Logic of double-digest restriction mapping

    Enzyme 1 cuts a linear DNA molecule into two fragments, implying a single cut site; Enzyme 2 produces three fragments, implying two cut sites. We start by arbitrarily placing the Enz1 cut site cloer to left end of the DNA (top map).  Comparison of the Enz2 single- and 1x2 double-digest patterns shows that the two larger fragments are conserved, so Enz1 must cut the smallest (3Kb) Enz2 fragment. The smallest fragment cannot be at the left end (2nd map), because Enz1 would cut the DNA beyond it. Similarly, the largest (8Kb) fragment produced by Enz2 cannot be at the left end of the map, since then the Enz1 cut site would fall within that fragment (4th map). Only if the middle-sized fragment (6Kb) were on the left, followed by the 3Kb fragment,  would Enz1 cut the 3Kb into the observed 1 and 2Kb fragments (3rd & 5th maps). The combined map shows the positions of the three RE sites.

    [HOMEWORK: Using the same logic, drawn a map starting with the assumption that the Enz1 cut site is closer to the right end of map].

Figure after © 2000 by Griffiths et al. ; text © 2010 by Steven M. Carr