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The electrophoretic mobility $\mu$ is the proportionality coefficient between drift velocity and a weak applied electric field. Its sign specifies motion relative to the field. When only travel distances are used, the mobility magnitude is often intended. For long linear DNA in a weak-field reptation regime, $|\mu |$ can scale inversely with chain length, whereas free-solution mobility is approximately length-independent. Neither law supplies a universal gel electrophoresis size calibration for arbitrary gel concentration, field strength or molecular topology.

A gel electrophoresis size calibration relates migration distance to known fragment lengths on the same gel. Here is an explicitly chosen model for linear double-stranded DNA, not measured data or a universal law. Let $L$ be the numerical length in base pairs and $d$ the numerical migration distance in millimetres from the wells:The logarithm has a dimensionless argument: $L/100$ is the length divided by 100 base pairs. The chosen DNA ladder fragments $L=100,250,500,1000$ give $d=55.00,50.22,46.61,43.00$, respectively. The gel bands therefore appear in the reverse order of length along the direction of migration.

To invert the calibration, rearrange the logarithm:Our chosen unknown $L=375$ gives $d=48.1116248\dots$, between the 250-base pair and 500-base pair references. Inserting that distance into the inverse recovers 375; retaining only $d=48.11$ gives about $375.12$ base pairs. The extra digits reflect rounding in this model, not the resolving power of a real gel.

For linear interpolation between those two reference gel bands, use the logarithm of length. Here the fraction of the distance from the 500-base pair reference toward the 250-base pair reference is $t={\log }_{10}(500/375)/{\log }_{10}2\approx 0.4150$, giving $L=500(250/500{)}^t=375$. Direct linear interpolation of lengths instead gives approximately $396.24$ base pairs. This difference explains why the choice of calibration coordinates matters. A real calibration must be checked over its usable range; folded RNA or circular DNA does not automatically share the linear double-stranded DNA calibration.

In the weak-field reptation regime of agarose gel electrophoresis, the electrophoretic mobility of a long linear DNA chain scales as $\mu \propto M^{-1}$, where $M$ is its number of base pairs. One way to see the scaling is that the constrained-chain diffusion coefficient scales as $D\propto M^{-2}$, whereas its effective electric charge scales as $M$; the drift response is proportional to $DM$. With the same electric field and running time, the migration distance is therefore $x=\mu Et\propto M^{-1}$. The time cancels from the ratio, givingHere “kbp” means a thousand base pairs, not a rate. The second gel band has traveled farther and corresponds to the shorter chain under this migration model. The inverse-length law applies only over an appropriate migration regime.^[ref].

At very low agarose concentration the mesh becomes too open to sieve these chains effectively. In the free-solution limit the chain's electric charge and friction are both approximately proportional to its length, so both chains have nearly the same electrophoretic mobility and their gel bands cease to separate well. At very high agarose concentration the pores become small and transport is strongly hindered; over a fixed experimental time both chains migrate very little, so their absolute spatial separation again becomes small. Increasing gel concentration can improve resolution over an intermediate range, but not indefinitely.

The numerical result is conditional on the inverse-length reptation law. Actual gel electrophoresis size calibration often uses an empirical approximately linear relation between distance and $\log M$ over a specified range. One known band alone cannot fix that relation's slope. The PDF supplies neither gel concentration nor a calibration curve, so $8.9\mathrm{kbp}$ is the standard model estimate rather than a uniquely calibrated experimental size.