Mechanism of extraordinary DNA digestion by pepsin.

Recently, the protein-specific enzyme pepsin was found be capable of digesting nucleic acids unexpectedly. In this study, the effects of DNA sequence specificity, purine content (AG content), depurination and length on the nucleic acid (NA) digestion by pepsin were investigated. The results showed that pepsin functioned similar as endonuclease, and presented a moderate sequence preference compared with restriction enzymes and non-specific nuclease. The digestion was specific (sequence dependent to some extent), and pepsin preferred to cleave purine-rich sequences. The digestion of favorable sequence was dramatically accelerated when the purine base at the cleavage site was removed (created an apurinic (AP) site). However, the AP site did not help to cleave the sequence that pepsin could not cleave originally. Moreover, the results indicated that pepsin preferred to digest longer DNA (e.g. > 59 bases) than shorter one, and sequence shorter than 30 bases was barely digested. The mechanism of DNA digestion by pepsin was also discussed.