Overview of restriction enzyme activity... - ...depending on number of bases flanking? (Mar/23/2007 )
I'm wondering if anyone knows a web site that lists the activity of restriction enzymes depending on how many bases are added to the restriction site (when designing primers). I know there is a list on the NEB web site but it only shows the activity for the restriciton site plus a few bases on each end. However if I amplify a DNA framgent with restriction site tailed primers, only the 5' flanking site of the restriciton site is that short (the 3' flanking region is the the whole PCR product). I'm wondering if it is easier for the restriction enzyme to cut the site if there is a long sequence flanking the 3' end compared to only 2-8 bases (as it is described on the NEB web site).
Any ideas? I would greatly appreciate your comments :-)!
I think once the base pair length flanking the restriction site has exceeded the restriction enzyme's footprint, additional length would not improve cutting efficiency.
I agree with perneseblue
As NEB suggest, you need certain number of bases for proper digestion. The efficiency doesnt change by adding more bases.