Biophysics of RNA-Protein Interactions
A Mechanistic View
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Open AccessRNA-guided RNA silencing by an Asgard archaeal Argonaute
Argonaute proteins are the central effectors of RNA-guided RNA silencing pathways in eukaryotes, playing crucial roles in gene repression and defense against viruses and transposons. Eukaryotic Argonautes are ...
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Article
Full-length single-molecule protein fingerprinting
Proteins are the primary functional actors of the cell. While proteoform diversity is known to be highly biologically relevant, current protein analysis methods are of limited use for distinguishing proteoform...
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Protocol
Single-Molecule FRET X
Fluorescence resonance energy transfer (FRET) is a photophysical phenomenon that has been repurposed as a biophysical tool to measure nanometer distances. With FRET by DNA eXchange, or FRET X, many points of i...
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Article
Author Correction: mRNA structural dynamics shape Argonaute-target interactions
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The emerging landscape of single-molecule protein sequencing technologies
Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of prot...
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mRNA structural dynamics shape Argonaute-target interactions
Small interfering RNAs (siRNAs) promote RNA degradation in a variety of processes and have important clinical applications. siRNAs direct cleavage of target RNAs by guiding Argonaute2 (AGO2) to its target site...
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Article
Open AccessTetrameric architecture of an active phenol-bound form of the AAA+ transcriptional regulator DmpR
The Pseudomonas putida phenol-responsive regulator DmpR is a bacterial enhancer binding protein (bEBP) from the AAA+ ATPase family. Even though it was discovered more than two decades ago and has been widely used...
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Selective loading and processing of prespacers for precise CRISPR adaptation
CRISPR–Cas immunity protects prokaryotes against invading genetic elements1. It uses the highly conserved Cas1–Cas2 complex to establish inheritable memory (spacers)2–5. How Cas1–Cas2 acquires spacers from foreig...
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Open AccessArgonaute bypasses cellular obstacles without hindrance during target search
Argonaute (Ago) proteins are key players in both gene regulation (eukaryotes) and host defense (prokaryotes). Acting on single-stranded nucleic-acid substrates, Ago relies on base pairing between a small nucle...
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Biophysics of RNA-Guided CRISPR Immunity
Prokaryotes are constantly threatened by a large array of viruses and other mobile genetic elements. The evolutionary arms’ race between these prokaryotes and their invaders has resulted in a wide arsenal of d...
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Article
Paving the way to single-molecule protein sequencing
Proteins are major building blocks of life. The protein content of a cell and an organism provides key information for the understanding of biological processes and disease. Despite the importance of protein a...
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Protocol
Probing RNA–Protein Interactions with Single-Molecule Pull-Down Assays
Recent advances in single-molecule techniques allow for dynamic observations of the interactions between various protein assemblies and RNA molecules with high spatiotemporal resolution. However, it remains ch...
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Article
Open AccessTRBP ensures efficient Dicer processing of precursor microRNA in RNA-crowded environments
The RNA-binding protein TRBP is a central component of the Dicer complex. Despite a decade of biochemical and structural studies, the essential functionality of TRBP in microRNA (miRNA) biogenesis remains unkn...
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A single vesicle-vesicle fusion assay for in vitro studies of SNAREs and accessory proteins
SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins are a highly regulated class of membrane proteins that drive the efficient merger of two distinct lipid bilayers into one int...
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Repetitive shuttling of a motor protein on DNA
Many helicases modulate recombination, an essential process that needs to be tightly controlled. Mutations in some human disease helicases cause increased recombination, genome instability and cancer. To eluci...
