Fluorescent probes for live-cell RNA detection.

No abstract is available for this paper.

• Publication year

  2009

• Venue

  Annual Review of Biomedical Engineering

• Publication date

  2009-07-10

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1146/annurev-bioeng-061008-124920PMID 19400712PMCID PMC2734976
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Molecular beacons in biomedical detection and clinical diagnosis.

  2008cited by this paper
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  2008cited by this paper
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  2008cited by this paper
• RNA visualization in live bacterial cells using fluorescent protein complementation

  2007influential reference
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  2007cited by this paper
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  2007cited by this paper
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  2006cited by this paper
• Quantification of mRNA in whole blood by assessing recovery of RNA and efficiency of cDNA synthesis.

  2006influential reference
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  2006cited by this paper
• Mechanistic model of bursts in mRNA synthesis

  2006cited by this paper
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  2006cited by this paper
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  2005influential reference
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  2005cited by this paper
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  2005cited by this paper
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  2005cited by this paper
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  2005cited by this paper
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  2005cited by this paper
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  2005cited by this paper
• Protein transduction technology

  2005cited by this paper
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  2004cited by this paper
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  2004cited by this paper
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  2004cited by this paper
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  2004cited by this paper
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  2004cited by this paper
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  2004cited by this paper
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  2003cited by this paper
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  2003cited by this paper
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  2003cited by this paper
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  2002cited by this paper
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  2002cited by this paper
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  2002cited by this paper
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  2002cited by this paper
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  2002cited by this paper
• Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes.

  2002cited by this paper
• [Serial analysis of gene expression].

  2002cited by this paper
• Detection of DNA Hybridization via Fluorescent Polymer Superquenching

  2002cited by this paper
• Protein/peptide transduction domains: potential to deliver large DNA molecules into cells.

  2001cited by this paper
• Methods for visualizing RNA processing and transport pathways in living cells

  2001cited by this paper
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  2001cited by this paper
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  2001cited by this paper
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  2001cited by this paper
• Modulation of RNA function by oligonucleotides recognizing RNA structure.

  2001cited by this paper
• Single-mismatch detection using gold-quenched fluorescent oligonucleotides

  2001cited by this paper
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  2001cited by this paper
• TAT-mediated protein transduction into mammalian cells.

  2001cited by this paper
• Linear 2' O-Methyl RNA probes for the visualization of RNA in living cells.

  2001influential reference
• Direct observation of specific messenger RNA in a single living cell under a fluorescence microscope.

  2000cited by this paper
• Wavelength-shifting molecular beacons

  2000cited by this paper
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  2000cited by this paper
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  2000cited by this paper
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  2000cited by this paper
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  2000cited by this paper
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  1999cited by this paper
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  1999cited by this paper
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  1999cited by this paper
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  1999cited by this paper
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  1998cited by this paper
• Real time detection of DNA.RNA hybridization in living cells.

  1998cited by this paper
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  1998cited by this paper
• Localization of signal recognition particle RNA in the nucleolus of mammalian cells.

  1998cited by this paper
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  1998cited by this paper
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  1998cited by this paper
• Multicolor molecular beacons for allele discrimination

  1998cited by this paper
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  1998cited by this paper
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  1998cited by this paper
• Cytoplasmic flows localize injected oskar RNA in Drosophila oocytes.

  1997cited by this paper
• Stochastic mechanisms in gene expression.

  1997cited by this paper
• In situ hybridization in living cells: detection of RNA molecules.

  1997cited by this paper
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  1996cited by this paper
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  1996cited by this paper
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  1996cited by this paper
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  1995cited by this paper
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  1995cited by this paper
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  1995cited by this paper
• Serial Analysis of Gene Expression

  1995cited by this paper
• Downregulation of amyloid precursor protein inhibits neurite outgrowth in vitro

  1995cited by this paper
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  1994cited by this paper
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  1993cited by this paper
• Identification of deoxyribonuclease II as an endonuclease involved in apoptosis.

  1993cited by this paper
• Sequence identification of 2,375 human brain genes

  1992cited by this paper
• Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction.

  1992cited by this paper
• Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia.

  1985influential reference
• Detection of specific RNAs or specific fragments of DNA by fractionation in gels and transfer to diazobenzyloxymethyl paper.

  1979cited by this paper
• Autoradiographic Detection of Molecular Hybrids between rRNA and DNA in Tissue Sections

  1970cited by this paper

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  2023cites this paper
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  2023cites this paper
• Exosomal MicroRNA Profiling.

  2023cites this paper
• Are We There Yet? Intracellular Sensing with Luminescent Nanoparticles and FRET.

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• Live-Cell Imaging of Endogenous RNA with a Genetically Encoded Fluorogenic Allosteric Aptamer.

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  2022cites this paper
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• Mismatched fluorescent probes with an enhanced strand displacement reaction rate for intracellular long noncoding RNA imaging.

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  2020cites this paper
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  2020cites this paper
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  2019cites this paper
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  2017cites this paper
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  2017cites this paper
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  2017cites this paper
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  2017cites this paper
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  2017cites this paper
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  2017cites this paper
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  2017cites this paper
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  2016cites this paper
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  2016cites this paper
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  2016cites this paper
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