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    1. Physics of Living Systems

    Measuring cis-regulatory energetics in living cells using allelic manifolds

    Talitha L Forcier, Andalus Ayaz ... Justin B Kinney
    A novel strategy is presented for quantitatively measuring protein-DNA and protein-protein interactions that regulate transcription in living cells.
    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics

    Homology sensing via non-linear amplification of sequence-dependent pausing by RecQ helicase

    Yeonee Seol, Gábor M Harami ... Keir C Neuman
    The rate of DNA unwinding by RecQ helicases is dramatically modulated by the DNA duplex stability in a geometry-dependent manner, providing an intrinsic mechanism for suppressing illegitimate recombination.
    1. Microbiology and Infectious Disease
    2. Structural Biology and Molecular Biophysics

    HIV-1 Env trimer opens through an asymmetric intermediate in which individual protomers adopt distinct conformations

    Xiaochu Ma, Maolin Lu ... Walther Mothes
    The identification of a single-CD4 bound asymmetric HIV-1 Envelope trimer intermediate provides new mechanistic insights into the activation of Envelope for fusion, and highlights the importance of asymmetry in biology.
    1. Structural Biology and Molecular Biophysics

    Dependence of nucleosome mechanical stability on DNA mismatches

    Thuy TM Ngo, Bailey Liu ... Taekjip Ha
    The mechanical stability of a nucleosome is enhanced upon the introduction of a single base pair mismatch that makes DNA more bendable, with implications on mismatch repair in vivo.
    1. Structural Biology and Molecular Biophysics

    Observation of long-range tertiary interactions during ligand binding by the TPP riboswitch aptamer

    Van K Duesterberg, Irena T Fischer-Hwang ... Steven M Block
    The combined use of optical trapping and single-molecule FRET permits the study of riboswitch structure formation and conformational dynamics at the same time.
    1. Physics of Living Systems

    Single molecule microscopy reveals key physical features of repair foci in living cells

    Judith Miné-Hattab, Mathias Heltberg ... Angela Taddei
    Upon DNA damage, Rad52 forms a membraneless sub-compartment where Rad52 molecules are highly dynamic and share properties with liquid-liquid phase-separated molecules, reflecting the existence of a liquid droplet around damaged DNA.
    1. Chromosomes and Gene Expression
    2. Genetics and Genomics

    Live-cell single-molecule tracking highlights requirements for stable Smc5/6 chromatin association in vivo

    Thomas J Etheridge, Desiree Villahermosa ... Johanne M Murray
    In vivo single-molecule imaging demonstrates that Smc5/6 chromatin association depends on ATP hydrolysis and dsDNA binding, requires Nse6 and is modulated by Brc1 after DNA damage.
    1. Structural Biology and Molecular Biophysics

    Top-down machine learning approach for high-throughput single-molecule analysis

    David S White, Marcel P Goldschen-Ohm ... Baron Chanda
    A new analysis algorithm (DISC) enables accurate analysis of data from high-throughput single-molecule paradigms and reveals a non-cooperative binding mechanism of cyclic nucleotide-binding domains from HCN ion channels.
    1. Biochemistry and Chemical Biology
    2. Microbiology and Infectious Disease

    The nanoscale organization of the Nipah virus fusion protein informs new membrane fusion mechanisms

    Qian Wang, Jinxin Liu ... Qian Liu
    Single-molecule localization imaging shows that the Nipah virus fusion protein forms nanoscale clusters on cell and viral membranes that favor membrane fusion activation.
    1. Chromosomes and Gene Expression
    2. Structural Biology and Molecular Biophysics

    ATP binding facilitates target search of SWR1 chromatin remodeler by promoting one-dimensional diffusion on DNA

    Claudia C Carcamo, Matthew F Poyton ... Taekjip Ha
    In vitro single-particle tracking reveals that ATP binding increases the one-dimensional diffusion of yeast chromatin remodeler SWR1 on DNA stretched between optical tweezers and diffusion is confined by protein roadblocks and nucleosomes.