A few facts about EcoP15I
- Cleaves inversely oriented sites that can be as far a a few kilobases apart Meisel et al., 1992.
- Cleavage is impaired by proteins bound between the sites Meisel et al., 1995.
- Positive bias for adenine stretches on the 5′ or 3′ side of CAGCAG Möncke-Buchner et al., 2009.
- Stimulated by AdoMet and sinefungin Raghavendra & Rao, 2005.
- Single-site cleavage is possible with higher concentration of enzyme (Ahmad and co., 2018).
Used in SuperSAGE, HELP-tagging, nanoCAGE, CAGE. (non-exhaustive list)
Ahmad I, Kulkarni M, Gopinath A, Saikrishnan K.
Nucleic Acids Res. 2018 Jul 6;46(12):6229-6237. doi:10.1093/nar/gky344
Single-site DNA cleavage by Type III restriction endonuclease requires a site-bound enzyme and a trans-acting enzyme that are ATPase-activated.
Nat Protoc. 2012 Feb 23;7(3):542-61. doi:10.1038/nprot.2012.005
Takahashi H, Lassmann T, Murata M, Carninci P.
5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing.
Nature. 1992 Jan 30;355(6359):467-9 doi:10.1038/355467a0
Meisel A, Bickle TA, Krüger DH, Schroeder C.
Type III restriction enzymes need two inversely oriented recognition sites for DNA cleavage.
Meisel A, Mackeldanz P, Bickle TA, Krüger DH, Schroeder C.
EMBO J. 1995 Jun 15;14(12):2958-66
Type III restriction endonucleases translocate DNA in a reaction driven by recognition site-specific ATP hydrolysis.
Protein bound to the DNA between the EcoP15I sites interfers negatively with cleavage.
Sinefungin promotes cleavage of the DNA molecules even if they contain only one EcoP15I site.
“Adenine stretches on the 5′ or 3′ side of CAGCAG led to preferred cleavage of this site.”