Base pairs nuclease specificity

The 5 - 3 exonuclease activity is much less specific in its requirements. A base-paired terminus is all that is required for its activity, irrespective of whether the 5 -terminal end is phosphoryl-ated or not. The 5 - 3 nuclease can remove oligonucleotides up to ten residues long from the 5 -end and the activity of this degrada-tive function is markedly enhanced by concomitant DNA synthesis. It is this property of the enzyme which allows the highly... 

It has been shown that cis - DDP, at low platinum/nucleotide ratios selectively inhibits the activity of several restriction endo - and exo nucleases when their cutting sites are adjacent to (d6)n (d )n sequences with n > 2 This demonstrates the sequence specificity of the binding of cis - DDP to DNA (17, 18, 19). GAG and GCG sequences also appear to be selectively involved in base - pair substitution mutagenesis and this suggests the possibility of platinum chelation by two guanines separated by a third base (20). 

One mechanism intrinsic to virtually aU DNA polymerases is a separate 3 5 exonuclease activity that double-checks each nucleotide after it is added. This nuclease activity permits the enzyme to remove a newly added nucleotide and is highly specific for mismatched base pairs (Fig. 25-7). If the polymerase has added the wrong nucleotide, translocation of the enzyme to the position where the next nucleotide is to be added is inhibited. This kinetic pause provides the opportunity for a correction. The 3 5 exonuclease activity removes the mispaired nucleotide, and the polymerase begins again. This activity, known as proofreading, is not simply the reverse of the polymerization reaction (Eqn... 

The specificity of RNase A for a pyrimidine on the 3 side of the phosphodiester bond that is cleaved is evidently ensured by the pair of hydrogen bonds from 0-2 of the pyrimidine to the backbone NH of Thr 45 and a second from the N-4 proton to the side chain OH of the same threonine (Fig. 12-25). Other nucleases, such as ribonuclease T2,762 with different specificities also make use of hydrogen bonding of the base at the 3 side of the cleavage point with backbone amide groupings. 

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