Base pair terminal fraying

The d(ATGCAT)2 Duplex. From NMR studies of the d(ATGCAT)2 duplex, it was known that, even at the lowest temperature studied, the terminal AT base-pairs were partially open or frayed . By partitioning the calorimetrically measured enthalpy into contributions from the internal AT and GC pairs using data from the d(GCGCGC)2 duplex and other measurements on AT pairs (not reproduced here), Breslauer and colleagues were able to show that what the NMR spectra interpreted as open pairs were also energetically ruptured. 

The 3 -+5 exonuclease activity plays an important role in polymerization in proof reading the base pair formed at each polymerization step. The enzyme checks the nature of each base-paired primer terminus before the polymerase proceeds to add the next nucleotide to the primer. It thus supplements the capacity of the polymerase to match the incoming nucleotide substrate to the template. A mismatched terminal nucleotide on the primer activates a site on the enzyme which results in the hydrolysis of the phosphodiester bond and the removal of the mismatched residue. The function of this 3 - 5 exonuclease activity is therefore to recognize and cleave incorrectly or non-base paired residues at the 3 -end of DNA chains. It will therefore degrade single stranded DNA and frayed or non-base paired residues at the ends of duplex DNA molecules provided they terminate in a 3 -hydroxyl group. 

---