Today, biology is virtually all based on massively parallel sequencing, long-strand sequencing, and metagenomic; looking back at old restriction mapping is not straightforward (at least for me).
For instance, in this seminal paper (Marini and Landy, Virology 1977;76:196 - https://www.sciencedirect.com/science/article/pii/0042682277902963), the authors used essentially three enzymes (Hinc, Hind II, Hind III) to determine the position of the "common core" of homology between Escherichia coli and lambda phage genomes that allows homology recombination, a segment known as att site. The phage att site was called POP’ and the bacteria att site was called POB’.
They had available two classes of phage mutants:
One class is comprised of those phage which carry a prophage att site in place of the normal phage att site. The second class of mutant phage, designated POΔ’ and ΔOP’, carry partial phage att sites. The “Δ” indicates the “non-att” DNA which has been transposed to lie adjacent to the common core by the deletion event.
The authors also reasoned that
To identify the att-containing Hind fragment, 11 deletion mutants of A centering around the crossover region for integration were used. Three of the deletions extend rightward from “0” [att] and should thus be missing the P’ arm of the att site. These comprise the POA’ class of mutants. Five of the deletions extend leftward from “0”. They should be missing the left arm of the att site and are designated ΔOP’ mutants. Two others contain deletions that began to the left of att and continue past att on the right; thus, these crossover deletions lack the entire POP’ region. A final mutant has a deletion slightly offset to the left of the att site. Every rightward deletion mutant, should lack the Hind fragment that contains the att site, since a portion of the site is in the deleted region of all POΔ’ phage. Similarly, the mutants with deletions extending to the left would fail to generate some of the wild-type restriction products.
And now for the punch line:
The Hind wild-type fragment containing POP’ [the core element of att, that is "O"] would be identified by virtue of the fact that it would be the only fragment missing from both rightward and leftward deletion mutants.
They drew an ideal map associated with these concepts:
Is it possible to explain such reasoning in a more accessible way?
Thank you
