Literature DB >> 27222403

A simple DNA handle attachment method for single molecule mechanical manipulation experiments.

Duyoung Min1, Mark A Arbing1, Robert E Jefferson1, James U Bowie1.   

Abstract

Manipulating single molecules and systems of molecules with mechanical force is a powerful technique to examine their physical properties. Applying force requires attachment of the target molecule to larger objects using some sort of molecular tether, such as a strand of DNA. DNA handle attachment often requires difficult manipulations of the target molecule, which can preclude attachment to unstable, hard to obtain, and/or large, complex targets. Here we describe a method for covalent DNA handle attachment to proteins that simply requires the addition of a preprepared reagent to the protein and a short incubation. The handle attachment method developed here provides a facile approach for studying the biomechanics of biological systems.
© 2016 The Protein Society.

Keywords:  SpyCatcher; SpyTag; forced unfolding; magnetic tweezers; membrane protein; optical tweezers; protein folding

Mesh:

Substances:

Year:  2016        PMID: 27222403      PMCID: PMC4972209          DOI: 10.1002/pro.2952

Source DB:  PubMed          Journal:  Protein Sci        ISSN: 0961-8368            Impact factor:   6.725


  41 in total

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Review 2.  Combining single-molecule manipulation and single-molecule detection.

Authors:  Juan Carlos Cordova; Dibyendu Kumar Das; Harris W Manning; Matthew J Lang
Journal:  Curr Opin Struct Biol       Date:  2014-10-17       Impact factor: 6.809

3.  Highly anisotropic stability and folding kinetics of a single coiled coil protein under mechanical tension.

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4.  Genetically encoded short peptide tag for versatile protein labeling by Sfp phosphopantetheinyl transferase.

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Journal:  Proc Natl Acad Sci U S A       Date:  2005-10-19       Impact factor: 11.205

5.  ClpX(P) generates mechanical force to unfold and translocate its protein substrates.

Authors:  Rodrigo A Maillard; Gheorghe Chistol; Maya Sen; Maurizio Righini; Jiongyi Tan; Christian M Kaiser; Courtney Hodges; Andreas Martin; Carlos Bustamante
Journal:  Cell       Date:  2011-04-29       Impact factor: 41.582

Review 6.  Review: Progresses in understanding N-ethylmaleimide sensitive factor (NSF) mediated disassembly of SNARE complexes.

Authors:  Je-Kyung Ryu; Reinhard Jahn; Tae-Young Yoon
Journal:  Biopolymers       Date:  2016-08       Impact factor: 2.505

7.  Spider Silk Peptide Is a Compact, Linear Nanospring Ideal for Intracellular Tension Sensing.

Authors:  Michael D Brenner; Ruobo Zhou; Daniel E Conway; Luca Lanzano; Enrico Gratton; Martin A Schwartz; Taekjip Ha
Journal:  Nano Lett       Date:  2016-02-03       Impact factor: 11.189

8.  Stretching single talin rod molecules activates vinculin binding.

Authors:  Armando del Rio; Raul Perez-Jimenez; Ruchuan Liu; Pere Roca-Cusachs; Julio M Fernandez; Michael P Sheetz
Journal:  Science       Date:  2009-01-30       Impact factor: 63.714

9.  Structural analysis and optimization of the covalent association between SpyCatcher and a peptide Tag.

Authors:  Long Li; Jacob O Fierer; Tom A Rapoport; Mark Howarth
Journal:  J Mol Biol       Date:  2013-10-23       Impact factor: 5.469

10.  Mechanical unzipping and rezipping of a single SNARE complex reveals hysteresis as a force-generating mechanism.

Authors:  Duyoung Min; Kipom Kim; Changbong Hyeon; Yong Hoon Cho; Yeon-Kyun Shin; Tae-Young Yoon
Journal:  Nat Commun       Date:  2013       Impact factor: 14.919

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  10 in total

Review 1.  Nucleic Acid-Barcoding Technologies: Converting DNA Sequencing into a Broad-Spectrum Molecular Counter.

Authors:  Glen Liszczak; Tom W Muir
Journal:  Angew Chem Int Ed Engl       Date:  2019-02-06       Impact factor: 15.336

2.  Accurate computational design of multipass transmembrane proteins.

Authors:  Peilong Lu; Duyoung Min; Frank DiMaio; Kathy Y Wei; Michael D Vahey; Scott E Boyken; Zibo Chen; Jorge A Fallas; George Ueda; William Sheffler; Vikram Khipple Mulligan; Wenqing Xu; James U Bowie; David Baker
Journal:  Science       Date:  2018-03-02       Impact factor: 47.728

Review 3.  Applications of Single-Molecule Methods to Membrane Protein Folding Studies.

Authors:  Robert E Jefferson; Duyoung Min; Karolina Corin; Jing Yang Wang; James U Bowie
Journal:  J Mol Biol       Date:  2017-05-23       Impact factor: 5.469

4.  Evolutionary balance between foldability and functionality of a glucose transporter.

Authors:  Hyun-Kyu Choi; Hyunook Kang; Chanwoo Lee; Hyun Gyu Kim; Ben P Phillips; Soohyung Park; Charlotte Tumescheit; Sang Ah Kim; Hansol Lee; Soung-Hun Roh; Heedeok Hong; Martin Steinegger; Wonpil Im; Elizabeth A Miller; Hee-Jung Choi; Tae-Young Yoon
Journal:  Nat Chem Biol       Date:  2022-04-28       Impact factor: 16.174

5.  Watching helical membrane proteins fold reveals a common N-to-C-terminal folding pathway.

Authors:  Hyun-Kyu Choi; Duyoung Min; Hyunook Kang; Min Ju Shon; Sang-Hyun Rah; Hak Chan Kim; Hawoong Jeong; Hee-Jung Choi; James U Bowie; Tae-Young Yoon
Journal:  Science       Date:  2019-11-29       Impact factor: 47.728

6.  Facile tethering of stable and unstable proteins for optical tweezers experiments.

Authors:  Kevin Maciuba; Fan Zhang; Christian M Kaiser
Journal:  Biophys J       Date:  2021-05-12       Impact factor: 3.699

7.  Protein folding modulates the chemical reactivity of a Gram-positive adhesin.

Authors:  Alvaro Alonso-Caballero; Daniel J Echelman; Rafael Tapia-Rojo; Shubhasis Haldar; Edward C Eckels; Julio M Fernandez
Journal:  Nat Chem       Date:  2020-11-30       Impact factor: 24.427

Review 8.  Methods to study folding of alpha-helical membrane proteins in lipids.

Authors:  Nicola J Harris; Grant A Pellowe; Laura R Blackholly; Samuel Gulaidi-Breen; Heather E Findlay; Paula J Booth
Journal:  Open Biol       Date:  2022-07-20       Impact factor: 7.124

9.  Integrated Method to Attach DNA Handles and Functionally Select Proteins to Study Folding and Protein-Ligand Interactions with Optical Tweezers.

Authors:  Yuxin Hao; Clare Canavan; Susan S Taylor; Rodrigo A Maillard
Journal:  Sci Rep       Date:  2017-09-07       Impact factor: 4.379

10.  Unfolding of a ClC chloride transporter retains memory of its evolutionary history.

Authors:  Duyoung Min; Robert E Jefferson; Yifei Qi; Jing Yang Wang; Mark A Arbing; Wonpil Im; James U Bowie
Journal:  Nat Chem Biol       Date:  2018-03-26       Impact factor: 15.040

  10 in total

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