9. Webster MW, Chen YH, Stowell JAW et al
(2018) mRNA Deadenylation is coupled to
translation rates by the differential activities of
Ccr4-not
nucleases.
Mol
Cell
70
(6):1089–1100 e1088. https://doi.org/10.
1016/j.molcel.2018.05.033
10. Harbers M (2015) Shift-Western blotting: separate analysis of protein and DNA from
protein-DNA complexes. Methods Mol Biol
1312:355–373.
https://doi.org/10.1007/
978-1-4939-2694-7_36
11. Blackwell TK, Weintraub H (1990) Differences
and similarities in DNA-binding preferences of
MyoD and E2A protein complexes revealed by
binding
site
selection.
Science
250
(4984):1104–1110
12. Beckert B, Masquida B (2011) Synthesis of
RNA by in vitro transcription. Methods Mol
Biol 703:29–41. https://doi.org/10.1007/
978-1-59745-248-9_3
13. Sambrook J, Russell DW (2006) Isolation of
DNA fragments from polyacrylamide gels by
the crush and soak method. CSH Protoc
2006(1).
https://doi.org/10.1101/pdb.
prot2936
14. Zarzosa-Alvarez AL, Sandoval-Cabrera A,
Torres-Huerta AL, Bermudez-Cruz RM
(2010) Electroeluting DNA fragments. J Vis
Exp 43. https://doi.org/10.3791/2136
15. Struhl K (2001) Reagents and radioisotopes
used to manipulate nucleic acids. Curr Protoc
Mol Biol. Chapter 3:Unit3 4. https://doi.org/
10.1002/0471142727.mb0304s09
16. Rueden CT, Schindelin J, Hiner MC, DeZonia
BE, Walter AE, Arena ET, Eliceiri KW (2017)
ImageJ2: ImageJ for the next generation of
scientific image data. BMC Bioinformatics 18
(1):529. https://doi.org/10.1186/s12859017-1934-z
17. Webster MW, Stowell JA, Passmore LA (2019)
RNA-binding proteins distinguish between
similar sequence motifs to promote targeted
deadenylation by Ccr4-not. Elife 8:e40670.
https://doi.org/10.7554/eLife.40670
18. Bhattacharyya D, Mirihana Arachchilage G,
Basu S (2016) Metal cations in G-Quadruplex
folding and stability. Front Chem 4:38.
https://doi.org/10.3389/fchem.2016.00038
19. Hulme EC, Trevethick MA (2010) Ligand
binding assays at equilibrium: validation and
interpretation.
Br
J
Pharmacol
161
(6):1219–1237. https://doi.org/10.1111/j.
1476-5381.2009.00604.x
EMSAs to Detect Protein-DNA/RNA Interactions
339
(2018) mRNA Deadenylation is coupled to
translation rates by the differential activities of
Ccr4-not
nucleases.
Mol
Cell
70
(6):1089–1100 e1088. https://doi.org/10.
1016/j.molcel.2018.05.033
10. Harbers M (2015) Shift-Western blotting: separate analysis of protein and DNA from
protein-DNA complexes. Methods Mol Biol
1312:355–373.
https://doi.org/10.1007/
978-1-4939-2694-7_36
11. Blackwell TK, Weintraub H (1990) Differences
and similarities in DNA-binding preferences of
MyoD and E2A protein complexes revealed by
binding
site
selection.
Science
250
(4984):1104–1110
12. Beckert B, Masquida B (2011) Synthesis of
RNA by in vitro transcription. Methods Mol
Biol 703:29–41. https://doi.org/10.1007/
978-1-59745-248-9_3
13. Sambrook J, Russell DW (2006) Isolation of
DNA fragments from polyacrylamide gels by
the crush and soak method. CSH Protoc
2006(1).
https://doi.org/10.1101/pdb.
prot2936
14. Zarzosa-Alvarez AL, Sandoval-Cabrera A,
Torres-Huerta AL, Bermudez-Cruz RM
(2010) Electroeluting DNA fragments. J Vis
Exp 43. https://doi.org/10.3791/2136
15. Struhl K (2001) Reagents and radioisotopes
used to manipulate nucleic acids. Curr Protoc
Mol Biol. Chapter 3:Unit3 4. https://doi.org/
10.1002/0471142727.mb0304s09
16. Rueden CT, Schindelin J, Hiner MC, DeZonia
BE, Walter AE, Arena ET, Eliceiri KW (2017)
ImageJ2: ImageJ for the next generation of
scientific image data. BMC Bioinformatics 18
(1):529. https://doi.org/10.1186/s12859017-1934-z
17. Webster MW, Stowell JA, Passmore LA (2019)
RNA-binding proteins distinguish between
similar sequence motifs to promote targeted
deadenylation by Ccr4-not. Elife 8:e40670.
https://doi.org/10.7554/eLife.40670
18. Bhattacharyya D, Mirihana Arachchilage G,
Basu S (2016) Metal cations in G-Quadruplex
folding and stability. Front Chem 4:38.
https://doi.org/10.3389/fchem.2016.00038
19. Hulme EC, Trevethick MA (2010) Ligand
binding assays at equilibrium: validation and
interpretation.
Br
J
Pharmacol
161
(6):1219–1237. https://doi.org/10.1111/j.
1476-5381.2009.00604.x
EMSAs to Detect Protein-DNA/RNA Interactions
339