Fluorescent Probes for Nucleic Acid Visualization in Fixed and Live Cells

RNA “Traffic Lights”: An Analytical Tool to Monitor siRNA Integrity

(2013) Carolin Holzhauser et al.   ACS Chemical Biology

Building Fluorescent DNA Nanodevices on Target Living Cell Surfaces

(2013) Guizhi Zhu et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Detection of miRNA in Live Cells by Using Templated RuII-Catalyzed Unmasking of a Fluorophore

(2013) Kalyan K. Sadhu et al.   CHEMISTRY-A EUROPEAN JOURNAL

Imaging cell biology in live animals: Ready for prime time

(2013) Roberto Weigert et al.   JOURNAL OF CELL BIOLOGY

Development of a New Method for Synthesis of Tandem Hairpin Pyrrole–Imidazole Polyamide Probes Targeting Human Telomeres

(2013) Yusuke Kawamoto et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A Targeted, Self-Delivered, and Photocontrolled Molecular Beacon for mRNA Detection in Living Cells

(2013) Liping Qiu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

High-throughput sequencing for biology and medicine

(2013) W. W. Soon et al.   Molecular Systems Biology

Quantitative visualization of DNA G-quadruplex structures in human cells

(2013) Giulia Biffi et al.   Nature Chemistry

Raman and SERS microscopy for molecular imaging of live cells

(2013) Almar F Palonpon et al.   Nature Protocols

Mediator regulates non-coding RNA transcription at fission yeast centromeres

(2013) Michael Thorsen et al.   Epigenetics & Chromatin

Tricolour fluorescence detection of sequence-specific DNA with a new molecular beacon and a nucleic acid dye TOTO-3

(2012) Dongshan Xiang et al.   ANALYST

Poly(A)-targeting molecular beacons: Fluorescence resonance energy transfer-based in vitro quantitation and time-dependent imaging in live cells

(2012) Min Young Kim et al.   ANALYTICAL BIOCHEMISTRY

Fluorescence assay of polyamide–DNA interactions

(2012) Cynthia M. Dupureur et al.   ANALYTICAL BIOCHEMISTRY

DNA Polyfluorophores for Real-Time Multicolor Tracking of Dynamic Biological Systems

(2012) Shenliang Wang et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Consecutive Signal Amplification for DNA Detection Based on De Novo Fluorophore Synthesis and Host-Guest Chemistry

(2012) Xiao-Hua Chen et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

RNA as a Structural and Regulatory Component of the Centromere

(2012) Jonathan I. Gent et al.   Annual Review of Genetics

PNA FIT-Probes for the Dual Color Imaging of Two Viral mRNA Targets in Influenza H1N1 Infected Live Cells

(2012) Susann Kummer et al.   BIOCONJUGATE CHEMISTRY

Quencher-free molecular beacon tethering 7-hydroxycoumarin detects targets through protonation/deprotonation

(2012) Hiromu Kashida et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Label-Free Live-Cell Imaging with Confocal Raman Microscopy

(2012) Katharina Klein et al.   BIOPHYSICAL JOURNAL

Single-dose pharmacokinetic and toxicity analysis of pyrrole–imidazole polyamides in mice

(2012) Timothy W. Synold et al.   CANCER CHEMOTHERAPY AND PHARMACOLOGY

Progress and Prospects of Pyrrole-Imidazole Polyamide-Fluorophore Conjugates as Sequence-Selective DNA Probes

(2012) Thangavel Vaijayanthi et al.   CHEMBIOCHEM

“DNA Traffic Lights”: Concept of Wavelength-Shifting DNA Probes and Application in an Aptasensor

(2012) Carolin Holzhauser et al.   CHEMBIOCHEM

DNA-Multichromophore Systems

(2012) Yin Nah Teo et al.   CHEMICAL REVIEWS

Combinatorial Strategies in Fluorescent Probe Development

(2012) Marc Vendrell et al.   CHEMICAL REVIEWS

Pericentric and centromeric transcription: a perfect balance required

(2012) Laura E. Hall et al.   CHROMOSOME RESEARCH

Pharmacokinetics of Py-Im Polyamides Depend on Architecture: Cyclic versus Linear

(2012) Jevgenij A. Raskatov et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Development of a Robust Model System of FRET using Base Surrogates Tethering Fluorophores for Strict Control of Their Position and Orientation within DNA Duplex

(2012) Tomohiro Kato et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

New Insights in the Study of Pyrene Excimer Fluorescence to Characterize Macromolecules and their Supramolecular Assemblies in Solution

(2012) Jean Duhamel   LANGMUIR

Visualising chromosomal replication sites and replicons in mammalian cells

(2012) Apolinar Maya-Mendoza et al.   METHODS

Mediator Promotes CENP-A Incorporation at Fission Yeast Centromeres

(2012) J. O. Carlsten et al.   MOLECULAR AND CELLULAR BIOLOGY

In vivo genome editing using a high-efficiency TALEN system

(2012) Victoria M. Bedell et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Transcription in the maintenance of centromere chromatin identity

(2012) F. L. Chan et al.   NUCLEIC ACIDS RESEARCH

Active transcription and essential role of RNA polymerase II at the centromere during mitosis

(2012) F. L. Chan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Crystal Structure of TAL Effector PthXo1 Bound to Its DNA Target

(2012) A. N.-S. Mak et al.   SCIENCE

Genetic encoding of fluorescent RNA ensures a bright future for visualizing nucleic acid dynamics

(2012) Jason Dictenberg   TRENDS IN BIOTECHNOLOGY

Non-Viral Nucleic Acid Delivery: Key Challenges and Future Directions

(2012) Mahmoud Elsabahy et al.   Current Drug Delivery

Recent trends in molecular beacon design and applications

(2011) Kewei Huang et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Fluorescent hybridization probes for nucleic acid detection

(2011) Jia Guo et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Fluorescence Imaging of Influenza H1N1 mRNA in Living Infected Cells Using Single-Chromophore FIT-PNA

(2011) Susann Kummer et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Nucleic Acid and Peptide Aptamers: Fundamentals and Bioanalytical Aspects

(2011) Marco Mascini et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

An Effective Minor Groove Binder as a Red Fluorescent Marker for Live-Cell DNA Imaging and Quantification

(2011) Xiaojun Peng et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

LNA for Optimization of Fluorescent Oligonucleotide Probes: Improved Spectral Properties and Target Binding

(2011) Irina V. Astakhova et al.   BIOCONJUGATE CHEMISTRY

Fluorescent DNA Nanotags Featuring Covalently Attached Intercalating Dyes: Synthesis, Antibody Conjugation, and Intracellular Imaging

(2011) Andrea L. Stadler et al.   BIOCONJUGATE CHEMISTRY

Improved Templated Fluorogenic Probes Enhance the Analysis of Closely Related Pathogenic Bacteria by Microscopy and Flow Cytometry

(2011) Raphael M. Franzini et al.   BIOCONJUGATE CHEMISTRY

Cellular Uptake and Intracellular Trafficking of Antisense and siRNA Oligonucleotides

(2011) Rudolph L. Juliano et al.   BIOCONJUGATE CHEMISTRY

A transformer of molecular beacon for sensitive and real-time detection of phosphatases with effective inhibition of the false positive signals

(2011) Chen Zhang et al.   BIOSENSORS & BIOELECTRONICS

Discrimination of the false-positive signals of molecular beacons by combination of heat inactivation and using single walled carbon nanotubes

(2011) Xin Su et al.   BIOSENSORS & BIOELECTRONICS

A Two-Color, Self-Controlled Molecular Beacon

(2011) Sarah M. Biner et al.   CHEMBIOCHEM

Triplex-Forming Twisted Intercalating Nucleic Acids (TINAs): Design Rules, Stabilization of Antiparallel DNA Triplexes and Inhibition of G-Quartet-Dependent Self-Association

(2011) Osman Doluca et al.   CHEMBIOCHEM

Development of a system to sensitively and specifically visualize c-fos mRNA in living cells using bispyrene-modified RNA probes

(2011) Reiko Waki et al.   CHEMICAL COMMUNICATIONS

Two Successive Reactions on a DNA Template: A Strategy for Improving Background Fluorescence and Specificity in Nucleic Acid Detection

(2011) Raphael M. Franzini et al.   CHEMISTRY-A EUROPEAN JOURNAL

Nucleic Acid Aptamers: Clinical Applications and Promising New Horizons

(2011) X. Ni et al.   CURRENT MEDICINAL CHEMISTRY

Making sense of therapeutics using antisense technology

(2011) Ravinder Malik et al.   Expert Opinion on Drug Discovery

Nucleic Acid-Templated Energy Transfer Leading to a Photorelease Reaction and its Application to a System Displaying a Nonlinear Response

(2011) Manuel Röthlingshöfer et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Enhancing the cellular uptake of Py–Im polyamides through next-generation aryl turns

(2011) Jordan L. Meier et al.   NUCLEIC ACIDS RESEARCH

Nucleic Acid Templated Uncaging of Fluorophores Using Ru-Catalyzed Photoreduction with Visible Light

(2011) Manuel Röthlingshöfer et al.   ORGANIC LETTERS

Multispectral labeling of antibodies with polyfluorophores on a DNA backbone and application in cellular imaging

(2011) Jia Guo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Oligo(2′-O-methylribonucleotides) containing insertions of 2′-bispyrenylmethylphosphorodiamidate nucleoside derivatives as prospective fluorescent probes for RNA detection

(2011) O. A. Krasheninina et al.   RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY

RNA Mimics of Green Fluorescent Protein

(2011) J. S. Paige et al.   SCIENCE

Homogeneous assays using aptamers

(2010) Audrey Sassolas et al.   ANALYST

Pyrene-Excimer Probes Based on the Hybridization Chain Reaction for the Detection of Nucleic Acids in Complex Biological Fluids

(2010) Jin Huang et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

The Discovery of Zinc Fingers and Their Applications in Gene Regulation and Genome Manipulation

(2010) Aaron Klug   Annual Review of Biochemistry

Small-molecule regulators that mimic transcription factors

(2010) José A. Rodríguez-Martínez et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Sandwich probes: two simultaneous reactions for templated nucleic acid detection

(2010) Daniel J. Kleinbaum et al.   CHEMICAL COMMUNICATIONS

Binary Probes for Nucleic Acid Analysis

(2010) Dmitry M. Kolpashchikov   CHEMICAL REVIEWS

An Efficient Fluorescence Resonance Energy Transfer (FRET) between Pyrene and Perylene Assembled in a DNA Duplex and Its Potential for Discriminating Single-Base Changes

(2010) Hiromu Kashida et al.   CHEMISTRY-A EUROPEAN JOURNAL

Synthesis and Optical Properties of Cyanine Dyes as Fluorescent DNA Base Substitutions for Live Cell Imaging

(2010) Carolin Holzhauser et al.   EUROPEAN JOURNAL OF ORGANIC CHEMISTRY

Targeting DNA Double-Strand Breaks with TAL Effector Nucleases

(2010) M. Christian et al.   GENETICS

A TALE nuclease architecture for efficient genome editing

(2010) Jeffrey C Miller et al.   NATURE BIOTECHNOLOGY

Genome editing with engineered zinc finger nucleases

(2010) Fyodor D. Urnov et al.   NATURE REVIEWS GENETICS

Telomeres: protecting chromosomes against genome instability

(2010) Roderick J. O'Sullivan et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Slow non-specific accumulation of 2′-deoxy and 2′-O-methyl oligonucleotide probes at mitochondria in live cells

(2010) Won Jong Rhee et al.   NUCLEIC ACIDS RESEARCH

Real time monitoring of endogenous cytoplasmic mRNA using linear antisense 2′-O-methyl RNA probes in living cells

(2010) Kohki Okabe et al.   NUCLEIC ACIDS RESEARCH

Ratiometric bimolecular beacons for the sensitive detection of RNA in single living cells

(2010) Antony K. Chen et al.   NUCLEIC ACIDS RESEARCH

Advances in Aptamers

(2010) Muhammad Ali Syed et al.   OLIGONUCLEOTIDES

Designed thiazole orange nucleotides for the synthesis of single labelled oligonucleotides that fluoresce upon matched hybridization

(2010) Lucas Bethge et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Locked Nucleic Acid Based Beacons for Surface Interaction Studies and Biosensor Development

(2009) Karen Martinez et al.   ANALYTICAL CHEMISTRY

Fluorescent Probes for Live-Cell RNA Detection

(2009) Gang Bao et al.   Annual Review of Biomedical Engineering

Hybridization-Sensitive Fluorescent Probe for Long-Term Monitoring of Intracellular RNA

(2009) Takeshi Kubota et al.   BIOCONJUGATE CHEMISTRY

Cell permeability of Py–Im-polyamide-fluorescein conjugates: Influence of molecular size and Py/Im content

(2009) Shigeki Nishijima et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Potent activity against K562 cells by polyamide–seco-CBI conjugates targeting histone H4 genes

(2009) Masafumi Minoshima et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Fluorophore Binding Aptamers as a Tool for RNA Visualization

(2009) Katja Eydeler et al.   BIOPHYSICAL JOURNAL

Simultaneous detection of mRNA and protein stem cell markers in live cells

(2009) Won Jong Rhee et al.   BMC BIOTECHNOLOGY

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

Radiolabelled Oligonucleotides for Imaging of Gene Expression with PET

(2009) G. Lendvai et al.   CURRENT MEDICINAL CHEMISTRY

Satellite DNA Spatial Localization and Transcriptional Activity in Mouse Embryonic E-14 and IOUD2 Stem Cells

(2009) N.I. Enukashvily et al.   CYTOGENETIC AND GENOME RESEARCH

Modifications at the C-Terminus To Improve Pyrrole−Imidazole Polyamide Activity in Cell Culture

(2009) Claire S. Jacobs et al.   JOURNAL OF MEDICINAL CHEMISTRY

Four-dimensional telomere analysis in recordings of living human cells acquired with Controlled Light Exposure Microscopy

(2009) W.H. DE VOS et al.   JOURNAL OF MICROSCOPY

Solution-Phase Synthesis of Pyrrole−Imidazole Polyamides

(2009) David M. Chenoweth et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Efficient Nucleic Acid Detection by Templated Reductive Quencher Release

(2009) Raphael M. Franzini et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Polyfluorophores on a DNA Backbone: A Multicolor Set of Labels Excited at One Wavelength

(2009) Yin Nah Teo et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Imaging intracellular RNA distribution and dynamics in living cells

(2009) Sanjay Tyagi   NATURE METHODS

Sub-cellular trafficking and functionality of 2′- O -methyl and 2′- O -methyl-phosphorothioate molecular beacons

(2009) Antony K. Chen et al.   NUCLEIC ACIDS RESEARCH

Red–white–blue emission switching molecular beacons: ratiometric multicolour DNA hybridization probes

(2009) Reji Varghese et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors

(2009) J. Boch et al.   SCIENCE

Target-Catalyzed Transfer Reactions for the Amplified Detection of RNA

(2008) Tom N. Grossmann et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Visualizing genetic loci and molecular machines in living bacteria

(2008) Xindan Wang et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Perylene Attached to 2′-Amino-LNA: Synthesis, Incorporation into Oligonucleotides, and Remarkable Fluorescence Propertiesin Vitroand in Cell Culture

(2008) Irina V. Astakhova et al.   BIOCONJUGATE CHEMISTRY

Perylene-conjugated pyrrole polyamide as a sequence-specific fluorescent probe

(2008) Jun Fujimoto et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Quantitating the concentration of Py-Im polyamide–fluorescein conjugates in live cells

(2008) Carey F. Hsu et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Symmetric cyanine dyes for detecting nucleic acids

(2008) SM Yarmoluk et al.   BIOTECHNIC & HISTOCHEMISTRY

Triplex Formation by Pyrene-Labelled Probes for Nucleic Acid Detection in Fluorescence Assays

(2008) Ineke Van Daele et al.   CHEMBIOCHEM

Hybridization-Sensitive On–Off DNA Probe: Application of the Exciton Coupling Effect to Effective Fluorescence Quenching

(2008) Shuji Ikeda et al.   Chemistry-An Asian Journal

Controlled light exposure microscopy reveals dynamic telomere microterritories throughout the cell cycle

(2008) Winnok H. De Vos et al.   CYTOMETRY PART A

Cyanine dyes for the detection of double stranded DNA

(2008) H. Hilal et al.  

Centromere mitotic recombination in mammalian cells

(2008) Isabel Jaco et al.   JOURNAL OF CELL BIOLOGY

Thiazole Orange and Cy3: Improvement of Fluorescent DNA Probes with Use of Short Range Electron Transfer

(2008) Florian Menacher et al.   JOURNAL OF ORGANIC CHEMISTRY

Microwave-Induced Multiple Functionalization of Carbon Nanotubes

(2008) Fulvio G. Brunetti et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Facile Decoration of Functionalized Single-Wall Carbon Nanotubes with Phthalocyanines via “Click Chemistry”

(2008) Stéphane Campidelli et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Two Color RNA Intercalating Probe for Cell Imaging Applications

(2008) Nathan Stevens et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Construction of three quadruple-fluorescent MDA435 cell lines that enable monitoring of the whole chromosome segregation process in the living state

(2008) Kenji Sugimoto et al.   MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS

Selective molecular imaging of viable cancer cells with pH-activatable fluorescence probes

(2008) Yasuteru Urano et al.   NATURE MEDICINE

Fluorescent probes for super-resolution imaging in living cells

(2008) Marta Fernández-Suárez et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The triple helix: 50 years later, the outcome

(2008) M. Duca et al.   NUCLEIC ACIDS RESEARCH

Targeting DNA with “light-up” pyrimidine triple-helical forming oligonucleotides conjugated to stabilizing fluorophores (LU-TFOs)

(2008) Brice-Loïc Renard et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

In vivo imaging of pyrrole-imidazole polyamides with positron emission tomography

(2008) D. A. Harki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functionalized Carbon Nanotubes in Drug Design and Discovery

(2007) Maurizio Prato et al.   ACCOUNTS OF CHEMICAL RESEARCH

A novel kinase-based ATP assay using molecular beacon

(2007) Changbei Ma et al.   ANALYTICAL BIOCHEMISTRY

New, stronger nucleophiles for nucleic acid-templated chemistry: Synthesis and application in fluorescence detection of cellular RNA

(2007) Gregory P. Miller et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Bis-pyrene-labeled molecular beacon: A monomer–excimer switching probe for the detection of DNA base alteration

(2007) Kazushige Yamana et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Carbon nanotube cell translocation and delivery of nucleic acidsin vitro and in vivo

(2007) Lara Lacerda et al.   JOURNAL OF MATERIALS CHEMISTRY