Quick questions on restriction enzymes?

[sameeralord]

Hello everyone,

[PLAIN]http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/R/RestrictionEnzymes.gif

1. Restriction enzymes cut only sugar phospahte bonds right. So in the formation of sticky bonds for example in BamHl, how does the hydrogen bonds between the molecules break. When sugar phophate bonds on each strand break, does it pull on the free side dissociating the hydrogen bonds. Can these pieces stick back easily again or do they need a ligase?

2. Can restriction enzymes cut single stranded DNA?

3. Also how do these detect specific sequences of DNA. Do they have some complementary area that binds with the specific region.

Thanks

 

[Ygggdrasil]

1. Restriction enzymes cut only sugar phospahte bonds right. So in the formation of sticky bonds for example in BamHl, how does the hydrogen bonds between the molecules break. When sugar phophate bonds on each strand break, does it pull on the free side dissociating the hydrogen bonds. Can these pieces stick back easily again or do they need a ligase?

Restriction enzymes typically leave sticky ends that are only a few nucleotides long. The energy from forming only a few hydrogen bonds is very low, comparable to thermal energy. Therefore, although the two sticky ends can bind together, the thermal energy present in solution is enough to break the two pieces apart. Therefore, the two ends only spend a fraction of time bound.

2. Can restriction enzymes cut single stranded DNA?

No. Restriction enzymes recognize only double-stranded DNA.

3. Also how do these detect specific sequences of DNA. Do they have some complementary area that binds with the specific region.

The answer varies with each restriction enzyme. Usually, the restriction enzyme will have some protein segment, such as an alpha helix, that inserts itself into the major groove of the DNA helix. There, the protein side chains can interact with exposed hydrogen bond donors and hydrogen bond acceptors.

Here's a site that talks about protein-DNA interactions in general and may be of some use:
http://higheredbcs.wiley.com/legacy/college/boyer/0471661791/structure/protein_dna/protein_dna.htm