xDNA has many applications in chemical and biological research, including expanding upon applications of natural DNA, such as scaffolding. In order to create self-assembling nanostructures, a scaffold is needed as a sort of trellis to support the growth. DNA has been used as a means to this end in the past, but expanded scaffolds make larger scaffolds for more complex self-assembly an option. xDNAs electrical conduction properties also make it a prime candidate as a molecular wire, as its π-π interactions help it efficiently conduct electricity. Its 8-letter alphabet (A, T, C, G, xA, xT, xC, xG) gives it the potential to store 2 times more states per sequence than DNA, where n' is the number of bases in the sequence. For example, combining 6 nucleotides of with B-DNA yields 4096 possible sequences, whereas a combination of the same number of nucleotides created with xDNA yields 262,144 possible sequences. Additionally, xDNA can be used as a fluorescent probe at enzyme active sites, as was its original application by Leonard et al.
xDNA has also been applied to the study of protein-DNA interactions. Due to xDNA's natural fluorescing properties, it can easily be visualized in both lab and living conditions. xDNA is becoming more easy to create and oligomerize, and its high-affinity binding to complementary DNA and RNA sequences means that it can not only help locate these sequences floating around in the cell, but also when they are already interacting with other structures within the cell. xDNA also has potential applications in assays that employ TdT as it may improve reporters, and can be used as an affinity tag for interstrand bonding.