 Gel electrophoresis size calibration

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.