Molecular Biology

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    Protocols in Current Issue
    Assay to Study the Phase-transition Behavior of Edc3, a Conserved Processing Body (P-body) Marker Protein
    Authors:  Raju Roy and Purusharth I. Rajyaguru, date: 08/20/2022, view: 1016, Q&A: 0
    [Abstract]

    RNA granules are conserved, non-membranous, biphasic structures predominantly composed of RNA and RNA-binding proteins. RNA granules often assemble as a result of cellular responses to a variety of stresses, including infection. Two types of RNA granules are best characterized: stress granules (SGs) and processing bodies (P-bodies). The mechanism

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    Purification of Mitochondrial Ribosomal Complexes from Trypanosoma cruzi and Leishmania tarentolae for Cryo-EM Analysis
    Authors:  Stéphanie Durrieu-Gaillard, Marie Sissler and Yaser Hashem, date: 05/20/2022, view: 1325, Q&A: 1
    [Abstract]

    Kinetoplastids are unicellular eukaryotic parasites responsible for human pathologies such as Chagas disease, sleeping sickness or Leishmaniasis, caused by Trypanosoma cruzi, Trypanosoma brucei, and various Leishmania spp., respectively. They harbor a single large mitochondrion that is essential for the survival of the parasite. Interestingly,

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    Normalized Ribo-Seq for Quantifying Absolute Global and Specific Changes in Translation
    Authors:  Katharina Hoerth, Sonja Reitter and Johanna Schott, date: 02/20/2022, view: 1493, Q&A: 0
    [Abstract] Ribosome profiling (Ribo-Seq) is a highly sensitive method to quantify ribosome occupancies along individual mRNAs on a genome-wide scale. Hereby, ribosome-protected fragments (= footprints) are generated by nuclease digestion, isolated, and sequenced together with the corresponding randomly fragmented input samples, to determine ribosome ...
    Pull-down of Biotinylated RNA and Associated Proteins
    Authors:  Jagadeesh K. Uppala, Chandrima Ghosh, Grzegorz Sabat and Madhusudan Dey, date: 02/20/2022, view: 1777, Q&A: 0
    [Abstract]

    Mapping networks of RNA-protein interactions in cells is essential for understanding the inner workings of many biological processes, including RNA processing, trafficking, and translation. Current in vivo methods for studying protein-RNA interactions rely mostly on purification of poly(A) transcripts, which represent only ~2–3% of total

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    An Aptamer-based mRNA Affinity Purification Procedure (RaPID) for the Identification of Associated RNAs (RaPID-seq) and Proteins (RaPID-MS) in Yeast
    Authors:  Rohini R. Nair, Gal Haimovich and Jeffrey E. Gerst, date: 01/05/2022, view: 1851, Q&A: 2
    [Abstract]

    RNA-RNA and RNA-protein interactions are involved in the regulation of gene expression. Here, we describe an updated and extended version of our RNA purification and protein identification (RaPID) protocol for the pulldown of aptamer-tagged mRNAs by affinity purification. The method takes advantage of the high affinity interaction between the MS2

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    Efficient and Rapid Analysis of Polysomes and Ribosomal Subunits in Cells and Tissues Using Ribo Mega-SEC
    [Abstract]

    Polysome profile analysis is a popular method for separating polysomes and ribosomal subunits and is typically achieved using a sucrose density gradient (SDG). This has remained the gold standard method since ribosomes were first discovered; however, this method is time-consuming and requires multiple steps from making the gradient and long

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    Antisense Oligo Pulldown of Circular RNA for Downstream Analysis
    Authors:  Debojyoti Das, Aniruddha Das and Amaresh C. Panda, date: 07/20/2021, view: 2341, 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

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    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: 8281, 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.

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    Biochemical Pulldown of mRNAs and Long Noncoding RNAs from Cellular Lysates Coupled with Mass Spectrometry to Identify Protein Binding Partners
    Authors:  Anca F. Savulescu, Stoyan Stoychev, Sipho Mamputha and Musa M. Mhlanga, date: 06/05/2020, view: 4363, Q&A: 2
    [Abstract] RNA binding proteins (RBPs) interact with cellular mRNAs, controlling various steps throughout the lifetime of these transcripts, including transcription, cellular transport, subcellular localization, translation and degradation. In addition to binding mRNA transcripts, a growing number of RBPs are shown to bind long noncoding RNAs (lncRNAs), ...
    Identification of RNase-sensitive LINE-1 Ribonucleoprotein Interactions by Differential Affinity Immobilization
    Authors:  Hua Jiang, Martin S. Taylor, Kelly R. Molloy, Ilya Altukhov and John LaCava, date: 04/05/2019, view: 5711, Q&A: 0
    [Abstract] Long Interspersed Nuclear Element-1 (LINE-1, L1) constitutes a family of autonomous, self-replicating genetic elements known as retrotransposons. Although most are inactive, copious L1 sequences populate the human genome. L1s proliferate in a ‘copy-and-paste’ fashion through an RNA intermediate; a full-length L1 transcript is ~6,000 nucleotides ...



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