Genomes and Genes
single molecule imaging
Summary: High resolution imaging techniques that allow visualization of individual molecules of proteins, lipids, or nucleic acids within cells or tissues.
- 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. ..
- 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. ..
- 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...
- 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. ..
- 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. ..
- 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. ..
- 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. ..
- 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. ..
- 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. ..
- 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. ..
- 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. ..
- 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. ..
- 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. ..
- Ashdown G, Burn G, Williamson D, PandÅ¾iÄ‡ 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. ..
- 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...
- 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. ..
- 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. ..
- 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. ..
- 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. ..
- 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. ..
- 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. ..