Difference between EcoRI and HindIII Restriction Enzymes

Restriction enzymes are enzymes that cleave DNA into fragments at particular sites, restriction sites seen in the DNA molecule. Such enzymes are seen in archaea and bacteria, and render a defense mechanism against invading viruses.

Since they are capable of identifying specific base sequences on the DNA and then cleaving each strand at a given place, they are also referred to as ‘molecular scissors’.

While there is a discrepancy in the number regarding the different types of restriction enzymes, (3, 4 or 5), four restriction enzymes have been recognized and categorized, for now, they are –

  • Type I
  • Type II
  • Type III
  • Type IV

These primarily differ in the cleavage site, structure, cofactors and specificity. The type II restriction enzymes differ from type I and III in the way that it cleaves DNA at specific sites in the recognition sites. Others randomly cleave DNA, at times hundreds of bases from the recognition sequence.

Type II enzymes cleave within or at short specific distances from the recognition site. Most of these require magnesium. They are single-function enzymes independent of methylase.

EcoRI and HindIII are two restriction enzymes belonging to the type II restriction enzyme class.

EcoRI Restriction Enzymes

  • These restriction endonuclease enzymes cleave the DNA double helix into fragments are particular sites
  • They form a part of the restriction-modification system
  • They create 4 nucleotide sticky terminals with 5′ end overhangs of AATT
  • Is a homodimer of a 31kDa containing one globular domain of the α/β architecture

HindIII Restriction Enzymes

  • These are type II site-specific deoxyribonuclease restriction enzymes isolated from the Haemophilus influenzae cleaving DNA palindromic sequences. The cofactor involved is Mg2+ through the process of hydrolysis
  • The process leads to the formation of overhanging palindromic sticky ends
  • The cleavage of the very sequence between the AAs leads to 5′ overhangs on the DNA, referred to as sticky ends

Key Difference between EcoRI and HindIII Restriction Enzymes

The table below depicts the difference between EcoRI and HindIII Restriction Enzymes

EcoRI Restriction Enzymes

HindIII Restriction Enzymes

Where is it isolated from?

E.coli species

Haemophilus influenza species

At which specific recognition site does it cut the DNA?



What is their palindromic sequence?



Can Mn2+ be used as a cofactor?



What is its molecular weight?




DNA screening, cloning

DNA sequencing and mapping

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