Literature DB >> 25212907

Single-molecule tools for enzymology, structural biology, systems biology and nanotechnology: an update.

Julia R Widom1, Soma Dhakal, Laurie A Heinicke, Nils G Walter.   

Abstract

Toxicology is the highly interdisciplinary field studying the adverse effects of chemicals on living organisms. It requires sensitive tools to detect such effects. After their initial implementation during the 1990s, single-molecule fluorescence detection tools were quickly recognized for their potential to contribute greatly to many different areas of scientific inquiry. In the intervening time, technical advances in the field have generated ever-improving spatial and temporal resolution and have enabled the application of single-molecule fluorescence to increasingly complex systems, such as live cells. In this review, we give an overview of the optical components necessary to implement the most common versions of single-molecule fluorescence detection. We then discuss current applications to enzymology and structural studies, systems biology, and nanotechnology, presenting the technical considerations that are unique to each area of study, along with noteworthy recent results. We also highlight future directions that have the potential to revolutionize these areas of study by further exploiting the capabilities of single-molecule fluorescence microscopy.

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Year:  2014        PMID: 25212907      PMCID: PMC4615698          DOI: 10.1007/s00204-014-1357-9

Source DB:  PubMed          Journal:  Arch Toxicol        ISSN: 0340-5761            Impact factor:   5.153


  115 in total

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Authors:  Jacek Krol; Inga Loedige; Witold Filipowicz
Journal:  Nat Rev Genet       Date:  2010-07-27       Impact factor: 53.242

Review 2.  DNA nanomachines.

Authors:  Jonathan Bath; Andrew J Turberfield
Journal:  Nat Nanotechnol       Date:  2007-05       Impact factor: 39.213

3.  Nuclear export of single native mRNA molecules observed by light sheet fluorescence microscopy.

Authors:  Jan Peter Siebrasse; Tim Kaminski; Ulrich Kubitscheck
Journal:  Proc Natl Acad Sci U S A       Date:  2012-05-21       Impact factor: 11.205

4.  Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation.

Authors:  Juan R Alvarez-Dominguez; Wenqian Hu; Bingbing Yuan; Jiahai Shi; Staphany S Park; Austin A Gromatzky; Alexander van Oudenaarden; Harvey F Lodish
Journal:  Blood       Date:  2013-11-07       Impact factor: 22.113

Review 5.  Advances in single-molecule fluorescence methods for molecular biology.

Authors:  Chirlmin Joo; Hamza Balci; Yuji Ishitsuka; Chittanon Buranachai; Taekjip Ha
Journal:  Annu Rev Biochem       Date:  2008       Impact factor: 23.643

6.  Visualization of dynamics of single endogenous mRNA labeled in live mouse.

Authors:  Hye Yoon Park; Hyungsik Lim; Young J Yoon; Antonia Follenzi; Chiso Nwokafor; Melissa Lopez-Jones; Xiuhua Meng; Robert H Singer
Journal:  Science       Date:  2014-01-24       Impact factor: 47.728

Review 7.  X-inactivation, imprinting, and long noncoding RNAs in health and disease.

Authors:  Jeannie T Lee; Marisa S Bartolomei
Journal:  Cell       Date:  2013-03-14       Impact factor: 41.582

8.  Characterization and development of photoactivatable fluorescent proteins for single-molecule-based superresolution imaging.

Authors:  Siyuan Wang; Jeffrey R Moffitt; Graham T Dempsey; X Sunney Xie; Xiaowei Zhuang
Journal:  Proc Natl Acad Sci U S A       Date:  2014-05-27       Impact factor: 11.205

Review 9.  Nuclear export dynamics of RNA-protein complexes.

Authors:  David Grünwald; Robert H Singer; Michael Rout
Journal:  Nature       Date:  2011-07-20       Impact factor: 49.962

10.  RNA-based fluorescent biosensors for live cell imaging of second messengers cyclic di-GMP and cyclic AMP-GMP.

Authors:  Colleen A Kellenberger; Stephen C Wilson; Jade Sales-Lee; Ming C Hammond
Journal:  J Am Chem Soc       Date:  2013-03-21       Impact factor: 15.419

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  7 in total

1.  Assembly of multienzyme complexes on DNA nanostructures.

Authors:  Jinglin Fu; Yuhe Renee Yang; Soma Dhakal; Zhao Zhao; Minghui Liu; Ting Zhang; Nils G Walter; Hao Yan
Journal:  Nat Protoc       Date:  2016-10-20       Impact factor: 13.491

Review 2.  Life under the Microscope: Single-Molecule Fluorescence Highlights the RNA World.

Authors:  Sujay Ray; Julia R Widom; Nils G Walter
Journal:  Chem Rev       Date:  2018-01-24       Impact factor: 60.622

3.  Nanoreporter of an Enzymatic Suicide Inactivation Pathway.

Authors:  Zvi Yaari; Justin M Cheung; Hanan A Baker; Rune S Frederiksen; Prakrit V Jena; Christopher P Horoszko; Fang Jiao; Simon Scheuring; Minkui Luo; Daniel A Heller
Journal:  Nano Lett       Date:  2020-10-29       Impact factor: 11.189

4.  Single Molecule Cluster Analysis dissects splicing pathway conformational dynamics.

Authors:  Mario R Blanco; Joshua S Martin; Matthew L Kahlscheuer; Ramya Krishnan; John Abelson; Alain Laederach; Nils G Walter
Journal:  Nat Methods       Date:  2015-09-28       Impact factor: 28.547

5.  Nanocaged enzymes with enhanced catalytic activity and increased stability against protease digestion.

Authors:  Zhao Zhao; Jinglin Fu; Soma Dhakal; Alexander Johnson-Buck; Minghui Liu; Ting Zhang; Neal W Woodbury; Yan Liu; Nils G Walter; Hao Yan
Journal:  Nat Commun       Date:  2016-02-10       Impact factor: 14.919

6.  Systems Toxicology.

Authors:  Ahmed Ghallab
Journal:  EXCLI J       Date:  2015-12-22       Impact factor: 4.068

7.  Caging and Photoactivation in Single-Molecule Förster Resonance Energy Transfer Experiments.

Authors:  Atieh Aminian Jazi; Evelyn Ploetz; Muhamad Arizki; Balasubramaniam Dhandayuthapani; Izabela Waclawska; Reinhard Krämer; Christine Ziegler; Thorben Cordes
Journal:  Biochemistry       Date:  2017-03-31       Impact factor: 3.162

  7 in total

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