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Article
Open AccessMyoD is a 3D genome structure organizer for muscle cell identity
The genome exists as an organized, three-dimensional (3D) dynamic architecture, and each cell type has a unique 3D genome organization that determines its cell identity. An unresolved question is how cell type...
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Article
Open Access1/f-noise-free optical sensing with an integrated heterodyne interferometer
Optical evanescent sensors can non-invasively detect unlabeled nanoscale objects in real time with unprecedented sensitivity, enabling a variety of advances in fundamental physics and biological applications. ...
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Article
A new metagenome binning method based on gene uniqueness
The human gut microbiome contains millions of genes and many undetected bacteria species. Recovering bacterial genomes from large complex metagenomes remains highly challenging, and current binning methods sho...
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Protocol
Delivering Molecular Beacons via an Electroporation-Based Approach Enables Live-Cell Imaging of Single RNA Transcripts and Genomic Loci
Molecular beacons (MBs) are synthetic oligonucleotide probes that are designed to fluoresce upon hybridization to complementary nucleic acid targets. In contrast to genetically encoded probes that can be readi...
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Protocol
Live-Cell Imaging of Genomic Loci Using CRISPR/Molecular Beacon Hybrid Systems
The ability to monitor the behavior of specific genomic loci in living cells can offer tremendous opportunities for deciphering the molecular basis driving cellular physiology and disease evolution. Toward thi...
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Protocol
Live-Cell Imaging of Long Noncoding RNAs Using Molecular Beacons
Long noncoding RNAs (lncRNAs) are a family of non-protein-coding RNA transcripts greater than 200 nucleotides in length that have been regarded as crucial modulators of gene expression in various biological an...
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Protocol
Single-Molecule Analysis of RNA Dynamics in Living Cells Using Molecular Beacons
Over the past decade, emerging evidence has indicated that long intergenic noncoding RNAs (lincRNAs), a class of RNA transcripts greater than 200 nt in length, function as key regulators of gene expression in ...
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Article
Open AccessInhibition of retroviral Gag assembly by non-silencing miRNAs promotes autophagic viral degradation
We recently reported an unconventional mechanism by which miRNAs inhibit HIV-1 viral production. This occurs when miRNAs bind nonspecifically to the viral structural protein Gag, interfering with viral RNA-med...
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Protocol
Quantifying Gene Expression in Living Cells with Ratiometric Bimolecular Beacons
Molecular beacons (MBs), a class of oligonucleotide-based probes, have enabled researchers to study various RNA molecules in their native live-cell contexts. However, it is also increasingly recognized that, w...
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Protocol
Optimizing Molecular Beacons for Intracellular Analysis of RNA
Conventional molecular beacons (MBs) have been used extensively for imaging specific endogenous RNAs in living cells, but their tendency to generate false-positive signals as a result of nuclease degradation a...
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Article
Open AccessA molecular beacon-based approach for live-cell imaging of RNA transcripts with minimal target engineering at the single-molecule level
Analysis of RNA dynamics and localization at the single-molecule level in living cells has been predominantly achieved by engineering target RNAs with large insertions of tandem repeat sequences that are bound...
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Article
Open AccessLong non-coding RNA Linc-RAM enhances myogenic differentiation by interacting with MyoD
Long non-coding RNAs (lncRNAs) are important regulators of diverse biological processes. Here we report on functional identification and characterization of a novel long intergenic non-coding RNA with MyoD-reg...
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Protocol
Delivery of Molecular Beacons for Live-Cell Imaging and Analysis of RNA
Over the past decade, a variety of oligonucleotide-based probes have been developed that allow for direct visualization of RNA molecules in living cells. Of these, molecular beacons have garnered a particularl...
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Article
Superparamagnetic Iron Oxide Nanoparticle Probes for Molecular Imaging
The field of molecular imaging has recently seen rapid advances in the development of novel contrast agents and the implementation of insightful approaches to monitor biological processes non-invasively. In pa...
