Single-molecule biophysics articles within Nature Communications

Featured

  • Article
    | Open Access

    DNA hybridization of two single-strands to form a double-stranded helix is widely used for genomic identification applications. Here, Vernicket al. record duplex formation of 20-mer oligonucleotide using a single-molecule field-effect transistor, where DNA kinetics is affected by electrostatic bias.

    • Sefi Vernick
    • , Scott M. Trocchia
    •  & Kenneth L. Shepard

  • Article
    | Open Access

    Neutrophil adhesion is tightly regulated to enforce protective immunity, but it is unclear how mechanochemical processes such as catch bonds and slip bonds modulate neutrophilsin vivo. Here the authors show that a point mutation in the adhesion molecule L-selectin alters mechanochemical regulation to affect neutrophil functions in mice.

    • Zhenghui Liu
    • , Tadayuki Yago
    •  & Rodger P. McEver

  • Article
    | Open Access

    Super-resolution localization microscopy produces biophysical information in the form of estimated positions of single molecules. Here, Lindénet al. estimate the uncertainty of single localizations, and show that this additional information can improve data analysis and localization precision.

    • Martin Lindén
    • , Vladimir Ćurić
    •  & Johan Elf

  • Article
    | Open Access

    Bacterial outer membrane TonB-dependent transporters (TBDTs) mediate the influx of several nutrients. Here the authors use single-molecule force spectroscopy to show that the interaction between TonB andEscherichia coliTBDT BtuB is mechanically resistant to the pulling that gates the BtuB channel.

    • Samuel J. Hickman
    • , Rachael E. M. Cooper
    •  & David J. Brockwell

  • Article
    | Open Access

    Cytoplasmic dynein 2 drives retrograde intraflagellar transport but little is known about its dynamics. Here the authors use fluorescence microscopy to track labelled dynein 2 inC. elegansat the single-molecule level and report diffusion at the ciliary base, and pausing and directional switches along the cilium.

    • Jona Mijalkovic
    • , Bram Prevo
    •  & Erwin J. G. Peterman

  • Article
    | Open Access

    Thanks to its base stacking structure, DNA can behave as an electric wire, but external control of its electronic properties has not been achieved yet. Here, the authors show that DNA conductance can be switched electrochemically when a DNA base is replaced by the redox molecule anthraquinone.

    • Limin Xiang
    • , Julio L. Palma
    •  & Nongjian Tao

  • Article
    | Open Access

    Interaction of fibronectin with αv-class and α5β1 integrins results in formation of cell adhesion complexes, but the initial events (<120 s) remain unclear. Here, the authors show that αv-class integrins bind fibronectin faster than α5β1 integrins and subsequently signal to α5ß1 integrins to strengthen the adhesion.

    • Mitasha Bharadwaj
    • , Nico Strohmeyer
    •  & Daniel J. Müller

  • Article
    | Open Access

    The human serotonin transporter (SERT) mediates the uptake of neurotransmitters to terminate neuronal signalling. Here the authors use single-molecule imaging to get insight into the molecular origin of SERT oligomerization and their pre-set stoichiometry at the plasma membrane.

    • Andreas Anderluh
    • , Tina Hofmaier
    •  & Gerhard J. Schütz

  • Article
    | Open Access

    Tracking single molecules in living cells is difficult or impractical owing to their high density. Here the authors introduce a technique of repeatedly photobleaching fluorophores at the boundary of a region of interest, thereby controlling the number of fluorescent particles for observation.

    • Vladislav Belyy
    • , Sheng-Min Shih
    •  & Ahmet Yildiz

  • Article
    | Open Access

    Kinesin-14s are commonly considered to be minus end-directed microtubule motor proteins. Here the authors show that KlpA, a fungal kinesin-14 orthologue, relies on its N-terminal nonmotor microtubule-binding tail to achieve context-dependent bidirectional motility.

    • Andrew R. Popchock
    • , Kuo-Fu Tseng
    •  & Weihong Qiu

  • Article
    | Open Access

    The RNA binding protein TRBP is a component of the Dicer complex but its role in microRNA biogenesis remains poorly understood. Here the authors use a crowded RNA environment and single-molecule imaging to show that TRBP acts as a gatekeeper to prevent Dicer engagement with pre miRNA-like substrates.

    • Mohamed Fareh
    • , Kyu-Hyeon Yeom
    •  & Chirlmin Joo

  • Article
    | Open Access

    Many super-resolution imaging techniques use fluorescence emission intensity to obtain precise positional information, but other spectral information is ignored. Here, the authors develop a method that records the spectrum and position of single dye molecules to map the hydrophobicity of a surface.

    • Marie N. Bongiovanni
    • , Julien Godet
    •  & Steven F. Lee

  • Article
    | Open Access

    Transcriptional bursting is a potential source of cell-to-cell variability but the molecular mechanisms are unclear. Here the authors use single molecule imaging to analyse the kinetics of bursting on DNA and observe that bursting is an intrinsic property of RNA polymerases on DNA.

    • Keisuke Fujita
    • , Mitsuhiro Iwaki
    •  & Toshio Yanagida

  • Article
    | Open Access

    Replicating the genome presents a major challenge to the maintenance of the epigenetic landscape. Here the authors use a minimal experimental system to show how nucleosomes are transferred to double-stranded DNA, with the transfer mediated by a quantitative loop formation model.

    • Lucy D. Brennan
    • , Robert A. Forties
    •  & Michelle D. Wang

  • Article
    | Open Access

    The bacterial cell wall is important for cell shape and stability, but how the activities of the biosynthetic machinery are coordinated are not clear. Here the authors use single-molecule imaging and chemical perturbations to determine factors that affect the localization dynamics of penicillin-binding proteins (PBP)1A and PBP1B.

    • Timothy K. Lee
    • , Kevin Meng
    •  & Kerwyn Casey Huang

  • Article
    | Open Access

    How molecular crowding affects membrane protein diffusion and function is not known. Here the authors measure diffusion of variant surface glycoprotein on trypanosomes and discover a molecular crowding threshold that limits diffusion, and find that N-linked glycans help to prevent retarding intermolecular interactions.

    • Andreas J. W. Hartel
    • , Marius Glogger
    •  & Markus Engstler

  • Article
    | Open Access

    CRISPR-Cas9 has enabled an unprecedented ability to manipulate the genome yet it is still poorly understood how target recognition functions at a molecular level. Here the authors use single-molecule FRET to probe Cas9-target interaction and identify distinct search and proofreading states.

    • Digvijay Singh
    • , Samuel H. Sternberg
    •  & Taekjip Ha

  • Article
    | Open Access

    HER2 is frequently overexpressed in breast cancer in association with increased metastatic potential. Here, the authors show that HER2 overexpression causes deformation of cell membranes in a signalling-independent manner that contributes to the disease phenotype by disrupting epithelial features.

    • Inhee Chung
    • , Mike Reichelt
    •  & Mark X. Sliwkowski

  • Article
    | Open Access

    Myosin X is a molecular motor unique in its ability to generate filopodia, but the mechanism explaining this behaviour is not known. Here, through a combination of structure, single-molecule assays and modelling the authors show that myosin X is optimized for transport along actin bundles.

    • Virginie Ropars
    • , Zhaohui Yang
    •  & Anne Houdusse

  • Article
    | Open Access

    Previous investigations have indicated that the model protein CspB folds in a simple two-state fashion. Here, the authors provide direct experimental evidence for that the energy landscape of two-state folding proteins is highly heterogeneous and that unfolding can occur via multiple pathways.

    • Jörg Schönfelder
    • , Raul Perez-Jimenez
    •  & Victor Muñoz

  • Article
    | Open Access

    Genomic instability can result from stalled or collapsed replication fork at sites of unrepaired DNA lesions. Here the authors uncover a new lesion bypass pathway for the T7 replisome, where leading strand template lesions can be overcome through interaction between the replisome's helicase and polymerase components.

    • Bo Sun
    • , Manjula Pandey
    •  & Michelle D. Wang

  • Article
    | Open Access

    Single molecule kinetics investigations and molecular simulations are useful tools in elucidating protein assembly mechanisms. Here, the authors use these to show that even naturally occurring tandem repeats undergo transient misfolding and that assembly is much more complex than we previously understood.

    • Alessandro Borgia
    • , Katherine R. Kemplen
    •  & Benjamin Schuler

  • Article
    | Open Access

    Single molecule methods for measuring load dependence are fundamental for molecular motor research. Here, Sung et al. introduce harmonic force spectroscopy, a method that randomly applies varying loads at high frequency, allowing the determination of load dependent parameters of human β-cardiac myosin at physiological ATP concentration.

    • Jongmin Sung
    • , Suman Nag
    •  & James A. Spudich

  • Article
    | Open Access

    During transcription, replication and repair, DNA-binding proteins must find specific interaction sites hidden within a vast excess of genomic DNA. Here the authors use single-molecule tracking to quantitatively determine the contributions of the different processes that underlie target search in human cells.

    • Davide Normanno
    • , Lydia Boudarène
    •  & Maxime Dahan

  • Article
    | Open Access

    Upf1 is a multifunctional helicase involved in various DNA- and RNA-related processes, including nonsense-mediated mRNA decay (NMD). Here the authors demonstrate that Upf1 is a highly processive ribonucleoprotein complex remodeler—a capability likely important for Upf1’s NMD function.

    • Francesca Fiorini
    • , Debjani Bagchi
    •  & Vincent Croquette

  • Article
    | Open Access

    The synthesis of ribosomes requires the orderly assembly of many proteins and large RNA molecules, a process that involves several assembly factors. Here the authors show that dedicated chaperones capture the N termini of specific nascent ribosomal proteins to promote folding and assembly into maturing ribosomes.

    • Patrick Pausch
    • , Ujjwala Singh
    •  & Dieter Kressler

  • Article
    | Open Access

    Chromatin effector proteins often employ multivalent interactions with histone post-translational modifications. Here by using chemically defined nucleosome array and single-molecule microscopy, the authors show that effector multivalency prolongs chromatin retention and accelerates the association rate.

    • Sinan Kilic
    • , Andreas L. Bachmann
    •  & Beat Fierz

  • Article |

    The existence of membrane rafts of higher lipid order in living cells is subject to ongoing debate. Here, Sevcsik et al. use a micropatterning approach to show that glycosylphosphatidylinositol-anchored proteins, typical raft constituents, do not influence their membrane nanoenvironment to promote raft phase formation.

    • Eva Sevcsik
    • , Mario Brameshuber
    •  & Gerhard J. Schütz

  • Article |

    Departure of ligands from cell surfaces can be slowed by rapid rebinding to nearby receptors. Here, the authors use single-molecule experiments and theory to show that rapid rebinding also can slow dissociation of an isolated molecular complex, allowing binding competitors to significantly raise dissociation rates.

    • Thayaparan Paramanathan
    • , Daniel Reeves
    •  & Jeff Gelles

  • Article |

    It remains unclear how the dynactin complex activates cytoplasmic dynein motor proteins. Ayloo et al.use single molecule imaging to observe dynein–dynactin behaviour on microtubules, and show that dynactin recruits dynein to microtubules and acts as a brake to slow the motor.

    • Swathi Ayloo
    • , Jacob E. Lazarus
    •  & Erika L. F. Holzbaur

  • Article |

    Unlike most processive motor proteins, the stepping motion of cytoplasmic dynein’s two linked motor domains is not precisely coordinated. Cleary et al.show that the ATPase activity of just one head is required for processive movement, and that tension on the linker gates the release of the motor from microtubules.

    • Frank B. Cleary
    • , Mark A. Dewitt
    •  & Ahmet Yildiz

  • Article
    | Open Access

    Lateral diffusion of transmembrane signalling molecules is implicated in neuronal communication but imaging in tissue is limited by poor temporal resolution. Here, the authors use quantum dots to label lipids and adhesion molecules, allowing them to track single-molecule motions in subcellular compartments.

    • B. Biermann
    • , S. Sokoll
    •  & M. Heine

  • Article |

    Messenger RNAs and their associated proteins are transported from the nucleus through highly selective nuclear pore complexes. Using ultrahigh resolution single-molecule imaging, the authors visualise the path taken by each messenger RNA as it negotiates the pore’s selectivity filter.

    • Jiong Ma
    • , Zhen Liu
    •  & Weidong Yang

  • Article
    | Open Access

    RecQ helicases are enzymes that play a central role in maintaining genome stability in the DNA repair cascade. Klaue et al. show that RecQ2 and RecQ3 from Arabidopsis thalianaprocess DNA by, respectively, unwinding and rewinding forked DNA substrates, using a frequent strand switching mechanism.

    • Daniel Klaue
    • , Daniela Kobbe
    •  & Ralf Seidel

  • Article
    | Open Access

    Tracking single molecules on long stretches of single-stranded DNA poses technical challenges due to its propensity to form hairpin structures. To solve this problem, the authors combine TIRF microscopy with optical tweezers to stretch the DNA and capture the dynamics of DNA unwinding by UvrD DNA helicase.

    • Kyung Suk Lee
    • , Hamza Balci
    •  & Taekjip Ha

  • Article
    | Open Access

    How the genome is physically organized is less understood in archaea than in eubacteria or eukaryotes. Laurens et al. measure DNA binding by the Sulfolobus solfataricusproteins Alba1 and Alba2 using single-molecule techniques and conclude that the presence of Alba2 leads to more bridging between DNA.

    • Niels Laurens
    • , Rosalie P.C. Driessen
    •  & Gijs J.L. Wuite

  • Article |

    The mitochondrial transcription factor A (TFAM) mediates both mitochondrial transcription and DNA compaction, but how it achieves these two functions is unknown. In this study, TFAM is shown to slide along DNA and cause local melting, suggesting a mechanism for how TFAM modulates both transcription and compaction.

    • Géraldine Farge
    • , Niels Laurens
    •  & Gijs J.L. Wuite

  • Article |

    Single-molecule force spectroscopy is used to study single molecule interactions, but probing short-lived events is difficult. Here, a nanomechanical interface is developed, which allows the study of microsecond timescale interactions.

    • Mingdong Dong
    •  & Ozgur Sahin

Browse broader subjects

Browse Single-molecule biophysics across other nature.com journals