in capillaries containing agarose solutions: Determination of DNA fragment sizes from concave Ferguson plots using program ElphoFit version 2.0. ______________________________________________________________________________ Component of DNA Nominal Predicted Predicted Predicted Ladder phiX174/HaeIII geometric geometric base pairs free mobility*b (bp) radius*a radius*b *c (10^-5 cm^2 V^-1 s^-1) (nm) (nm) ______________________________________________________________________________ 118 3.7 3.93+-0.14 141+-15 41.2+-0.5*d 3.78+-0.05 125+-5 40.0+-0.2*e ------------------------------------------------------------------------------ 271,286*f 4.92 4.93+-0.18 278+-31 39.4+-0.6*d 4.91+-0.06 275+-10 39.9+-0.2*e ______________________________________________________________________________ *a Calculated from base pairs using Eq.10 of (8). *b Computed from the concave Ferguson plots (Fig.1) using program ElphoFit version 2.0. Part of this program is an algorithm which allows for the simultaneous evaluation of all five Ferguson plots using the nonlinear Eqs.1 to 3. *c Determined from predicted geometric mean radius. *d Assumption of no common free mobility intercept. *e Assumption of a single common free mobility intercept. *f Anomalous electrophoretic migration reported by the manufacturer.Table 1. Electrophoresis
Table 2. Effective fiber parameters derived from the convex Ferguson plots of bacteriophages (Fig.5) in agarose gel electrophoresis*a. _____________________________________________________________________ Fiber Gel concentration (%) parameter 0.4 0.7 1.0 1.3 1.6 ____________________ ______________________________________________ Radius (nm) 24.6 24.0 22.9 21.3 19.3 Total length (10^11 cm/g) 6.8 7.1 7.7 9.0 10.9 Volume (mL/g) 12.8 12.8 12.8 12.8 12.8 Mean pore radius (nm)*b,d 71.7 47.1 33.9 25.0 18.5 Median pore radius (nm)*c,d 52.2 32.7 22.4 15.7 10.9 _____________________________________________________________________ *a Calculation of fiber and pore parameters by program ElphoFit is based on loge(mobility). *b Average pore size; radius of a sphere that can be placed in the spacings of a randomly and uniformly distributed fiber network. *c Size of the most frequent pore population. *d Calculation according to Section (i) of Approximations (1), considering n2L = 0.01*T*l', where n is the number of fibers (fiber centers) in a particular volume, L is half of the individual fiber length, T is the gel concentration in % (g/100 mL) and l' the total fiber length in cm/g [based on loge(mobility)]. The calulation uses P(r>0) = P(r=0) - r, where r is the fiber radius and P the mean or median pore radius.
Table 3. Characterization of two bacteriophages based on
analysis of convex Ferguson plots (Fig.5) using program ElphoFit
version 2.0.
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Bacteriophage Nominal Predicted Predicted
radius*a radius*b free mobility*b
(nm) (nm) (10 5cm V 1 s 1
_____________ _________________________________________________
T3 30.1 29.6 +- 0.4 8.7 +- 0.1
9-P22 31.4 30.2 +- 0.4 14.8 +- 0.2
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*a Determined by low-angle X-ray scattering.
*b Computed from the Ferguson plot (Fig.5) using Eqs.1, 4 and 5