by Pyrene‐Labeled Probes , 2009, Chembiochem : a European journal of chemical biology.

[96]  H. Xiong,et al.  8-Aza-7-deazaguanine nucleosides and oligonucleotides with octadiynyl side chains: synthesis, functionalization by the azide-alkyne 'click' reaction and nucleobase specific fluorescence quenching of coumarin dye conjugates. , 2009, Organic & biomolecular chemistry.

[97]  Imrich Géci,et al.  Identification of a new G-quadruplex motif in the KRAS promoter and design of pyrene-modified G4-decoys with antiproliferative activity in pancreatic cancer cells. , 2009, Journal of medicinal chemistry.

[98]  Colin D. Medley,et al.  Molecular engineering of DNA: molecular beacons. , 2009, Angewandte Chemie.

[99]  I. V. Astakhova,et al.  Highly fluorescent conjugated pyrenes in nucleic acid probes: (phenylethynyl)pyrenecarbonyl-functionalized locked nucleic acids. , 2008, Chemistry.

[100]  I. V. Astakhova,et al.  1-, 2-, and 4-ethynylpyrenes in the structure of twisted intercalating nucleic acids: structure, thermal stability, and fluorescence relationship. , 2008, Chemistry.

[101]  A. Venyaminova,et al.  Oligo(2′-O-methylribonucleotides) and their derivatives: III. 5′-Mono- and 5′-bispyrenyl derivatives of oligo(2′-O-methylribonucleotides) and their 3′-modified analogues: Synthesis and properties , 2008, Russian Journal of Bioorganic Chemistry.

[102]  E. Pedersen,et al.  High physiological thermal triplex stability optimization of twisted intercalating nucleic acids (TINA). , 2008, Organic & biomolecular chemistry.

[103]  Nayoung Kim,et al.  Gene mutations of 23S rRNA associated with clarithromycin resistance in Helicobacter pylori strains isolated from Korean patients. , 2008, Journal of microbiology and biotechnology.

[104]  Xiang-Jun Lu,et al.  3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures , 2008, Nature Protocols.

[105]  Mitsunobu Nakamura,et al.  Pyrene-zipper array assembled via RNA duplex formation. , 2008, Journal of the American Chemical Society.

[106]  A. Murakami,et al.  Microarray-based label-free detection of RNA using bispyrene-modified 2'-O-methyl oligoribonucleotide as capture and detection probe. , 2008, Bioorganic & medicinal chemistry letters.

[107]  S. Balasubramanian,et al.  Rigid cyanine dye nucleic acid labels. , 2008, Chemical communications.

[108]  A. Ustinov,et al.  A Convenient Synthesis of Cyanine Dyes: Reagents for the Labeling of Biomolecules , 2008 .

[109]  Young Jun Seo,et al.  Quencher-free molecular beacons: a new strategy in fluorescence based nucleic acid analysis. , 2008, Chemical Society reviews.

[110]  A. Marx,et al.  Nucleotide insertion and bypass synthesis of pyrene- and BODIPY-modified oligonucleotides by DNA polymerases. , 2008, Chemical communications.

[111]  S. L. Bondarev,et al.  1-Phenylethynylpyrene (1-PEPy) as refined excimer forming alternative to pyrene: case of DNA major groove excimer. , 2007, Bioconjugate chemistry.

[112]  S. L. Bondarev,et al.  5(6)-carboxyfluorescein revisited: new protecting group, separation of isomers, and their spectral properties on oligonucleotides. , 2007, Bioconjugate chemistry.

[113]  Mitsunobu Nakamura,et al.  Pyrene aromatic arrays on RNA duplexes as helical templates. , 2007, Organic & biomolecular chemistry.

[114]  J. Šponer,et al.  Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers , 2007 .

[115]  S. Jockusch,et al.  Fluorescent hybridization probes for sensitive and selective DNA and RNA detection. , 2007, Accounts of chemical research.

[116]  R. S. Coleman,et al.  Coumarin base-pair replacement as a fluorescent probe of ultrafast DNA dynamics , 2007 .

[117]  M. Parrinello,et al.  Canonical sampling through velocity rescaling. , 2007, The Journal of chemical physics.

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

[119]  P. T. Jørgensen,et al.  Twisted Intercalating Nucleic Acids – Intercalator Influence on Parallel Triplex Stabilities , 2006 .

[120]  V. Govorun,et al.  Phenylethynylpyrene-labeled oligonucleotide probes for excimer fluorescence SNP analysis of 23S rRNA gene in clarithromycin-resistant Helicobacter pylori strains. , 2006, Mutation research.

[121]  E. Pedersen,et al.  Synthesis of twisted intercalating nucleic acids possessing acridine derivatives. Thermal stability studies. , 2006, Bioconjugate chemistry.

[122]  Mitsunobu Nakamura,et al.  Pyrene-modified DNA aptamer as a fluorescent biosensor with high affinity and specificity for ATP sensing , 2006 .

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

[124]  K. Fujimoto,et al.  Alkynylpyrenes as improved pyrene-based biomolecular probes with the advantages of high fluorescence quantum yields and long absorption/emission wavelengths. , 2006, Chemistry.

[125]  Tom Brown,et al.  Fluorescence based strategies for genetic analysis. , 2005, Chemical communications.

[126]  Mitsunobu Nakamura,et al.  Pyrene is highly emissive when attached to the RNA duplex but not to the DNA duplex: the structural basis of this difference , 2005, Nucleic acids research.

[127]  Mitsunobu Nakamura,et al.  Helical pyrene-array along the outside of duplex RNA. , 2005, Chemical communications.

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

[129]  E. Pedersen,et al.  Stable and selective formation of hoogsteen-type triplexes and duplexes using twisted intercalating nucleic acids (TINA) prepared via postsynthetic Sonogashira solid-phase coupling reactions. , 2005, Journal of the American Chemical Society.

[130]  K. Hwang,et al.  Electronic polarization reversal and excited state intramolecular charge transfer in donor/acceptor ethynylpyrenes. , 2005, The journal of physical chemistry. B.

[131]  Mitsunobu Nakamura,et al.  DNA mismatch detection using a pyrene-excimer-forming probe. , 2005, Chemical communications.

[132]  T. Oretskaya,et al.  Oligonucleotides with 2'-O-carboxymethyl group: synthesis and 2'-conjugation via amide bond formation on solid phase. , 2004, Organic & biomolecular chemistry.

[133]  Akimitsu Okamoto,et al.  Pyrene-labeled oligodeoxynucleotide probe for detecting base insertion by excimer fluorescence emission. , 2004, Journal of the American Chemical Society.

[134]  K. Burgess,et al.  On the stability of furanopyrimidin-2-one bases in oligonucleotides. , 2004, Chemical communications.

[135]  V. Korshun,et al.  Oligonucleotides containing new fluorescent 1-phenylethynylpyrene and 9,10-bis(phenylethynyl)anthracene uridine-2′-carbamates: synthesis and properties , 2004 .

[136]  Kazuhisa Fujimoto,et al.  Unambiguous detection of target DNAs by excimer-monomer switching molecular beacons. , 2004, The Journal of organic chemistry.

[137]  Robert M Dickson,et al.  DNA-templated Ag nanocluster formation. , 2004, Journal of the American Chemical Society.

[138]  D. Stetsenko,et al.  1-(Phenylethynyl)pyrene and 9,10-Bis(phenylethynyl)anthracene, Useful Fluorescent Dyes for DNA Labeling: Excimer Formation and Energy Transfer , 2004 .

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

[140]  R. Efremov,et al.  Pyrenemethyl ara‐Uridine‐2′‐carbamate: A Strong Interstrand Excimer in the Major Groove of a DNA Duplex , 2003, Chembiochem : a European journal of chemical biology.

[141]  K. Yamana,et al.  Detection of acceptor sites for antisense oligonucleotides on native folded RNA by fluorescence spectroscopy. , 2003, Bioorganic & medicinal chemistry.

[142]  Gang Bao,et al.  Hybridization of 2'-O-methyl and 2'-deoxy molecular beacons to RNA and DNA targets. , 2002, Nucleic acids research.

[143]  Yusuke Ohtani,et al.  Bis-pyrene-labeled oligonucleotides: sequence specificity of excimer and monomer fluorescence changes upon hybridization with DNA. , 2002, Bioconjugate chemistry.

[144]  K. Yamana,et al.  Bispyrene-conjugated 2'-O-methyloligonucleotide as a highly specific RNA-recognition probe. , 2002, Angewandte Chemie.

[145]  J. Monti,et al.  New ligand combinations for the efficient stabilization of short nucleic acid hairpins , 2002 .

[146]  D. Stetsenko,et al.  Novel uridin-2′-yl carbamates: synthesis, incorporation into oligodeoxyribonucleotides, and remarkable fluorescence properties of 2′-pyren-1-ylmethylcarbamate , 2002 .

[147]  V. Korshun,et al.  Synthesis and Fluorescent Characteristics of Oligodeoxynucleotides Containing a Novel Fluorescent Label, p-(2-Benzoxazolyl)tolane , 2001, Russian Journal of Bioorganic Chemistry.

[148]  V. Vlassov,et al.  5'-bis-pyrenylated oligonucleotides displaying excimer fluorescence provide sensitive probes of RNA sequence and structure. , 2001, Nucleic acids research.

[149]  S. Pathak,et al.  Hydroxylated quantum dots as luminescent probes for in situ hybridization. , 2001, Journal of the American Chemical Society.

[150]  K. Yamana,et al.  Fluorescence Detection of Specific RNA Sequences Using 2'-Pyrene-Modified Oligoribonucleotides We are very grateful to Professor Hiroshi Sugiyama, Dr. Tetsuji Yamaoka, and Dr. Takashi Morii for ion-spray mass spectrometric measurements and helpful comments on this research. , 2001, Angewandte Chemie.

[151]  F. Mégraud,et al.  Detection of Point Mutations Associated with Resistance of Helicobacter pylori to Clarithromycin by Hybridization in Liquid Phase , 1998, Journal of Clinical Microbiology.

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

[153]  Norman C. Nelson,et al.  Advantages of 2'-O-methyl oligoribonucleotide probes for detecting RNA targets. , 1998, Nucleic acids research.

[154]  S. Kumamoto,et al.  Homopyrimidine Oligonucleotides Modified by a Pyrenylmethyl Group at the Terminal Position: Enhanced Fluorescence upon Binding to Double Helical DNA , 1997 .

[155]  K. Balakin,et al.  New Pyrene Derivatives for Fluorescent Labeling of Oligonucleotides , 1997 .

[156]  R. Strömberg,et al.  Removal of t-butyldimethylsilyl protection in RNA-synthesis. Triethylamine trihydrofluoride (TEA, 3HF) is a more reliable alternative to tetrabutylammonium fluoride (TBAF). , 1994, Nucleic acids research.

[157]  M. Pirrung,et al.  A convenient procedure for the deprotection of silylated nucleosides and nucleotides using triethylamine trihydrofluoride , 1994 .

[158]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[159]  P. Theisen,et al.  Fluorescent dye phosphoramidite labelling of oligonucleotides. , 1992, Nucleic acids symposium series.

[160]  H. Ozaki,et al.  Enhanced Fluorescence in the Binding of Oligonucleotides With a Pyrene Group in the Sugar Fragment to Complementary Polynucleotides , 1992 .

[161]  K. Yamana,et al.  Synthesis of oligonucleotide derivatives with pyrene group at sugar fragment , 1991 .

[162]  A. Trzeciak,et al.  A Simple and Effective Chemical Phosphorylation Procedure for Biomolecules , 1987 .

[163]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[164]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[165]  E. Wang,et al.  DNA-templated fluorescent silver nanoclusters , 2011, Analytical and Bioanalytical Chemistry.

[166]  I. V. Astakhova,et al.  Phenylethynylpyrene excimer forming hybridization probes for fluorescence SNP detection. , 2009, Methods in molecular biology.

[167]  Yalin Tang,et al.  Nucleosides, Nucleotides and Nucleic Acids , 2008 .

[168]  Kazushige Yamana,et al.  Bis-pyrene-labeled molecular beacon: a monomer-excimer switching probe for the detection of DNA base alteration. , 2008, Bioorganic & medicinal chemistry.

[169]  V. Korshun,et al.  Synthesis and fluorescent properties of 5-(1-pyrenylethynyl)-2′-deoxyuridine-containing oligodeoxynucleotides , 2007, Russian Journal of Bioorganic Chemistry.

[170]  K. Yamana,et al.  2'-Pyrene modified oligonucleotide provides a highly sensitive fluorescent probe of RNA. , 1999, Nucleic acids research.

[171]  M. Caruthers,et al.  Chemical synthesis of deoxyoligonucleotides by the phosphoramidite method. , 1987, Methods in enzymology.