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1.
Figure 3.

Figure 3. From: A single zinc finger optimizes the DNA interactions of the nucleocapsid protein of the yeast retrotransposon Ty3.

Structure of (a) wild-type Ty3 NC, (b) Δ1-NCp9, (c) Δ2-NCp9, (d) NCp9 dd and (e) Δ2-NCp9 dd. Basic residues shown in blue and zinc coordinating residues shown in green.

Kathy R. Chaurasiya, et al. Nucleic Acids Res. 2012 January;40(2):751-760.
2.
Figure 4.

Figure 4. From: A single zinc finger optimizes the DNA interactions of the nucleocapsid protein of the yeast retrotransposon Ty3.

Typical force-extension (solid) and release (dashed) curves of (a) DNA only (black) and in the presence of (a and b) 20 nM Ty3 NC mutant Δ1-NCp9. First stretch–release curve shown in green (a and b), and second stretch–release curve shown in blue (b).

Kathy R. Chaurasiya, et al. Nucleic Acids Res. 2012 January;40(2):751-760.
3.
Figure 6.

Figure 6. From: A single zinc finger optimizes the DNA interactions of the nucleocapsid protein of the yeast retrotransposon Ty3.

Typical force-extension (solid) and release (dashed) curves of (a) DNA only (black) and in the presence of (a and b) 3 nM Ty3 NC mutant NCp9 dd. First stretch–release curve shown in green (a and b), and second stretch–release curve shown in blue (b).

Kathy R. Chaurasiya, et al. Nucleic Acids Res. 2012 January;40(2):751-760.
4.
Figure 7.

Figure 7. From: A single zinc finger optimizes the DNA interactions of the nucleocapsid protein of the yeast retrotransposon Ty3.

Typical force-extension (solid) and release (dashed) curves of (a) DNA only (black) and in the presence of (a and b) 13 nM Ty3 NC mutant Δ2-NCp9 dd. First stretch–release curve shown in green (a and b), and second stretch–release curve shown in blue (b).

Kathy R. Chaurasiya, et al. Nucleic Acids Res. 2012 January;40(2):751-760.
5.
Figure 5.

Figure 5. From: A single zinc finger optimizes the DNA interactions of the nucleocapsid protein of the yeast retrotransposon Ty3.

Typical force-extension (solid) and release (dashed) curves of (a) DNA only (black) and in the presence of (ac) 50 nM Ty3 NC mutant Δ2-NCp9. First stretch–release curve shown in green (a and b), second stretch–release curve shown in blue (b and c), and third stretch-release curve shown in red (c).

Kathy R. Chaurasiya, et al. Nucleic Acids Res. 2012 January;40(2):751-760.
6.
Figure 2.

Figure 2. From: A single zinc finger optimizes the DNA interactions of the nucleocapsid protein of the yeast retrotransposon Ty3.

(a and b) Typical force-extension (solid) and release (dashed) curves of λ-DNA in the presence of wild type Ty3 NC. (a) DNA only (black) and 5 nM wild type Ty3 NC (green). (b) 5 nM (green) and 25 nM (blue) wild type Ty3 NC. (c) Change in the transition width ΔF of DNA force-induced melting as a function of wild type Ty3 NC concentration. ΔF = δF – δF0, where δF is the melting transition width in the presence of protein and δF0 = 3.6 (±0.3) pN, the melting transition width of DNA only. Standard error determined from at least three measurements was used to compute error bars for ΔF. A χ2 fit (blue line) to a simple DNA binding isotherm [ and ] yields Kd = 3.5 (±0.5) nM and ΔFsat = 6.2 (±0.4) pN. Protein concentrations significantly above saturation (80–150 nM) were also included in the χ2 fit (data not shown).

Kathy R. Chaurasiya, et al. Nucleic Acids Res. 2012 January;40(2):751-760.
7.
Figure 1.

Figure 1. From: A single zinc finger optimizes the DNA interactions of the nucleocapsid protein of the yeast retrotransposon Ty3.

(a) Typical force-extension (solid) and release (dashed) curves of λ-DNA (black) obtained with optical tweezers. The WLC model (blue line) describes dsDNA. Near the dsDNA contour length, the molecule undergoes a force-induced melting transition, from dsDNA to ssDNA. The FJC model describes ssDNA (red line). Minimal hysteresis is evident in these solution conditions (50 mM Na+, 10 mM HEPES, pH 7.5). (b) Quantification of the hysteresis area ratio for a typical DNA extension and release curve. Force–extension (solid) and release (dashed) curve of DNA in the presence of Ty3 NC Δ2-NCp9 dd are shown in green. The WLC and FJC models are shown in blue and red, respectively. A linear combination of these two models is shown in black, indicating the fraction of ssDNA exposed to solution upon DNA extension. Relative hysteresis is the ratio of A1, the area between the stretch (solid green) and release (dashed green) curves, and A2, the area between the stretch (solid green) and melted DNA fraction (black) curves. (c) Equilibrium dissociation constant Kd determined from change in average melting force ΔFm as a function of protein concentration c fit to a simple DNA binding isotherm [ and ]. Data points for mutant Δ2-NCp9 dd are shown with standard error bars, with a fit (blue line) that yields Kd = 20 (± 1) nM and saturated melting force ΔFmsat = 16 (± 0.5) pN. Kd was estimated for mutants Δ1-NCp9 and NCp9 dd with this method, but could not be obtained for mutant Δ2-NCp9, which did not affect DNA melting force.

Kathy R. Chaurasiya, et al. Nucleic Acids Res. 2012 January;40(2):751-760.

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