Endonuclease-polynucleotide complex

For the complexation of double-stranded DNA, a more elaborate polynucleotide morphology has been designed via the introduction of homopolynucleotide sequences on the ends for SPG binding [54]. Poly(dA) 80-mer was introduced at both ends of DNA, forming loops which provide protection from degradation by endonucleases, an approach adopted from viruses. 

If naked DNA (that is, DNA that is not protein-complexed) is partially digested with a nonspecific endonuclease that randomly cuts double strands, a broad smear of polynucleotide fragments is observed in an electrophoresis gel. If the same experiment is conducted with chromatin, or even with whole nuclei (which the nuclease can easily penetrate through the nuclear pores), the random DNA cleavage yields a series of bands that are multiples of approximately 200 base pairs. This indicates that "naked" DNA is present only at regularly spaced points. 

Whereas the structure of mRNA determines its susceptibility to degradative enzymes, the detailed mechanisms are complex. In prokaryotes, the enzymes involved include two endonucleases (RNase E and RNase III) and two exonucleases (polynucleotide phosphorylase and RNase II). Other nucleases may be active in particular cases such as phage infection. In eukaryotes, a major pathway involves removal of the 3 poly(A) tail (deadenylation), followed by removal of the 5 cap, which renders the mRNA susceptible to rapid endonucleolytic degradation in the 5 3 ... 

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