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Literature DB >> 28673677

Studying protein-DNA interactions using atomic force microscopy.

Emily C Beckwitt¹, Muwen Kong¹, Bennett Van Houten².

Abstract

Atomic force microscopy (AFM) has made significant contributions to the study of protein-DNA interactions by making it possible to topographically image biological samples. A single protein-DNA binding reaction imaged by AFM can reveal protein binding specificity and affinity, protein-induced DNA bending, and protein binding stoichiometry. Changes in DNA structure, complex conformation, and cooperativity, can also be analyzed. In this review we highlight some important examples in the literature and discuss the advantages and limitations of these measurements. We also discuss important advances in technology that will facilitate the progress of AFM in the future.

Entities: Chemical Disease Gene Mutation Species

Keywords: Atomic force microscopy; Binding specificity; DNA bending; Protein-DNA interaction; Stoichiometry

Mesh：

Substances：
Proteins
DNA

Year: 2017 PMID： 28673677 PMCID： PMC5762137 DOI： 10.1016/j.semcdb.2017.06.028

Source DB: PubMed Journal: Semin Cell Dev Biol ISSN： 1084-9521 Impact factor: 7.727

142 in total

1. Substrate preparation for reliable imaging of DNA molecules with the scanning force microscope.

Authors: J Vesenka; M Guthold; C L Tang; D Keller; E Delaine; C Bustamante
Journal: Ultramicroscopy Date: 1992-07 Impact factor: 2.689

2. Imaging and mapping protein-binding sites on DNA regulatory regions with atomic force microscopy.

Authors: F Moreno-Herrero; P Herrero; J Colchero; A M Baró; F Moreno
Journal: Biochem Biophys Res Commun Date: 2001-01-12 Impact factor: 3.575

3. Atomic force microscopy captures the initiation of methyl-directed DNA mismatch repair.

Authors: Eric A Josephs; Tianli Zheng; Piotr E Marszalek
Journal: DNA Repair (Amst) Date: 2015-09-21

4. Following the assembly of RNA polymerase-DNA complexes in aqueous solutions with the scanning force microscope.

Authors: M Guthold; M Bezanilla; D A Erie; B Jenkins; H G Hansma; C Bustamante
Journal: Proc Natl Acad Sci U S A Date: 1994-12-20 Impact factor: 11.205

5. New insights into the regulatory mechanisms of ppGpp and DksA on Escherichia coli RNA polymerase-promoter complex.

Authors: Nicola Doniselli; Piere Rodriguez-Aliaga; Davide Amidani; Jorge A Bardales; Carlos Bustamante; Daniel G Guerra; Claudio Rivetti
Journal: Nucleic Acids Res Date: 2015-04-27 Impact factor: 16.971

6. Cooperative cluster formation, DNA bending and base-flipping by O6-alkylguanine-DNA alkyltransferase.

Authors: Ingrid Tessmer; Manana Melikishvili; Michael G Fried
Journal: Nucleic Acids Res Date: 2012-06-22 Impact factor: 16.971

7. Two high-mobility group box domains act together to underwind and kink DNA.

Authors: R Sánchez-Giraldo; F J Acosta-Reyes; C S Malarkey; N Saperas; M E A Churchill; J L Campos
Journal: Acta Crystallogr D Biol Crystallogr Date: 2015-06-30

8. Insights into the architecture and stoichiometry of Escherichia coli PepA*DNA complexes involved in transcriptional control and site-specific DNA recombination by atomic force microscopy.

Authors: Phu Nguyen Le Minh; Neel Devroede; Jan Massant; Dominique Maes; Daniel Charlier
Journal: Nucleic Acids Res Date: 2009-01-09 Impact factor: 16.971

9. Determination of protein-DNA binding constants and specificities from statistical analyses of single molecules: MutS-DNA interactions.

Authors: Yong Yang; Lauryn E Sass; Chunwei Du; Peggy Hsieh; Dorothy A Erie
Journal: Nucleic Acids Res Date: 2005-08-01 Impact factor: 16.971

10. High-resolution AFM imaging of single-stranded DNA-binding (SSB) protein--DNA complexes.

Authors: Loïc Hamon; David Pastré; Pauline Dupaigne; Cyrille Le Breton; Eric Le Cam; Olivier Piétrement
Journal: Nucleic Acids Res Date: 2007-03-28 Impact factor: 16.971

15 in total

1. Atomic Force Microscopy Reveals that the Drosophila Telomere-Capping Protein Verrocchio Is a Single-Stranded DNA-Binding Protein.

Authors: Alessandro Cicconi; Emanuela Micheli; Grazia Daniela Raffa; Stefano Cacchione
Journal: Methods Mol Biol Date: 2021

Studying protein-DNA interactions using atomic force microscopy.

1. Substrate preparation for reliable imaging of DNA molecules with the scanning force microscope.

2. Imaging and mapping protein-binding sites on DNA regulatory regions with atomic force microscopy.

3. Atomic force microscopy captures the initiation of methyl-directed DNA mismatch repair.

4. Following the assembly of RNA polymerase-DNA complexes in aqueous solutions with the scanning force microscope.

5. New insights into the regulatory mechanisms of ppGpp and DksA on Escherichia coli RNA polymerase-promoter complex.

6. Cooperative cluster formation, DNA bending and base-flipping by O6-alkylguanine-DNA alkyltransferase.

7. Two high-mobility group box domains act together to underwind and kink DNA.

8. Insights into the architecture and stoichiometry of Escherichia coli PepA*DNA complexes involved in transcriptional control and site-specific DNA recombination by atomic force microscopy.

9. Determination of protein-DNA binding constants and specificities from statistical analyses of single molecules: MutS-DNA interactions.

10. High-resolution AFM imaging of single-stranded DNA-binding (SSB) protein--DNA complexes.

1. Atomic Force Microscopy Reveals that the Drosophila Telomere-Capping Protein Verrocchio Is a Single-Stranded DNA-Binding Protein.

2. Bending and looping of long DNA by Polycomb repressive complex 2 revealed by AFM imaging in liquid.

3. High-Speed Atomic Force Microscopy Visualization of Protein-DNA Interactions Using DNA Origami Frames.

Review 4. Dynamic action of DNA repair proteins as revealed by single molecule techniques: Seeing is believing.

5. AP-endonuclease 1 sculpts DNA through an anchoring tyrosine residue on the DNA intercalating loop.

6. Effects of size, cooperativity, and competitive binding on protein positioning on DNA.

7. Design, assembly, and characterization of membrane-spanning DNA nanopores.

8. Impact of DNA sequences on DNA 'opening' by the Rad4/XPC nucleotide excision repair complex.

Review 9. Friction Determination by Atomic Force Microscopy in Field of Biochemical Science.

10. Accurate nanoscale flexibility measurement of DNA and DNA-protein complexes by atomic force microscopy in liquid.