Double digest problem

The double digest problem is a formulation of the problem of generating a physical gene map with the help of restriction enzymes . The idea is to use two different restriction enzymes RE1 and RE2 that cut at different recognition sequences. To do this, the DNA to be examined is first copied several times and then three reactions are carried out:

complete digestion with restriction enzyme RE1
complete digestion with restriction enzyme RE2
complete digestion with both restriction enzymes RE1 and RE2

The DNA fragments obtained are then separated, for example with the aid of gel electrophoresis , and the different fragment lengths are thus obtained. This results in three sets of fragment lengths RE1, RE2 and RE1RE2. The task is then to derive the cutting positions of the restriction enzymes from these quantities. Since the recognition sequences of the restriction enzymes used are known, positions on the sequence have been clearly identified. ${\ displaystyle \ Delta}$ ${\ displaystyle \ Delta}$ ${\ displaystyle \ Delta}$

example

(the interfaces are marked with *, the DNA sequence is 15kb)

RE1 cuts at points 4, 7 and 11,

RE2 cuts at points 5 and 10,

both cut together at points 4, 5, 7, 10 and 11.

0kB 5kb 10kb 15kb

| ------- * - | ---- * ----- | - * ------- | only RE1

| ---------- * ---------- * ---------- | only RE2

| ------- * - * ---- * ----- * - * ------- | both together

${\ displaystyle \ Delta}$ RE1 = {4kb, 3kb, 4kb, 4kb}

${\ displaystyle \ Delta}$ RE2 = {5kb, 5kb, 5kb}

${\ displaystyle \ Delta}$ RE1RE2 = {4kb, 1kb, 2kb, 3kb, 1kb, 4kb}

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

literature

João Setubal, João Meidanis: Introduction to Computational Molecular Biology . PWS Publishing Company, 1999, ISBN 0-534-95262-3 , pp. 145-146 . - double digest problem is there as a Restriction Site Mapping referred