Molecular Biology

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    GeneWeld: Efficient Targeted Integration Directed by Short Homology in Zebrafish

    Efficient precision genome engineering requires high frequency and specificity of integration at the genomic target site. Multiple design strategies for zebrafish gene targeting have previously been reported with widely varying frequencies for

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    Modeling Perturbations in Protein Filaments at the Micro and Meso Scale Using NAMD and PTools/Heligeom
    Authors:  Benjamin Boyer, Benoist Laurent, Charles H. Robert and Chantal Prévost, date: 07/20/2021, view: 114, Q&A: 0

    Protein filaments are dynamic entities that respond to external stimuli by slightly or substantially modifying the internal binding geometries between successive protomers. This results in overall changes in the filament architecture, which are

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    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: 48, Q&A: 0

    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

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    Extraction of DNA and RNA from Formalin-fixed Paraffin-embedded Tissue Specimens

    One of the most common methods for isolating biomolecules from clinical samples is using TRIzol. While many tissues are freshly frozen, a large number of tissues are formalin-fixed paraffin-embedded (FFPE) blocks for pathology and diagnostics.

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    A Gel-Based Assay for Probing Protein Translocation on dsDNA
    Authors:  Christiane Brugger and Alexandra M. Deaconescu, date: 07/20/2021, view: 68, Q&A: 0

    Protein translocation on DNA represents the key biochemical activity of ssDNA translocases (aka helicases) and dsDNA translocases such as chromatin remodelers. Translocation depends on DNA binding but is a distinct process as it typically involves

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    A Simple Method to Generate Super-sensitive AID (ssAID)-based Conditional Knockouts using CRISPR-based Gene Knockout in Various Vertebrate Cell Lines
    Authors:  Kohei Nishimura and Tatsuo Fukagawa, date: 07/20/2021, view: 44, Q&A: 0

    Inducing loss of function of a target protein using methods such as gene knockout is a powerful and useful strategy for analyzing protein function in cells. In recent years, the CRISPR/Cas-9-based gene knockout technology has been widely used across

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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: 75, Q&A: 0

    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

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    PCR-mediated One-day Synthesis of Guide RNA for the CRISPR/Cas9 System
    Authors:  Naim Hassan, Farhana Easmin, Keisuke Ekino and Satoshi Harashima, date: 07/05/2021, view: 1072, Q&A: 0

    Nowadays, CRISPR (clustered regularly interspaced short palindromic repeats) and the CRISPR-associated protein (Cas9) system play a major role in genome editing. To target the desired sequence of the genome successfully, guide RNA (gRNA) is

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    Measurement of Transgene Copy Number in Plants Using Droplet Digital PCR
    Authors:  Yao-Min Cai, Quentin M. Dudley and Nicola J. Patron, date: 07/05/2021, view: 954, Q&A: 0

    Transgenic plants are produced both to investigate gene function and to confer desirable traits into crops. Transgene copy number is known to influence expression levels, and consequently, phenotypes. Similarly, knowledge of transgene zygosity is

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    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

    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

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