scholarly journals Single-molecule pull-down for investigating protein–nucleic acid interactions

Methods ◽  
2016 ◽  
Vol 105 ◽  
pp. 99-108 ◽  
Author(s):  
Mohamed Fareh ◽  
Luuk Loeff ◽  
Malwina Szczepaniak ◽  
Anna C. Haagsma ◽  
Kyu-Hyeon Yeom ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Single Molecule ◽  
Protein Nucleic Acid ◽  
Nucleic Acid Interactions

scholarly journals Single-Stranded DNA Curtains for Real-Time Single-Molecule Visualization of Protein–Nucleic Acid Interactions

2012 ◽  
Vol 84 (18) ◽  
pp. 7607-7612 ◽  
Author(s):  
Bryan Gibb ◽  
Tim D. Silverstein ◽  
Ilya J. Finkelstein ◽  
Eric C. Greene
Keyword(s):  
Nucleic Acid ◽  
Real Time ◽  
Single Molecule ◽  
Single Stranded Dna ◽  
Protein Nucleic Acid ◽  
Nucleic Acid Interactions

scholarly journals Argonaute bypasses cellular obstacles without hindrance during target search

2019 ◽  
Author(s):  
Tao Ju Cui ◽  
Misha Klein ◽  
Jorrit W. Hegge ◽  
Stanley D. Chandradoss ◽  
John van der Oost ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Single Molecule ◽  
High Efficiency ◽  
Lateral Diffusion ◽  
Secondary Structures ◽  
Single Molecule Fret ◽  
Tight Contact ◽  
Dna Backbone ◽  
Protein Nucleic Acid ◽  
Nucleic Acid Interactions

Argonaute (Ago) proteins are key players in gene regulation in eukaryotes and host defense in prokaryotes. For specific interference, Ago relies on base pairing between small nucleic acid guides and complementary target sequences. To efficiently scan nucleic acid chains for potential targets, Ago must bypass both secondary structures in mRNA and single stranded DNA as well as protein barriers. Through single-molecule FRET, we reveal that lateral diffusion is mediated mainly through protein-nucleic acid interactions, rather than interactions between the guide and targeted strand. This allows Ago to scan for targets with high efficiency but without maintaining tight contact with the DNA backbone. Real-time observations show that Ago “glides” short distances over secondary structures while using intersegmental jumps to reduce scanning redundancy and bypass protein barriers. Our single-molecule method in combination with kinetic analysis may serve as a novel platform to study the effect of sequence on search kinetics for other nucleic acid-guided proteins.

scholarly journals Single-Stranded DNA Curtains for Real-Time Single-Molecule Visualization of Protein−Nucleic Acid Interactions

2013 ◽  
Vol 104 (2) ◽  
pp. 178a
Author(s):  
Bryan Gibb ◽  
Tim D. Silverstein ◽  
Ilya J. Finkelstein ◽  
Eric C. Greene
Keyword(s):  
Nucleic Acid ◽  
Real Time ◽  
Single Molecule ◽  
Single Stranded Dna ◽  
Protein Nucleic Acid ◽  
Nucleic Acid Interactions

scholarly journals Argonaute bypasses cellular obstacles without hindrance during target search

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Tao Ju Cui ◽  
Misha Klein ◽  
Jorrit W. Hegge ◽  
Stanley D. Chandradoss ◽  
John van der Oost ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Host Defense ◽  
Single Molecule ◽  
Kinetic Modelling ◽  
Secondary Structures ◽  
Single Molecule Fret ◽  
Search Processes ◽  
Protein Nucleic Acid ◽  
Nucleic Acid Interactions ◽  
Modelling Approach

Abstract Argonaute (Ago) proteins are key players in both gene regulation (eukaryotes) and host defense (prokaryotes). Acting on single-stranded nucleic-acid substrates, Ago relies on base pairing between a small nucleic-acid guide and its complementary target sequences for specificity. To efficiently scan nucleic-acid chains for targets, Ago diffuses laterally along the substrate and must bypass secondary structures as well as protein barriers. Using single-molecule FRET in conjunction with kinetic modelling, we reveal that target scanning is mediated through loose protein-nucleic acid interactions, allowing Ago to slide short distances over secondary structures, as well as to bypass protein barriers via intersegmental transfer. Our combined single-molecule experiment and kinetic modelling approach may serve as a platform to dissect search processes and study the effect of sequence on search kinetics for other nucleic acid-guided proteins.

Snapshot blotting: The transfer of nucleic acids and nucleoprotein complexes from electrophoresis gels to EM grids

1992 ◽  
Vol 50 (1) ◽  
pp. 762-763
Author(s):  
Stephen D. Jett
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Nucleic Acid Binding ◽  
Mobility Shift ◽  
Carbon Coated ◽  
Nucleoprotein Complexes ◽  
Mobility Shift Assay ◽  
Protein Nucleic Acid ◽  
Gel Mobility Shift ◽  
Nucleic Acid Interactions

The electrophoresis gel mobility shift assay is a popular method for the study of protein-nucleic acid interactions. The binding of proteins to DNA is characterized by a reduction in the electrophoretic mobility of the nucleic acid. Binding affinity, stoichiometry, and kinetics can be obtained from such assays; however, it is often desirable to image the various species in the gel bands using TEM. Present methods for isolation of nucleoproteins from gel bands are inefficient and often destroy the native structure of the complexes. We have developed a technique, called “snapshot blotting,” by which nucleic acids and nucleoprotein complexes in electrophoresis gels can be electrophoretically transferred directly onto carbon-coated grids for TEM imaging.

Use of difference boundary sedimentation velocity to investigate nonspecific protein-nucleic acid interactions

Biochemistry ◽  
1980 ◽  
Vol 19 (15) ◽  
pp. 3516-3522 ◽  
Author(s):  
Timothy M. Lohman ◽  
C. Glen Wensley ◽  
Jeffrey Cina ◽  
Richard R. Burgess ◽  
M. Thomas Record
Keyword(s):  
Nucleic Acid ◽  
Sedimentation Velocity ◽  
Protein Nucleic Acid ◽  
Nucleic Acid Interactions

Protein—nucleic acid interactions Folding and binding Web alert

1998 ◽  
Vol 8 (1) ◽  
pp. 9-10 ◽  
Author(s):  
PhilipE Bourne ◽  
Judith Murray-Rust ◽  
JeremyH Lakey
Keyword(s):  
Nucleic Acid ◽  
Protein Nucleic Acid ◽  
Nucleic Acid Interactions

Single-molecule nucleic acid interactions monitored on a label-free microcavity biosensor platform

2014 ◽  
Vol 9 (11) ◽  
pp. 933-939 ◽  
Author(s):  
Martin D. Baaske ◽  
Matthew R. Foreman ◽  
Frank Vollmer
Keyword(s):  
Nucleic Acid ◽  
Single Molecule ◽  
Label Free ◽  
Nucleic Acid Interactions

Nonspecific Prion Protein–Nucleic Acid Interactions Lead to Different Aggregates and Cytotoxic Species

Biochemistry ◽  
2012 ◽  
Vol 51 (27) ◽  
pp. 5402-5413 ◽  
Author(s):  
Bruno Macedo ◽  
Thiago A. Millen ◽  
Carolina A. C. A. Braga ◽  
Mariana P. B. Gomes ◽  
Priscila S. Ferreira ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Prion Protein ◽  
Protein Nucleic Acid ◽  
Nucleic Acid Interactions
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