Mechanisms of restriction endonucleases:

Restriction enzymes have a specific mechanism of action towards their target sequences. The enzyme attaches to DNA sequence and recognizes short specific palindrome sequences as it slides down the DNA. Once it recognizes the restriction site, it cleaves the DNA and finally the enzyme is released from the complex.

 

Usually in English language palindromes are the words that spell similarly even though when they are read in the reverse order.

Palindromes with rotational symmetry also exist, which can be found in the double stranded DNA. The complimentary strands of DNA illustrate this type of arrangement rarely and such sequences serve as the restriction sites for the restriction enzymes. These sequences are very specific for each of the enzymes as their sequences differs from one another

E.G: GAATTC

      CTTAAG

The phosphodiester bonds are broken down between the nucleotides in order to cut the DNA into two. The cutting of DNA by the restriction endonucleases generally results in two types of ends. They are

(i)     Staggered (or) cohesive (or) sticky ends:

Staggered ends are produced by some restriction endonucleases, when the double stranded DNA is cut unevenly. They cut both the strands at different sites which leave single complimentary strands protruding from each of the cut ends. This phenomenon is illustrated below by a sequence from the restriction site of EcoR I.

Even (or) blunt (or) non-sticky ends: Blunt ends are produced when the endonucleases cut the both the strands of the double stranded DNA evenly or in other words at the same place. As a result it will not leave any single strands protruding from the cut ends. This phenomenon is better illustrated below using the results of Hae III enzyme

See Also: Nomenclature of Restriction Endonuclease Classification of Restriction Endonuclease

The fact that different enzymes act in different modes according to its specificity of the short palindrome sequences and in turn produces two ends of either staggered or blunt ends is greatly exploited in gene cloning and r-DNA technology. DNA ligases are the enzymes that are used to seal or stick the DNA fragments together. They are of two types namely Ecoli DNA ligase and T4 DNA ligase, which can seal staggered ends and blunt ends respectively.
The staggered ends are more advantageous than the blunt ends, since the staggered or sticky ends have a complimentary single strand at the end that tends to get bind again exactly as before in the presence of Ecoli DNA ligase enzymes. However it’s not the case with the blunt ends as they are free to bind with any other blunt ends in vicinity in the presence of T4 DNA ligase enzymes.