Literature DB >> 31509386

Measuring DNA Hybridization Kinetics in Live Cells Using a Time-Resolved 3D Single-Molecule Tracking Method.

Yuan-I Chen1, Yin-Jui Chang2, Trung Duc Nguyen1, Cong Liu1, Stephanie Phillion1, Yu-An Kuo1, Huong T Vu1, Angela Liu1, Yen-Liang Liu1, Soonwoo Hong1, Pengyu Ren1, Thomas E Yankeelov1,3,4,5,6, Hsin-Chih Yeh1,7.   

Abstract

Single-molecule detection enables direct characterization of annealing/melting kinetics of nucleic acids without the need for synchronization of molecular states, but the current experiments are not carried out in a native cellular context. Here we describe an integrated 3D single-molecule tracking and lifetime measurement method that can follow individual DNA molecules diffusing inside a mammalian cell and observe multiple annealing and melting events on the same molecules. By comparing the hybridization kinetics of the same DNA strand in vitro, we found the association constants can be 13- to 163-fold higher in the molecular crowding cellular environment.

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Year:  2019        PMID: 31509386      PMCID: PMC7179573          DOI: 10.1021/jacs.9b08036

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  29 in total

1.  Three-dimensional tracking of single mRNA particles in Saccharomyces cerevisiae using a double-helix point spread function.

Authors:  Michael A Thompson; Jason M Casolari; Majid Badieirostami; Patrick O Brown; W E Moerner
Journal:  Proc Natl Acad Sci U S A       Date:  2010-10-04       Impact factor: 11.205

2.  Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami.

Authors:  Ralf Jungmann; Christian Steinhauer; Max Scheible; Anton Kuzyk; Philip Tinnefeld; Friedrich C Simmel
Journal:  Nano Lett       Date:  2010-11-10       Impact factor: 11.189

3.  Control of DNA strand displacement kinetics using toehold exchange.

Authors:  David Yu Zhang; Erik Winfree
Journal:  J Am Chem Soc       Date:  2009-12-02       Impact factor: 15.419

4.  Continuous throughput and long-term observation of single-molecule FRET without immobilization.

Authors:  Swati Tyagi; Virginia VanDelinder; Niccolò Banterle; Gustavo Fuertes; Sigrid Milles; Morgane Agez; Edward A Lemke
Journal:  Nat Methods       Date:  2014-01-19       Impact factor: 28.547

5.  Segmentation of 3D Trajectories Acquired by TSUNAMI Microscope: An Application to EGFR Trafficking.

Authors:  Yen-Liang Liu; Evan P Perillo; Cong Liu; Peter Yu; Chao-Kai Chou; Mien-Chie Hung; Andrew K Dunn; Hsin-Chih Yeh
Journal:  Biophys J       Date:  2016-11-15       Impact factor: 4.033

6.  Duplex stabilities of phosphorothioate, methylphosphonate, and RNA analogs of two DNA 14-mers.

Authors:  L Kibler-Herzog; G Zon; B Uznanski; G Whittier; W D Wilson
Journal:  Nucleic Acids Res       Date:  1991-06-11       Impact factor: 16.971

7.  Kinetic fingerprinting to identify and count single nucleic acids.

Authors:  Alexander Johnson-Buck; Xin Su; Maria D Giraldez; Meiping Zhao; Muneesh Tewari; Nils G Walter
Journal:  Nat Biotechnol       Date:  2015-06-22       Impact factor: 54.908

8.  Single-Molecule Tracking and Its Application in Biomolecular Binding Detection.

Authors:  Cong Liu; Yen-Liang Liu; Evan P Perillo; Andrew K Dunn; Hsin-Chih Yeh
Journal:  IEEE J Sel Top Quantum Electron       Date:  2016-05-17       Impact factor: 4.544

9.  Full characterization of GPCR monomer-dimer dynamic equilibrium by single molecule imaging.

Authors:  Rinshi S Kasai; Kenichi G N Suzuki; Eric R Prossnitz; Ikuko Koyama-Honda; Chieko Nakada; Takahiro K Fujiwara; Akihiro Kusumi
Journal:  J Cell Biol       Date:  2011-02-07       Impact factor: 10.539

10.  Predicting DNA hybridization kinetics from sequence.

Authors:  Jinny X Zhang; John Z Fang; Wei Duan; Lucia R Wu; Angela W Zhang; Neil Dalchau; Boyan Yordanov; Rasmus Petersen; Andrew Phillips; David Yu Zhang
Journal:  Nat Chem       Date:  2017-11-06       Impact factor: 24.427

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  5 in total

1.  Three-Dimensional Two-Color Dual-Particle Tracking Microscope for Monitoring DNA Conformational Changes and Nanoparticle Landings on Live Cells.

Authors:  Yen-Liang Liu; Evan P Perillo; Phyllis Ang; Mirae Kim; Duc Trung Nguyen; Katherine Blocher; Yu-An Chen; Cong Liu; Ahmed M Hassan; Huong T Vu; Yuan-I Chen; Andrew K Dunn; Hsin-Chih Yeh
Journal:  ACS Nano       Date:  2020-07-15       Impact factor: 15.881

Review 2.  Real-Time Feedback-Driven Single-Particle Tracking: A Survey and Perspective.

Authors:  Bertus van Heerden; Nicholas A Vickers; Tjaart P J Krüger; Sean B Andersson
Journal:  Small       Date:  2022-06-27       Impact factor: 15.153

3.  Kinetics of heterochiral strand displacement from PNA-DNA heteroduplexes.

Authors:  Nandini Kundu; Brian E Young; Jonathan T Sczepanski
Journal:  Nucleic Acids Res       Date:  2021-06-21       Impact factor: 16.971

4.  Recent developments in the characterization of nucleic acid hybridization kinetics.

Authors:  Yuan-I Chen; Manasa P Sripati; Trung Duc Nguyen; Yin-Jui Chang; Yu-An Kuo; Soonwoo Hong; Hsin-Chih Yeh
Journal:  Curr Opin Biomed Eng       Date:  2021-06-12

5.  Generative adversarial network enables rapid and robust fluorescence lifetime image analysis in live cells.

Authors:  Yuan-I Chen; Yin-Jui Chang; Shih-Chu Liao; Trung Duc Nguyen; Jianchen Yang; Yu-An Kuo; Soonwoo Hong; Yen-Liang Liu; H Grady Rylander; Samantha R Santacruz; Thomas E Yankeelov; Hsin-Chih Yeh
Journal:  Commun Biol       Date:  2022-01-11
  5 in total

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