enzymes that break down dna catalyze the hydrolysis of the covalent bonds that join nucleotides together. what would happen to dna molecules treated with these enzymes? enzymes that break down dna catalyze the hydrolysis of the covalent bonds that join nucleotides together. what would happen to dna molecules treated with these enzymes? the phosphodiester linkages of the polynucleotide backbone would be broken. the two strands of the double helix would separate. the pyrimidines would be separated from the deoxyribose sugars. all bases would be separated from the deoxyribose sugars.