There is no particular “advantage for bacteria” other than “it works”. There is also a PDB Molecule of the Month item on this, although unfortunately the bending of the DNA is not apparent in the images there.Ĭomment on Last Two Sentences of Question This answer is based on chapter sections 9.3.2 and 9.3.3 of Berg et al., which is available online at NCBI Bookshelf and is well worth reading in full. DNA lacking the recognition site is not cleaved by the restriction enzyme because it does not bind specifically to the protein so that the magnesium ion remains too far away. Methylation of the adenine nucleotide in the recognition sequence prevents hydrogen bonding of the enzyme to the DNA. Compare bending a thin pipe over one’s knee, applying equal force with both hands.) (The dimeric nature of enzyme allows force to be exerted at two points, to produce the bend. This binding causes the DNA to bend (C) bringing a catalytic magnesium ion into a position in which it can interact with phosphate of the phosphodiester bond that is being cleaved (D). The ‘palindromic’ nature of the recognition/cleavage site of restriction endonucleases, such as EcoRV (illustrated here) results in a form of symmetry (A) that allows a dimeric enzyme - that forms a tunnel - to bind symmetrically at that site in the DNA (B). Way that facilitates the endonuclease reaction. Another blunt cutter is EcoRV with a recognition sequence of GAT | ATC.The palindromic symmetry of the restriction site allows a dimericĮnzyme to bind the DNA in a manner that bends the double helix in a DNA digested with EcoRI can be ligated back together with another piece of DNA digested with EcoRI, but not to a piece digested with SmaI. While endonucleases cut DNA, ligases join them back together. This distinction in cutting is important because an EcoRI sticky end can be used to match up a piece of DNA cut with the same enzyme in order to glue or ligate them back together. Restriction enzymes hydrolyze covalent phosphodiester bonds of the DNA to leave either “sticky/cohesive” ends or “blunt” ends. By using 6-cutters or 8-cutters, the sequences occur throughout large stretches rarely, but often enough to be of utility. Calculate the reverse complement of the whole forward strand to finish. Reverse the order of the reverse complement ( CTA) and add it to the end of the forward strand - TAGCTA. Calculate the reverse complement of the sequence - ATC. Molecular biologists also tend to use these special molecular scissors that recognize palindromes of 6 or 8. Starting with the original sequence - TAG. Therefore, the reverse complement of one strand is identical to the other. With respect to DNA, there are 2 strands that run antiparallel to each other. Some examples of palindromes: RACE CAR, CIVIC, A MAN A PLAN A CANAL PANAMA. Palindromic sequences are the same sequence forwards and backwards. The restriction that is useful to biologists is usually palindromic DNA sequences. This is a very strong covalent bond while the weaker hydrogen bonds maintain their interactions and double strandedness.Īs the name implies, restriction endonucleases (or restriction enzymes) are “ restricted” in their ability to cut or digest DNA.
Endonucleases are enzymes that can hydrolyze the nucleic acid polymer by breaking the phosphodiester bond between the phosphate and the pentose on the nucleic acid backbone. \)ĭNA can be cut by restriction endonucleases ( RE).
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