The backbone of double-stranded DNA has a structure that is to a large extent independent of the base sequence, although minor variations in local conformational parameters certainly occur. Consequently, the intrinsic chemical reactivity of each phosphodiester bond (or sugar ring) is independent of its position in the polynucleotide chain, as is evidenced by the near-random distribution of sites of modification or cleavage by small chemical reagents (Nielsen 1990). On the other hand, the reactivity of phosphodiester bonds in double-stranded DNA to enzymes such as nucleases can vary widely from position to position. This reflects the relatively large surface of interaction between DNA and proteins, which permits sequence preferences through a number of sequence- or conformation-sensitive bonds. Thus, many proteins have been found to act on DNA only at sites with unique nucleotide sequences. Even "sequence nonspecific" enzymes frequently display some degree of sequence preference. The structural basis of sequence-specific interactions...
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Mizuuchi et al. (1993) studied this question.