11. When the ligand is DNA, it has been suggested that the result
needs to be multiplied by a factor of 0.78 because the response
associated with nucleic acid binding to the surface is not the
same as that for a protein of equivalent mass [1, 3]. Unless it is
already known, it is best to assume that the stoichiometry is 1:1
and the concentrations of protein should be calculated based
on the molecular weight of the monomer.
Acknowledgments
The work was carried out using the John Innes Centre Biophysical
Analysis Facility with funding from the Biotechnology and
Biological Sciences Research Council (UK) Institute Strategic
Programme Grant BB/P012523/1. We would like to thank Julia
Mundy for critically reading the chapter.
References
1. Buckle M (2001) Surface plasmon resonance
applied to DNA-protein complexes. Methods
Mol Biol 148:535–546. https://doi.org/10.
1385/1-59259-208-2:535
2. Majka J, Speck C (2007) Analysis of proteinDNA interactions using surface plasmon resonance. Adv Biochem Eng Biotechnol
104:13–36
3. Stockley PG, Persson B (2009) Surface plasmon resonance assays of DNA-protein interactions. Methods Mol Biol 543:653–669.
https://doi.org/10.1007/978-1-60327-0151_38
4. Buckle M, Williams RM, Negroni M, Buc H
(1996) Real time measurements of elongation
by a reverse transcriptase using surface plasmon
resonance. Proc Natl Acad Sci U S A 93
(2):889–894
5. Katsamba PS, Park S, Laird-Offringa IA (2002)
Kinetic studies of RNA-protein interactions
using surface plasmon resonance. Methods 26
(2):95–104.
https://doi.org/10.1016/
S1046-2023(02)00012-9
6. Park S, Myszka DG, Yu M, Littler SJ, LairdOffringa IA (2000) HuD RNA recognition
motifs play distinct roles in the formation of a
stable complex with AU-rich RNA. Mol Cell
Biol 20(13):4765–4772
7. Stevenson CE, Assaad A, Chandra G et al
(2013) Investigation of DNA sequence recognition by a streptomycete MarR family transcriptional regulator through surface plasmon
resonance and X-ray crystallography. Nucleic
Acids Res 41(14):7009–7022. https://doi.
org/10.1093/nar/gkt523
8. Tran NT, Stevenson CE, Som NF et al (2018)
Permissive zones for the centromere-binding
protein ParB on the Caulobacter crescentus
chromosome. Nucleic Acids Res 46
(3):1196–1209. https://doi.org/10.1093/
nar/gkx1192
9. Bekiesch P, Forchhammer K, Apel AK (2016)
Characterization of DNA binding sites of
RokB, a ROK-family regulator from Streptomyces coelicolor reveals the RokB regulon. PLoS
One 11(5):e0153249. https://doi.org/10.
1371/journal.pone.0153249
10. Bekiesch P, Franz-Wachtel M, Kulik A et al
(2016) DNA affinity capturing identifies new
regulators of the heterologously expressed
novobiocin gene cluster in Streptomyces coelicolor M512. Appl Microbiol Biotechnol 100
(10):4495–4509. https://doi.org/10.1007/
s00253-016-7306-1
11. Campilongo R, Fung RKY, Little RH et al
(2017) One ligand, two regulators and three
binding sites: how KDPG controls primary carbon metabolism in Pseudomonas. PLoS Genet
13(6):e1006839. https://doi.org/10.1371/
journal.pgen.1006839
12. Fernandes GC, Hauf K, Sant’Anna FH et al
(2017) Glutamine synthetase stabilizes the
binding of GlnR to nitrogen fixation gene
operators. FEBS J 284(6):903–918. https://
doi.org/10.1111/febs.14021
378
Clare E. M. Stevenson and David M. Lawson
needs to be multiplied by a factor of 0.78 because the response
associated with nucleic acid binding to the surface is not the
same as that for a protein of equivalent mass [1, 3]. Unless it is
already known, it is best to assume that the stoichiometry is 1:1
and the concentrations of protein should be calculated based
on the molecular weight of the monomer.
Acknowledgments
The work was carried out using the John Innes Centre Biophysical
Analysis Facility with funding from the Biotechnology and
Biological Sciences Research Council (UK) Institute Strategic
Programme Grant BB/P012523/1. We would like to thank Julia
Mundy for critically reading the chapter.
References
1. Buckle M (2001) Surface plasmon resonance
applied to DNA-protein complexes. Methods
Mol Biol 148:535–546. https://doi.org/10.
1385/1-59259-208-2:535
2. Majka J, Speck C (2007) Analysis of proteinDNA interactions using surface plasmon resonance. Adv Biochem Eng Biotechnol
104:13–36
3. Stockley PG, Persson B (2009) Surface plasmon resonance assays of DNA-protein interactions. Methods Mol Biol 543:653–669.
https://doi.org/10.1007/978-1-60327-0151_38
4. Buckle M, Williams RM, Negroni M, Buc H
(1996) Real time measurements of elongation
by a reverse transcriptase using surface plasmon
resonance. Proc Natl Acad Sci U S A 93
(2):889–894
5. Katsamba PS, Park S, Laird-Offringa IA (2002)
Kinetic studies of RNA-protein interactions
using surface plasmon resonance. Methods 26
(2):95–104.
https://doi.org/10.1016/
S1046-2023(02)00012-9
6. Park S, Myszka DG, Yu M, Littler SJ, LairdOffringa IA (2000) HuD RNA recognition
motifs play distinct roles in the formation of a
stable complex with AU-rich RNA. Mol Cell
Biol 20(13):4765–4772
7. Stevenson CE, Assaad A, Chandra G et al
(2013) Investigation of DNA sequence recognition by a streptomycete MarR family transcriptional regulator through surface plasmon
resonance and X-ray crystallography. Nucleic
Acids Res 41(14):7009–7022. https://doi.
org/10.1093/nar/gkt523
8. Tran NT, Stevenson CE, Som NF et al (2018)
Permissive zones for the centromere-binding
protein ParB on the Caulobacter crescentus
chromosome. Nucleic Acids Res 46
(3):1196–1209. https://doi.org/10.1093/
nar/gkx1192
9. Bekiesch P, Forchhammer K, Apel AK (2016)
Characterization of DNA binding sites of
RokB, a ROK-family regulator from Streptomyces coelicolor reveals the RokB regulon. PLoS
One 11(5):e0153249. https://doi.org/10.
1371/journal.pone.0153249
10. Bekiesch P, Franz-Wachtel M, Kulik A et al
(2016) DNA affinity capturing identifies new
regulators of the heterologously expressed
novobiocin gene cluster in Streptomyces coelicolor M512. Appl Microbiol Biotechnol 100
(10):4495–4509. https://doi.org/10.1007/
s00253-016-7306-1
11. Campilongo R, Fung RKY, Little RH et al
(2017) One ligand, two regulators and three
binding sites: how KDPG controls primary carbon metabolism in Pseudomonas. PLoS Genet
13(6):e1006839. https://doi.org/10.1371/
journal.pgen.1006839
12. Fernandes GC, Hauf K, Sant’Anna FH et al
(2017) Glutamine synthetase stabilizes the
binding of GlnR to nitrogen fixation gene
operators. FEBS J 284(6):903–918. https://
doi.org/10.1111/febs.14021
378
Clare E. M. Stevenson and David M. Lawson