It's important for the cell to distinguish message (RNA) from gene (DNA) in order to preserve the genes intact in an environment where the message is continually broken down and resynthesized. Substituting U for T provides another criterion of specificity to ensure that RNAases will not attack the DNA sequence.


U and T also have somewhat different H bonding potentials that have minor impact in a double helix but have a more significant effect for a single stranded molecule that will form short regions of base pairing. This is important in RNA secondary structure, e.g. the cloverleafs of tRNA.