of effective geometric parameters using a conventional fluorimeter. Anal Chem 81:420–426
11. Lewis JS, Jergic S, Dixon NE (2016) The E.
coli DNA replication fork. Enzyme 39:31–88
12. Schaeffer PM, Headlam MJ, Dixon NE (2005)
Protein–protein interactions in the eubacterial
replisome. IUBMB Life 57:5–12
13. Glover BP, McHenry CS (1998) The chi psi
subunits of DNA polymerase III holoenzyme
bind to single-stranded DNA-binding protein
(SSB) and facilitate replication of an
SSB-coated
template.
J
Biol
Chem
273:23476–23484
14. Georgescu RE, Kurth I, O’Donnell ME
(2011) Single-molecule studies reveal the function of a third polymerase in the replisome. Nat
Struct Mol Biol 19:113–116
15. Simonetta KR, Kazmirski SL, Goedken ER et al
(2009) The mechanism of ATP-dependent
primer-template recognition by a clamp loader
complex. Cell 137:659–671
16. Schuck P (1997) Use of surface plasmon resonance to probe the equilibrium and dynamic
aspects of interactions between biological
macromolecules. Annu Rev Biophys Biomol
Struct 26:541–566
17. Mao H, Hart SA, Schink A, Pollok BA (2004)
Sortase-mediated protein ligation: a new
method for protein engineering. J Am Chem
Soc 126:2670–2671
18. Bloom LB, Turner J, Kelman Z et al (1996)
Dynamics of loading the beta sliding clamp of
DNA polymerase III onto DNA. J Biol Chem
271:30699–30708
19. Brown PH, Balbo A, Schuck P (2008) Characterizing protein-protein interactions by sedimentation
velocity
analytical
ultracentrifugation. Curr Protoc Immunol
Chapter 18:Unit 18.15
20. Dam J, Velikovsky CA, Mariuzza RA et al
(2005) Sedimentation velocity analysis of heterogeneous
protein-protein
interactions:
Lamm equation modeling and sedimentation
coefficient distributions c(s). Biophys J
89:619–634
21. Naue N, Curth U (2012) Investigation of
protein-protein interactions of single-stranded
DNA-binding proteins by analytical ultracentrifugation. Methods Mol Biol 922:133–149
22. Schuck P (2010) Diffusion of the reaction
boundary of rapidly interacting macromolecules in sedimentation velocity. Biophys J
98:2741–2751
23. Schuck P (2000) Size-distribution analysis of
macromolecules by sedimentation velocity
ultracentrifugation and Lamm equation modeling. Biophys J 78:1606–1619
24. Lohman TM, Overman LB (1985) Two binding modes in Escherichia coli single strand binding protein-single stranded DNA complexes.
Modulation by NaCl concentration. J Biol
Chem 260:3594–3603
25. Bogutzki A, Naue N, Litz L, Pich A, Curth U
(2019) E. coli primase and DNA polymerase III
holoenzyme are able to bind concurrently to a
primed template during DNA replication. Sci
Rep 9:14460
26. Ton-That H, Liu G, Mazmanian SK, Faull KF,
Schneewind O (1999) Purification and characterization of sortase, the transpeptidase that
cleaves surface proteins of Staphylococcus aureus
at the LPXTG motif. Proc Natl Acad Sci U S A
96:12424–12429
27. Alegria-Schaffer A, Lodge A, Vattem K (2009)
Performing and optimizing Western blots with
an emphasis on chemiluminescent detection.
Methods Enzymol 463:573–599
28. Brautigam CA (2015) Calculations and
publication-quality illustrations for analytical
ultracentrifugation data. Methods Enzymol
562:109–133
29. Zhao H, Schuck P (2015) Combining biophysical methods for the analysis of protein complex
stoichiometry and affinity in SEDPHAT. Acta
Crystallogr D Biol Crystallogr 71:3–14
30. Laue MT, Shah BD, Rigdeway TM, Pelletier
SL (1992) Computer-aided interpretation of
analytical sedimentation data for proteins. In:
Harding SE et al (eds) Analytical ultracentrifugation in biochemistry and polymer science.
The Royal Society of Chemistry, Cambridge,
pp 90–125
31. Owczarzy R, Tataurov AV, Wu Y et al (2008)
IDT SciTools: a suite for analysis and design of
nucleic acid oligomers. Nucleic Acids Res 36:
W163–W169
32. Zhao H, Mayer ML, Schuck P (2014) Analysis
of protein interactions with picomolar binding
affinity by fluorescence-detected sedimentation
velocity. Anal Chem 86:3181–3187
33. Wilfinger WW, Mackey K, Chomczynski P
(1997) Effect of pH and ionic strength on the
spectrophotometric assessment of nucleic acid
purity. BioTechniques 22:474–476, 478–481
34. Zhao H, Casillas E Jr, Shroff H et al (2013)
Tools for the quantitative analysis of sedimentation boundaries detected by fluorescence
optical analytical ultracentrifugation. PLoS
One 8:e77245
Analysis of Protein-DNA Interactions by AUC
421
11. Lewis JS, Jergic S, Dixon NE (2016) The E.
coli DNA replication fork. Enzyme 39:31–88
12. Schaeffer PM, Headlam MJ, Dixon NE (2005)
Protein–protein interactions in the eubacterial
replisome. IUBMB Life 57:5–12
13. Glover BP, McHenry CS (1998) The chi psi
subunits of DNA polymerase III holoenzyme
bind to single-stranded DNA-binding protein
(SSB) and facilitate replication of an
SSB-coated
template.
J
Biol
Chem
273:23476–23484
14. Georgescu RE, Kurth I, O’Donnell ME
(2011) Single-molecule studies reveal the function of a third polymerase in the replisome. Nat
Struct Mol Biol 19:113–116
15. Simonetta KR, Kazmirski SL, Goedken ER et al
(2009) The mechanism of ATP-dependent
primer-template recognition by a clamp loader
complex. Cell 137:659–671
16. Schuck P (1997) Use of surface plasmon resonance to probe the equilibrium and dynamic
aspects of interactions between biological
macromolecules. Annu Rev Biophys Biomol
Struct 26:541–566
17. Mao H, Hart SA, Schink A, Pollok BA (2004)
Sortase-mediated protein ligation: a new
method for protein engineering. J Am Chem
Soc 126:2670–2671
18. Bloom LB, Turner J, Kelman Z et al (1996)
Dynamics of loading the beta sliding clamp of
DNA polymerase III onto DNA. J Biol Chem
271:30699–30708
19. Brown PH, Balbo A, Schuck P (2008) Characterizing protein-protein interactions by sedimentation
velocity
analytical
ultracentrifugation. Curr Protoc Immunol
Chapter 18:Unit 18.15
20. Dam J, Velikovsky CA, Mariuzza RA et al
(2005) Sedimentation velocity analysis of heterogeneous
protein-protein
interactions:
Lamm equation modeling and sedimentation
coefficient distributions c(s). Biophys J
89:619–634
21. Naue N, Curth U (2012) Investigation of
protein-protein interactions of single-stranded
DNA-binding proteins by analytical ultracentrifugation. Methods Mol Biol 922:133–149
22. Schuck P (2010) Diffusion of the reaction
boundary of rapidly interacting macromolecules in sedimentation velocity. Biophys J
98:2741–2751
23. Schuck P (2000) Size-distribution analysis of
macromolecules by sedimentation velocity
ultracentrifugation and Lamm equation modeling. Biophys J 78:1606–1619
24. Lohman TM, Overman LB (1985) Two binding modes in Escherichia coli single strand binding protein-single stranded DNA complexes.
Modulation by NaCl concentration. J Biol
Chem 260:3594–3603
25. Bogutzki A, Naue N, Litz L, Pich A, Curth U
(2019) E. coli primase and DNA polymerase III
holoenzyme are able to bind concurrently to a
primed template during DNA replication. Sci
Rep 9:14460
26. Ton-That H, Liu G, Mazmanian SK, Faull KF,
Schneewind O (1999) Purification and characterization of sortase, the transpeptidase that
cleaves surface proteins of Staphylococcus aureus
at the LPXTG motif. Proc Natl Acad Sci U S A
96:12424–12429
27. Alegria-Schaffer A, Lodge A, Vattem K (2009)
Performing and optimizing Western blots with
an emphasis on chemiluminescent detection.
Methods Enzymol 463:573–599
28. Brautigam CA (2015) Calculations and
publication-quality illustrations for analytical
ultracentrifugation data. Methods Enzymol
562:109–133
29. Zhao H, Schuck P (2015) Combining biophysical methods for the analysis of protein complex
stoichiometry and affinity in SEDPHAT. Acta
Crystallogr D Biol Crystallogr 71:3–14
30. Laue MT, Shah BD, Rigdeway TM, Pelletier
SL (1992) Computer-aided interpretation of
analytical sedimentation data for proteins. In:
Harding SE et al (eds) Analytical ultracentrifugation in biochemistry and polymer science.
The Royal Society of Chemistry, Cambridge,
pp 90–125
31. Owczarzy R, Tataurov AV, Wu Y et al (2008)
IDT SciTools: a suite for analysis and design of
nucleic acid oligomers. Nucleic Acids Res 36:
W163–W169
32. Zhao H, Mayer ML, Schuck P (2014) Analysis
of protein interactions with picomolar binding
affinity by fluorescence-detected sedimentation
velocity. Anal Chem 86:3181–3187
33. Wilfinger WW, Mackey K, Chomczynski P
(1997) Effect of pH and ionic strength on the
spectrophotometric assessment of nucleic acid
purity. BioTechniques 22:474–476, 478–481
34. Zhao H, Casillas E Jr, Shroff H et al (2013)
Tools for the quantitative analysis of sedimentation boundaries detected by fluorescence
optical analytical ultracentrifugation. PLoS
One 8:e77245
Analysis of Protein-DNA Interactions by AUC
421