Molecular Biology

Categories

    Protocols in Current Issue
    Antisense Oligo Pulldown of Circular RNA for Downstream Analysis
    Authors:  Debojyoti Das, Aniruddha Das and Amaresh C. Panda, date: 07/20/2021, view: 76, Q&A: 0
    [Abstract]

    Circular RNAs (circRNAs) are a large family of noncoding RNA molecules that have emerged as novel regulators of gene expression by sequestering microRNAs (miRNAs) and RNA-binding proteins (RBPs). Several computational tools have been developed to predict circRNA interaction with target miRNAs and RBPs with a view to studying their potential effect

    ...
    A Multi-color Bicistronic Biosensor to Compare the Translation Dynamics of Different Open Reading Frames at Single-molecule Resolution in Live Cells
    Authors:  Amanda L. Koch, Tatsuya Morisaki and Timothy J. Stasevich, date: 07/20/2021, view: 49, Q&A: 0
    [Abstract]

    Here, we describe how to image and quantitate the translation dynamics of a bicistronic biosensor that we recently created to fairly compare cap-dependent and IRES-mediated translation at single-molecule resolution in live human cells. This technique employs a pair of complementary intrabodies loaded into living cells that co-translationally bind

    ...
    Transcriptional Run-on: Measuring Nascent Transcription at Specific Genomic Sites in Yeast
    Authors:  Victoria Begley, Lola de Miguel-Jiménez and Sebastián Chávez, date: 06/20/2021, view: 724, Q&A: 0
    [Abstract]

    DNA transcription by RNA polymerases has always interested the scientific community as it is one of the most important processes involved in genome expression. This has led scientists to come up with different protocols allowing analysis of this process in specific locations across the genome by quantitating the amount of RNA polymerases

    ...
    Mechanical Fractionation of Cultured Neuronal Cells into Cell Body and Neurite Fractions
    Authors:  Ankita Arora, Raeann Goering, Hei-Yong G. Lo and J. Matthew Taliaferro, date: 06/05/2021, view: 1396, Q&A: 0
    [Abstract]

    Many cells contain spatially defined subcellular regions that perform specialized tasks enabled by localized proteins. The subcellular distribution of these localized proteins is often facilitated by the subcellular localization of the RNA molecules that encode them. A key question in the study of this process of RNA localization is the

    ...
    A New Method for Studying RNA-binding Proteins on Specific RNAs
    Authors:  Weiping Sun, Ziheng Zhang, Ji-Long Liu and Min Zhuang, date: 05/20/2021, view: 4076, Q&A: 0
    [Abstract]

    Proximity-based protein labeling has been developed to identify protein-nucleic acid interactions. We have reported a novel method termed CRUIS (CRISPR-based RNA-United Interacting System), which captures RNA-protein interactions in living cells by combining the RNA-binding capacity of CRISPR/Cas13 and the proximity-tagging activity of PUP-IT.

    ...
    In vivo CD40 Silencing by siRNA Infusion in Rodents and Evaluation by Kidney Immunostaining
    [Abstract]

    The co-stimulatory molecule CD40 and its ligand CD40L play a key role in the regulation of immunological processes and are involved in the pathophysiology of autoimmune and inflammatory diseases. Inhibition of the CD40-CD40L axis is a promising therapy, and a number of strategies and techniques have been designed to hinder its functionality. Our

    ...
    Identification of R-loop-forming Sequences in Drosophila melanogaster Embryos and Tissue Culture Cells Using DRIP-seq
    Authors:  Célia Alecki and Nicole J. Francis, date: 05/05/2021, view: 2712, Q&A: 0
    [Abstract]

    R-loops are non-canonical nucleic structures composed of an RNA–DNA hybrid and a displaced ssDNA. Originally identified as a source of genomic instability, R-loops have been shown over the last decade to be involved in the targeting of proteins and to be associated with different histone modifications, suggesting a regulatory function. In

    ...
    Colorimetric RT-LAMP and LAMP-sequencing for Detecting SARS-CoV-2 RNA in Clinical Samples
    [Abstract]

    During pandemics, such as the one caused by SARS-CoV-2 coronavirus, simple methods to rapidly test large numbers of people are needed. As a faster and less resource-demanding alternative to detect viral RNA by conventional qPCR, we used reverse transcription loop-mediated isothermal amplification (RT-LAMP). We previously established colorimetric

    ...
    Trypanosomatid, fluorescence-based in vitro U-insertion/U-deletion RNA-editing (FIDE)
    Authors:  Wolf-Matthias Leeder, Elisabeth Kruse and H. Ulrich Göringer, date: 03/05/2021, view: 1632, Q&A: 0
    [Abstract]

    Gene expression within the mitochondria of African trypanosomes and other protozoan organisms relies on a nucleotide-specific RNA-editing reaction. In the process exclusively uridine (U)-nucleotides are site-specifically inserted into and deleted from sequence-deficient primary transcripts to convert them into translatable mRNAs. The reaction is

    ...
    Primer ID Next-Generation Sequencing for the Analysis of a Broad Spectrum Antiviral Induced Transition Mutations and Errors Rates in a Coronavirus Genome
    [Abstract]

    Next generations sequencing (NGS) has become an important tool in biomedical research. The Primer ID approach combined with the MiSeq platform overcomes the limitation of PCR errors and reveals the true sampling depth of population sequencing, making it an ideal tool to study mutagenic effects of potential broad-spectrum antivirals on RNA viruses.

    ...



    We use cookies on this site to enhance your user experience. By using our website, you are agreeing to allow the storage of cookies on your computer.