« Back to Glossary Index

a nuclease is a DNA or RNA cutter (endonuclease) or chewer (exonuclease). “Nuclease” is an umbrella term for protein enzymes (reaction mediators/speed uppers) that cleave the phosphodiester bond connecting DNA or RNA letters (nucleotides). Endonucleases cut somewhere in the middle of the chain, whereas exonucleases chew from one or both ends of the chains (starting at the 5′ end and working towards the 3′ end or going from the 3′ end towards the 5′ end). You can can remember this by thinking of an endoscopy. If you have an endoscopy your doctor sticks a tube with a camera *inside* you to look at your insides. If you use an endo-something-ase, you cut that something *inside* of its sequence. On the other side of things, when scientists look for exoplanets, they’re looking for planets on the “outskirts.” When scientists use exo-something-ases they’re using enzymes (biochemical reaction mediators/speed-uppers) to chew that something from the ends. 

Nucleases have various degrees of specificity. DNases only cut DNA, RNases only cut RNA. Then they subspecialize…

Some endonucleases are really picky – “restriction enzymes” are endonucleases that recognize specific sequences of DNA & cleave them – they’re useful for things like molecular cloning (moving pieces of DNA from one place to another) or mystery-solving – you can use analytical digests for things like seeing if those sequences are present (maybe in one suspect but not another, or in patients with a disease but not those without) – restriction polymorph fragment analysis can be used to cut (or try to cut) DNA & see what pieces you end up with.

Instead of recognizing specific sequences, some nucleases recognize things like structural features and “you don’t belong here’s.” For example, RNase H recognizes DNA hybrids (1 strand DNA bound to 1 strand RNA) & cuts the RNA (but NOT the DNA). If you want to cut single-stranded regions around hybrids, go for S1 nuclease, which can cut up single-stranded DNA or RNA (though it prefers DNA) while leaving alone double-stranded regions – great for seeing where probes bind and stuff. 

If you want to cut DNA but Not RNA, go for DNaseI, which cuts DNA “non-specifically.” But if you want to protect the RNA, make sure that the DNaseI you use is “RNase free” – typically the RNases you’re most worried about are RNase I, which cuts single-stranded RNA “non-specifically” and RNase A, which cuts single-stranded RNA 3’ of C’s & U’s (and leaves a tell-tale signature of a 3’ phosphate & 5’ OH).