Consider the goal for the deletions when you are choosing your restriction system. A record of the rationale should be contained in your notebook. The joined ends may be from a single DNA molecule or from different molecules. It is also possible to ligate any two blunt-ended DNA molecules together, although this is considerably less efficient since there is nothing to hold the DNA molecules next to each other. Ligations are used in our experiment to create stable recombinant DNA molecules for use in transformations.
Ligations require planning.
Restriction fragments with protruding ends to be ligated must contain compatible complementary sequences. If orientation of an insert is important, two different ends will increase the probability of the correct orientation. However, in this course, we do not have time to convert protruding ends to blunt ends. The components to be ligated are mixed in a ratio determined by the desired product. If a product is to be inserted, such as in a cloning procedure, an excess of insert of 2 to 3 x the vector concentration is used, and the concentration of DNA is higher to increase the occurrences of intermolecular ligation.