single molecule imaging


Summary: High resolution imaging techniques that allow visualization of individual molecules of proteins, lipids, or nucleic acids within cells or tissues.

Top Publications

  1. Wadsworth G, Parikh R, Choy J, Kim H. mRNA detection in budding yeast with single fluorophores. Nucleic Acids Res. 2017;45:e141 pubmed publisher
    ..Our FISH protocol with single-fluorophore sensitivity significantly reduces cost and time compared to the conventional FISH protocols and opens up new opportunities to investigate small changes in RNA at the single cell level...
  2. Geng J, Klionsky D. Direct quantification of autophagic flux by a single molecule-based probe. Autophagy. 2017;13:639-641 pubmed publisher
    ..Since the key index of this probe is the degradation of GFP-LC3, it can be used to measure the cumulative effect of basal autophagy. The assay is applicable to high-throughput drug discovery as well as in vivo analysis...
  3. Bryan L, Weilandt D, Bachmann A, Kiliç S, Lechner C, Odermatt P, et al. Single-molecule kinetic analysis of HP1-chromatin binding reveals a dynamic network of histone modification and DNA interactions. Nucleic Acids Res. 2017;45:10504-10517 pubmed publisher
    ..Multiple weak protein and DNA interactions result in a multivalent interaction network that targets effectors to a specific chromatin modification state, where their activity is required...
  4. Huang D, Bax N, Buckley C, Weis W, Dunn A. Vinculin forms a directionally asymmetric catch bond with F-actin. Science. 2017;357:703-706 pubmed publisher
    ..The directional and force-stabilized binding of vinculin to F-actin may be a mechanism by which adhesion complexes maintain front-rear asymmetry in migrating cells. ..
  5. Jiao Y, Peluso P, Shi J, Liang T, Stitzer M, Wang B, et al. Improved maize reference genome with single-molecule technologies. Nature. 2017;546:524-527 pubmed publisher
    ..In addition, comparative optical mapping of two other inbred maize lines revealed a prevalence of deletions in regions of low gene density and maize lineage-specific genes. ..
  6. Murata A, Itoh Y, Mano E, Kanbayashi S, Igarashi C, Takahashi H, et al. One-Dimensional Search Dynamics of Tumor Suppressor p53 Regulated by a Disordered C-Terminal Domain. Biophys J. 2017;112:2301-2314 pubmed publisher
    ..These results suggest that p53 modulates the quaternary structure of the complex between p53 and DNA under different [Mg2+] and that it maintains the target search along DNA. ..
  7. Li X, Xiong X, Zhang M, Wang K, Chen Y, Zhou J, et al. Base-Resolution Mapping Reveals Distinct m1A Methylome in Nuclear- and Mitochondrial-Encoded Transcripts. Mol Cell. 2017;68:993-1005.e9 pubmed publisher
    ..Collectively, our approaches reveal distinct classes of m1A methylome and provide a resource for functional studies of m1A-mediated epitranscriptomic regulation. ..
  8. von Diezmann A, Shechtman Y, Moerner W. Three-Dimensional Localization of Single Molecules for Super-Resolution Imaging and Single-Particle Tracking. Chem Rev. 2017;117:7244-7275 pubmed publisher
  9. Mollazade M, Tabarin T, Nicovich P, Soeriyadi A, Nieves D, Gooding J, et al. Can single molecule localization microscopy be used to map closely spaced RGD nanodomains?. PLoS ONE. 2017;12:e0180871 pubmed publisher
    ..We therefore conclude that SMLM is a promising technique to directly map the distribution and nanoscale organization of ligands and would benefit from an improved localization precision. ..

More Information


  1. Mickolajczyk K, Hancock W. Kinesin Processivity Is Determined by a Kinetic Race from a Vulnerable One-Head-Bound State. Biophys J. 2017;112:2615-2623 pubmed publisher
    ..Overall, our results provide a kinetic framework for explaining kinesin processivity and for mapping structural differences to functional differences in diverse kinesin isoforms. ..
  2. Pitchiaya S, Heinicke L, Park J, Cameron E, Walter N. Resolving Subcellular miRNA Trafficking and Turnover at Single-Molecule Resolution. Cell Rep. 2017;19:630-642 pubmed publisher
    ..Probing single cells for miRNA activity, trafficking, and metabolism promises to facilitate screening for effective miRNA mimics and anti-miRNA drugs. ..
  3. Toulmin A, Baltierra Jasso L, Morten M, Sabir T, McGlynn P, Schröder G, et al. Conformational Heterogeneity in a Fully Complementary DNA Three-Way Junction with a GC-Rich Branchpoint. Biochemistry. 2017;56:4985-4991 pubmed publisher
    ..This structural diversity has implications for branch interactions and processing in vivo and for technological applications...
  4. Kieffer Kwon K, Nimura K, Rao S, Xu J, Jung S, Pekowska A, et al. Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation. Mol Cell. 2017;67:566-578.e10 pubmed publisher
    ..Our results thus define the nature and transcriptional impact of chromatin decondensation and reveal an unexpected role for Myc in the establishment of nuclear topology in mammalian cells. ..
  5. Aryal R, Kwak P, Tamayo A, Gebert M, Chiu P, Walz T, et al. Macromolecular Assemblies of the Mammalian Circadian Clock. Mol Cell. 2017;67:770-782.e6 pubmed publisher
    ..Our results define the macromolecular assemblies comprising the circadian feedback loop and provide an initial structural view of endogenous eukaryotic clock machinery. ..
  6. Srinivasan S, Hazra J, Singaraju G, Deb D, Rakshit S. ESCORTing proteins directly from whole cell-lysate for single-molecule studies. Anal Biochem. 2017;535:35-42 pubmed publisher
    ..We anticipate that this method will substantially reduce the investment by way of time, money and energy in the area of single molecule studies. ..
  7. Manteca A, Alonso Caballero A, Fertin M, Poly S, De Sancho D, Perez Jimenez R. The influence of disulfide bonds on the mechanical stability of proteins is context dependent. J Biol Chem. 2017;292:13374-13380 pubmed publisher
  8. Hsu S, Gilgenast T, Bartman C, Edwards C, Stonestrom A, Huang P, et al. The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries. Mol Cell. 2017;66:102-116.e7 pubmed publisher
    ..These findings indicate that BRD2 supports boundary activity, and they raise the possibility that pharmacologic BET inhibitors can influence gene expression in part by perturbing domain boundary function. ..
  9. Gregorio G, Masureel M, Hilger D, Terry D, Juette M, Zhao H, et al. Single-molecule analysis of ligand efficacy in ?2AR-G-protein activation. Nature. 2017;547:68-73 pubmed publisher
  10. Jiang S, Park S, Challapalli S, Fei J, Wang Y. Robust nonparametric quantification of clustering density of molecules in single-molecule localization microscopy. PLoS ONE. 2017;12:e0179975 pubmed publisher
    ..As an example, this descriptor was applied to estimate the clustering density of ptsG mRNA in E. coli bacteria. ..
  11. Krebs A, Imanci D, Hoerner L, Gaidatzis D, Burger L, Schübeler D. Genome-wide Single-Molecule Footprinting Reveals High RNA Polymerase II Turnover at Paused Promoters. Mol Cell. 2017;67:411-422.e4 pubmed publisher
    ..Our study provides a framework to quantify protein binding at single-molecule resolution and refines concepts of transcriptional pausing. ..
  12. Coleman R, Qiao Z, Singh S, Peng C, Cianfrocco M, Zhang Z, et al. p53 Dynamically Directs TFIID Assembly on Target Gene Promoters. Mol Cell Biol. 2017;37: pubmed publisher
    ..Collectively, these findings indicate that p53 dynamically escorts and loads TFIID onto its target promoters. ..
  13. Cuculis L, Schroeder C. A Single-Molecule View of Genome Editing Proteins: Biophysical Mechanisms for TALEs and CRISPR/Cas9. Annu Rev Chem Biomol Eng. 2017;8:577-597 pubmed publisher
    ..Here, we discuss the DNA search and recognition process for TALEs and Cas9 that have been revealed by recent single-molecule experiments. ..
  14. Burghardt T, Sun X, Wang Y, Ajtai K. Auxotonic to isometric contraction transitioning in a beating heart causes myosin step-size to down shift. PLoS ONE. 2017;12:e0174690 pubmed publisher
    ..Overall, the approach is a unique bottom-up single molecule mechanical characterization of a hierarchically functional native muscle myosin. ..
  15. Suzuki Y, Tsutsumi K, Miyamoto T, Yamamura H, Imaizumi Y. Heterodimerization of two pore domain K+ channel TASK1 and TALK2 in living heterologous expression systems. PLoS ONE. 2017;12:e0186252 pubmed publisher
    ..These results suggested that heterodimerization of TASK1 and TALK2 provides cells with the ability to make multiple responses to a variety of physiological and pharmacological stimuli. ..
  16. Ashdown G, Burn G, Williamson D, Pandžić E, Peters R, Holden M, et al. Live-Cell Super-resolution Reveals F-Actin and Plasma Membrane Dynamics at the T Cell Synapse. Biophys J. 2017;112:1703-1713 pubmed publisher
    ..We hypothesize that this apparent cytoskeletal-membrane coupling could provide a mechanism for driving the observed retrograde flow of signaling molecules such as the TCR, Lck, ZAP70, LAT, and SLP76. ..
  17. Czaplinski K. Techniques for Single-Molecule mRNA Imaging in Living Cells. Adv Exp Med Biol. 2017;978:425-441 pubmed publisher
  18. Lamichhane R, Hammond J, Pauszek R, Anderson R, Pedron I, van der Schans E, et al. A DEAD-box protein acts through RNA to promote HIV-1 Rev-RRE assembly. Nucleic Acids Res. 2017;45:4632-4641 pubmed publisher
  19. Horvathova I, Voigt F, Kotrys A, Zhan Y, Artus Revel C, Eglinger J, et al. The Dynamics of mRNA Turnover Revealed by Single-Molecule Imaging in Single Cells. Mol Cell. 2017;68:615-625.e9 pubmed publisher
    ..This methodology provides a framework for investigating the entire life history of individual mRNAs from birth to death in single cells...
  20. Halpern K, Shenhav R, Matcovitch Natan O, Tóth B, Lemze D, Golan M, et al. Single-cell spatial reconstruction reveals global division of labour in the mammalian liver. Nature. 2017;542:352-356 pubmed publisher
    ..These include a spatial order of bile acid biosynthesis enzymes that matches their position in the enzymatic cascade. Our approach can facilitate the reconstruction of similar spatial genomic blueprints for other mammalian organs. ..
  21. Myler L, Gallardo I, Soniat M, Deshpande R, Gonzalez X, Kim Y, et al. Single-Molecule Imaging Reveals How Mre11-Rad50-Nbs1 Initiates DNA Break Repair. Mol Cell. 2017;67:891-898.e4 pubmed publisher
    ..Our results provide a mechanism for how MRN promotes homologous recombination on nucleosome-coated DNA. ..
  22. Bugaud O, Barbier N, Chommy H, Fiszman N, Le Gall A, Dulin D, et al. Kinetics of CrPV and HCV IRES-mediated eukaryotic translation using single-molecule fluorescence microscopy. RNA. 2017;23:1626-1635 pubmed publisher
  23. Kriegel F, Ermann N, Forbes R, Dulin D, Dekker N, Lipfert J. Probing the salt dependence of the torsional stiffness of DNA by multiplexed magnetic torque tweezers. Nucleic Acids Res. 2017;45:5920-5929 pubmed publisher
    ..5 pN) torsional stiffness values of C = 103 ± 4 nm are identical, within experimental errors, for all tested salt concentration, suggesting that the intrinsic torsional stiffness of DNA does not depend on salt. ..
  24. Ouenzar F, Lalonde M, Laprade H, Morin G, Gallardo F, Tremblay Belzile S, et al. Cell cycle-dependent spatial segregation of telomerase from sites of DNA damage. J Cell Biol. 2017;216:2355-2371 pubmed publisher
    ..This study reveals novel roles for Pif1, Rad52, and Siz1-dependent sumoylation in the spatial exclusion of telomerase from sites of DNA repair. ..
  25. Pan H, Bilinovich S, Kaur P, Riehn R, Wang H, Williams D. CpG and methylation-dependent DNA binding and dynamics of the methylcytosine binding domain 2 protein at the single-molecule level. Nucleic Acids Res. 2017;45:9164-9177 pubmed publisher
    ..These results suggest that MBD2 targets NuRD to unmethylated or methylated CpG islands where its distinct dynamic binding modes help maintain open or closed chromatin, respectively. ..
  26. Shen H, Tauzin L, Baiyasi R, Wang W, Moringo N, Shuang B, et al. Single Particle Tracking: From Theory to Biophysical Applications. Chem Rev. 2017;117:7331-7376 pubmed publisher
    ..We then highlight some applications of SPT to study various biological and synthetic materials systems. Finally, we provide our perspective regarding several directions for future advancements in the theory and application of SPT. ..