You won't change the chemical at all”it's still DNA with every one of its nucleotides present and accounted for...
You're making the mistake here of thinking that isomers of the same chemical should act the same. They don't at all. Benzene, 2,4-hexadiyne, and 1,5-hexadiyne each have six carbons and six hydrogens, but are very distinct chemically. Two DNAs with differenr ordering of the same bases are just as different as two proteins with different ordering of the same amino acids - and that can be VERY different.