Fluorescence titrations of SSB and SSB with poly(dT) at 22°C and different salt conditions

<p><b>Copyright information:</b></p><p>Taken from "Single-stranded DNA-binding protein of : a biophysical characterization"</p><p>Nucleic Acids Research 2005;33(5):1662-1670.</p><p>Published online 21 Mar 2005</p><p>PMCID:PMC1069009.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p> Solid lines are theoretical binding isotherms for the binding of a multidentate ligand to a linear polymer () with binding site size and cooperative affinity ω· as indicated below. () Circles: 0.375 μM SSB in 0.3 M NaCl, 20 mM KP, 100 p.p.m. Tween-20; = 53.9, ω· = 1.2 × 10 M, = 86.2%. Triangles: 0.375 μM SSB in 1 mM NaCl, 1 mM KP, 100 p.p.m. Tween-20; = 47.5, ω· = 5 × 10 M, = 74.9%. () Circles: 0.29 μM SSB in 0.3 M NaCl, 20 mM KP, 0.1 mM EDTA, 100 p.p.m. Tween-20; = 63.7, ω· = 1.5 × 10 M, = 92%. Triangles: 0.44 μM SSB in 1 mM NaCl, 1 mM KP, 0.1 mM EDTA, 100 p.p.m. Tween-20; = 39.5, ω· = 9.3 × 10 M, = 70%

Interaction of SSB and DNA polymerase III χ subunit detected by analytical ultracentrifugation

<p><b>Copyright information:</b></p><p>Taken from "Single-stranded DNA-binding protein of : a biophysical characterization"</p><p>Nucleic Acids Research 2005;33(5):1662-1670.</p><p>Published online 21 Mar 2005</p><p>PMCID:PMC1069009.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p> Analytical sedimentation velocity centrifugation of 2.65 μM SSB (dotted line) and a mixture of 2.65 μM SSB and 31.8 μM χ (solid line) in 0.3 M NaCl, 20 mM KP at 20°C and 50 000 r.p.m. Differential sedimentation coefficient distributions were obtained using the program SEDFIT (). In the presence of χ, a complex is formed which sediments faster than any of the free proteins. Inset: for different mixtures concentrations of free and bound χ were determined from the areas under the separated peaks of the differential sedimentation coefficient distributions and were used to construct a binding isotherm. The solid line represents the best non-linear least squares fit for independent binding of 2.2 χ molecules to a SSB dimer with = 7.4 × 10 M

SSB and SSB show different influence on the melting behavior of poly(dA–dT)

<p><b>Copyright information:</b></p><p>Taken from "Single-stranded DNA-binding protein of : a biophysical characterization"</p><p>Nucleic Acids Research 2005;33(5):1662-1670.</p><p>Published online 21 Mar 2005</p><p>PMCID:PMC1069009.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p> Samples containing 38 μM nucleotides of poly(dA–dT) in a buffer containing 75 mM NaCl and 20 mM KP were melted in the presence of 3.25 μM SSB (a), 3.25 μM SSB (b) and in the absence of protein (c)

Domain architectures of () protein families sharing homology with the BpuJI nuclease domain identified in this study and () previously characterized Type III Res subunits and the McrBC system

<p><b>Copyright information:</b></p><p>Taken from "Restriction endonuclease BpuJI specific for the 5′-CCCGT sequence is related to the archaeal Holliday junction resolvase family"</p><p></p><p>Nucleic Acids Research 2007;35(7):2377-2389.</p><p>Published online 28 Mar 2007</p><p>PMCID:PMC1874659.</p><p>© 2007 The Author(s)</p> AHJR, the archaeal Holliday junction resolvase domain similar to the C-terminal catalytic domain of BpuJI; for domains of superfamily II helicases, SF-II, the closest homolog of known structure is indicated; HSP90N, the N-terminal domain of HSP90; McrB-N and McrB-C, respectively, the N-terminal DNA binding and the C-terminal GTPase domains of the McrB subunit of 5′-methylcytosine-specific restriction enzyme; DBD?, unclassified putative DNA binding domain; UPF0102, uncharacterized protein family with the predicted single-domain nuclease fold related to AHJRs; Region X and PD-(D/E)XK, endonuclease domains of Type III and McrC restriction enzymes, respectively. Each architecture in (A) is illustrated with a single representative and corresponds to the grouping in the alignment (Supplementary Figure 5B)

The 3′-end directed endonucleolytic activity of the isolated C-terminal domain of BpuJI

<p><b>Copyright information:</b></p><p>Taken from "Restriction endonuclease BpuJI specific for the 5′-CCCGT sequence is related to the archaeal Holliday junction resolvase family"</p><p></p><p>Nucleic Acids Research 2007;35(7):2377-2389.</p><p>Published online 28 Mar 2007</p><p>PMCID:PMC1874659.</p><p>© 2007 The Author(s)</p> () Cleavage of the PCR fragment by the C-terminal domain. Total of 1 nM of the PCR fragment, 5′-labelled in bottom strand, was incubated with 3 μM of the C-terminal domain at 4°C. Aliquots were removed at timed intervals (indicated above the relevant lanes) and analysed by electrophoresis through the standard sequencing gel. Lanes G, A, T, C are sequence ladders. () Cleavage of oligonucleotide duplexes by the C-terminal domain. Total of 2 nM of oligoduplex, 3′-labelled (upper gels) or 5′-labelled (lower gels) in top strand, was incubated with 100 nM of the C-terminal domain at 25°C. Aliquots were removed at timed intervals (indicated above the relevant lanes) and analysed by electrophoresis through denaturing 20% polyacrylamide. In cartoons below the gels the position of the label is indicated by a star, the arrows show the position of initial cleavage

Analytical gel filtration experiments to determine the MvaI oligomeric state and the stoichiometry of DNA binding for the oligoduplex 1 shown in ()

<p><b>Copyright information:</b></p><p>Taken from "Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically"</p><p></p><p>Nucleic Acids Research 2007;35(6):2035-2046.</p><p>Published online 7 Mar 2007</p><p>PMCID:PMC1874612.</p><p>© 2007 The Author(s)</p> Elution profiles were recorded simultaneously at 260 and 280 nm and deconvoluted to obtain separate curves for the MvaI (blue) and DNA (red) concentration. () MvaI alone, () DNA alone, () mixture with a 2:1 molar excess of MvaI over DNA, () stoichiometric mixture, () mixture with a 2:1 molar excess of DNA over MvaI, () calibration curve for Superose ™ 12 HR 10/30 column (Amersham Biosciences) with standards from Biorad (vitamin B-12, 1.35 kDa; myoglobin, 17 kDa; ovalbumin, 44kDa; IgG, 150 kDa and thyroglobin, 670 kDa)