The Nitrogenous bases of dna form the rungs, linking the Nucleotides strands together through Phosphodiester bonds . Each rung is made up of two bases that link together and because of their chemical nature, A (adenine ) will only link with T (thymine) and G (guanine ) will only link with C (cytosine). Nucleotides are joined together to form two long strands that spiral to build a structure called a double helix. If it looks like a ladder, the phosphate and sugar molecules would be the sides, while the bases would be the rungs.