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DNA on one side of the recognition sequence, within twenty nucleotides of the recognition site. Type II restriction enzymes discovered to date collectively recognize over 200 different DNA sequences.

Type II restriction enzymes can cleave DNA in one of three possible ways. In one case, these enzymes cleave both DNA strands in the middle of a recognition sequence, generating blunt ends. For example:

(The notations 5' and 3' are used to indicate the orientation of a DNA molecule. The numbers 5 and 3 refer to specific carbon atoms in the deoxyri-bose sugar in DNA.)

These blunt ended fragments can be joined to any other DNA fragment with blunt ends, making these enzymes useful for certain types of DNA cloning experiments.

Different restriction enzymes cleave DNA at specific recognition sequences. Cleaving a single piece of DNA with multiple restriction enzymes creates a "DNA fingerprint." The pattern of fragments can be compared to similar DNA from another source treated with the same enzymes, to determine if the two are identical or different.

Type II restriction enzymes can also cleave DNA to leave a 3' ("three prime") overhang. (An overhang means that the restriction enzyme leaves a short single-stranded "tail" of DNA at the site where the DNA was cut.) These 3' overhanging ends can only join to another compatible 3' overhanging end (that is, an end with the same sequence in the overhang).

Finally, some type II enzymes can generate 5' overhanging DNA ends, which can only be joined to a compatible 5' end. ▼

In the type II restriction enzymes discovered to date, the recognition sequences range from 4 bp to 9 bp long. Cleavage will not occur unless the full length of the recognition sequence is encountered. Enzymes with a short recognition sequence cut DNA frequently; restriction enzymes with 8 or 9 bp sequences typically cut DNA very infrequently, because these longer sequences are less common in the target DNA.

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