The nucleotides used to build DNA are Adenine, Cytosine, Guanine, and Thymine. For RNA, there is no Thymine; it is replaced with another nucleotide called Uracil. These are actually the names of the nitrogenous bases that nucleotides contain.A nucleotide is made up of a Deoxyribose Sugar, a Phosphate Molecule, and a Nitrogenous Base. We refer to them though by the name of their nitrogenous base.hese are actually the names of the nitrogenous bases that nucleotides contain. A nucleotide is made up of a Deoxyribose Sugar, a Phosphate Molecule, and a Nitrogenous Base. We refer to them though by the name of their nitrogenous base.