Restriction map

The double digest problem is a formulation of the problem to create a genetic map physical with the aid of restriction enzymes. The idea is, two different restriction enzymes RE1 and RE2 to use that intersect at different recognition sequences. For this, the DNA to be investigated is first copied several times, and it then performed three reactions:

The obtained DNA fragments are subsequently separated, for example, with the aid of gel electrophoresis and therefore obtained the different fragment lengths. It thus creates three fragment length amounts RE1, RE2 and RE1RE2. The task is then to deduce from these quantities, the average positions of the restriction enzymes. As is known, the recognition sequences of the restriction enzymes used, has hence uniquely identifies locations in the sequence.

Example

( the interface is marked with a *, the DNA sequence has a length of 15 kb )

RE1 cuts at the points 4, 7 and 11,

RE2 cuts at the points 5 and 10,

Both blades together at the points 4, 5, 7, 10 and 11

0KB 5kb 10kb 15kb

| ------- * - | ---- * ----- | - * ------- | Only RE1

| ---------- * ---------- * ---------- | Only RE2

| ------- * - * ---- * ----- * - * ------- | Both together

RE1 = { 4kb, 3kb, 4kb, 4kb }

RE2 = { 5 kb, 5 kb, 5 kb }

RE1RE2 = { 4kb, 1kb, 2kb, 3kb, 1kb, 4kb }

Although the double digest problem is NP-complete, a solution might not be unique and the number of solutions grows exponentially, it is a popular mapping method, since the required experiments are easy to perform.