Metal ions play critical roles in chemical, biological, and environmental processes. Various biomolecules have the ability to coordinate with metal ions and form various materials. Nucleobases, nucleosides, and nucleotides, as the essential components of DNA, have emerged as a useful building block for the construction of functional nanomaterials. In recent years, DNA oligonucleotides have also been used for this purpose. We herein review the strategies for the synthesis of soft nanomaterials through the assembly of nucleotides (or DNA) and metal ions to yield various nanoparticles, fibers, and hydrogels. Such coordination methods are simple to operate and can be carried out under ambient conditions. The luminescent, catalytic, and molecular recognition properties of these coordination materials are described with representative recent examples. Their applications ranging from biosensing, enzyme encapsulation, catalysis, templated shell growth to cancer therapy are highlighted. Finally, challenges of this field and future perspectives are discussed.