Literature DB >> 33159061

The smfBox is an open-source platform for single-molecule FRET.

Benjamin Ambrose1, James M Baxter1, John Cully1, Matthew Willmott1, Elliot M Steele2, Benji C Bateman3, Marisa L Martin-Fernandez3, Ashley Cadby2, Jonathan Shewring1, Marleen Aaldering1, Timothy D Craggs4.   

Abstract

Single-molecule Förster Resonance Energy Transfer (smFRET) is a powerful technique capable of resolving both relative and absolute distances within and between structurally dynamic biomolecules. High instrument costs, and a lack of open-source hardware and acquisition software have limited smFRET's broad application by non-specialists. Here, we present the smfBox, a cost-effective confocal smFRET platform, providing detailed build instructions, open-source acquisition software, and full validation, thereby democratising smFRET for the wider scientific community.

Entities:  

Year:  2020        PMID： 33159061      PMCID： PMC7648814          DOI： 10.1038/s41467-020-19468-4

Source DB:  PubMed          Journal:  Nat Commun        ISSN： 2041-1723            Impact factor:   14.919


  27 in total

1.  Fluorescence-aided molecule sorting: analysis of structure and interactions by alternating-laser excitation of single molecules.

Authors:  Achillefs N Kapanidis; Nam Ki Lee; Ted A Laurence; Sören Doose; Emmanuel Margeat; Shimon Weiss
Journal:  Proc Natl Acad Sci U S A       Date:  2004-06-02       Impact factor: 11.205

2.  Detection of structural dynamics by FRET: a photon distribution and fluorescence lifetime analysis of systems with multiple states.

Authors:  Stanislav Kalinin; Alessandro Valeri; Matthew Antonik; Suren Felekyan; Claus A M Seidel
Journal:  J Phys Chem B       Date:  2010-06-17       Impact factor: 2.991

3.  Periodic acceptor excitation spectroscopy of single molecules.

Authors:  Sören Doose; Mike Heilemann; Xavier Michalet; Shimon Weiss; Achillefs N Kapanidis
Journal:  Eur Biophys J       Date:  2007-02-06       Impact factor: 1.733

4.  Complete architecture of the archaeal RNA polymerase open complex from single-molecule FRET and NPS.

Authors:  Julia Nagy; Dina Grohmann; Alan C M Cheung; Sarah Schulz; Katherine Smollett; Finn Werner; Jens Michaelis
Journal:  Nat Commun       Date:  2015-01-30       Impact factor: 14.919

5.  Conformational landscapes of DNA polymerase I and mutator derivatives establish fidelity checkpoints for nucleotide insertion.

Authors:  Johannes Hohlbein; Louise Aigrain; Timothy D Craggs; Oya Bermek; Olga Potapova; Pouya Shoolizadeh; Nigel D F Grindley; Catherine M Joyce; Achillefs N Kapanidis
Journal:  Nat Commun       Date:  2013       Impact factor: 14.919

6.  FRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET.

Authors:  Antonino Ingargiola; Eitan Lerner; SangYoon Chung; Shimon Weiss; Xavier Michalet
Journal:  PLoS One       Date:  2016-08-17       Impact factor: 3.240

7.  Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study.

Authors:  Björn Hellenkamp; Sonja Schmid; Olga Doroshenko; Oleg Opanasyuk; Ralf Kühnemuth; Soheila Rezaei Adariani; Benjamin Ambrose; Mikayel Aznauryan; Anders Barth; Victoria Birkedal; Mark E Bowen; Hongtao Chen; Thorben Cordes; Tobias Eilert; Carel Fijen; Christian Gebhardt; Markus Götz; Giorgos Gouridis; Enrico Gratton; Taekjip Ha; Pengyu Hao; Christian A Hanke; Andreas Hartmann; Jelle Hendrix; Lasse L Hildebrandt; Verena Hirschfeld; Johannes Hohlbein; Boyang Hua; Christian G Hübner; Eleni Kallis; Achillefs N Kapanidis; Jae-Yeol Kim; Georg Krainer; Don C Lamb; Nam Ki Lee; Edward A Lemke; Brié Levesque; Marcia Levitus; James J McCann; Nikolaus Naredi-Rainer; Daniel Nettels; Thuy Ngo; Ruoyi Qiu; Nicole C Robb; Carlheinz Röcker; Hugo Sanabria; Michael Schlierf; Tim Schröder; Benjamin Schuler; Henning Seidel; Lisa Streit; Johann Thurn; Philip Tinnefeld; Swati Tyagi; Niels Vandenberk; Andrés Manuel Vera; Keith R Weninger; Bettina Wünsch; Inna S Yanez-Orozco; Jens Michaelis; Claus A M Seidel; Timothy D Craggs; Thorsten Hugel
Journal:  Nat Methods       Date:  2018-08-31       Impact factor: 28.547

8.  Dynamic anticipation by Cdk2/Cyclin A-bound p27 mediates signal integration in cell cycle regulation.

Authors:  Maksym Tsytlonok; Hugo Sanabria; Yuefeng Wang; Suren Felekyan; Katherina Hemmen; Aaron H Phillips; Mi-Kyung Yun; M Brett Waddell; Cheon-Gil Park; Sivaraja Vaithiyalingam; Luigi Iconaru; Stephen W White; Peter Tompa; Claus A M Seidel; Richard Kriwacki
Journal:  Nat Commun       Date:  2019-04-11       Impact factor: 14.919

9.  PAM: A Framework for Integrated Analysis of Imaging, Single-Molecule, and Ensemble Fluorescence Data.

Authors:  Waldemar Schrimpf; Anders Barth; Jelle Hendrix; Don C Lamb
Journal:  Biophys J       Date:  2018-04-10       Impact factor: 4.033

10.  Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase.

Authors:  Timothy D Craggs; Marko Sustarsic; Anne Plochowietz; Majid Mosayebi; Hendrik Kaju; Andrew Cuthbert; Johannes Hohlbein; Laura Domicevica; Philip C Biggin; Jonathan P K Doye; Achillefs N Kapanidis
Journal:  Nucleic Acids Res       Date:  2019-11-18       Impact factor: 16.971
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  5 in total

1.  Open microscopy in the life sciences: quo vadis?

Authors:  Johannes Hohlbein; Benedict Diederich; Barbora Marsikova; Emmanuel G Reynaud; Séamus Holden; Wiebke Jahr; Robert Haase; Kirti Prakash
Journal:  Nat Methods       Date:  2022-09       Impact factor: 47.990

2.  High-Force Application by a Nanoscale DNA Force Spectrometer.

Authors:  Michael Darcy; Kyle Crocker; Yuchen Wang; Jenny V Le; Golbarg Mohammadiroozbahani; Mahmoud A S Abdelhamid; Timothy D Craggs; Carlos E Castro; Ralf Bundschuh; Michael G Poirier
Journal:  ACS Nano       Date:  2022-04-06       Impact factor: 18.027

Review 3.  FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices.

Authors:  Eitan Lerner; Anders Barth; Jelle Hendrix; Benjamin Ambrose; Victoria Birkedal; Scott C Blanchard; Richard Börner; Hoi Sung Chung; Thorben Cordes; Timothy D Craggs; Ashok A Deniz; Jiajie Diao; Jingyi Fei; Ruben L Gonzalez; Irina V Gopich; Taekjip Ha; Christian A Hanke; Gilad Haran; Nikos S Hatzakis; Sungchul Hohng; Seok-Cheol Hong; Thorsten Hugel; Antonino Ingargiola; Chirlmin Joo; Achillefs N Kapanidis; Harold D Kim; Ted Laurence; Nam Ki Lee; Tae-Hee Lee; Edward A Lemke; Emmanuel Margeat; Jens Michaelis; Xavier Michalet; Sua Myong; Daniel Nettels; Thomas-Otavio Peulen; Evelyn Ploetz; Yair Razvag; Nicole C Robb; Benjamin Schuler; Hamid Soleimaninejad; Chun Tang; Reza Vafabakhsh; Don C Lamb; Claus Am Seidel; Shimon Weiss
Journal:  Elife       Date:  2021-03-29       Impact factor: 8.140

Review 4.  Single molecule imaging of protein aggregation in Dementia: Methods, insights and prospects.

Authors:  John S H Danial; David Klenerman
Journal:  Neurobiol Dis       Date:  2021-03-09       Impact factor: 5.996

5.  Construction of a Three-Color Prism-Based TIRF Microscope to Study the Interactions and Dynamics of Macromolecules.

Authors:  Max S Fairlamb; Amy M Whitaker; Fletcher E Bain; Maria Spies; Bret D Freudenthal
Journal:  Biology (Basel)       Date:  2021-06-23
  5 in total

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