[2] Mirkin is known for his development of nanoparticle-based biodetection schemes, the invention of dip-pen nanolithography (recognized by National Geographic as one of the top 100 scientific discoveries that changed the world), and contributions to supramolecular chemistry, nanoelectronics, and nanooptics.

[2][7] He was a NSF postdoctoral research fellow at Massachusetts Institute of Technology where he worked with Professor Mark S. Wrighton on microelectrode devices for electrocatalysis.

[2][7] A common strategy used by Mirkin's group is the use of the unique properties of spherical nucleic acids (SNAs), spherical arrangements of nucleic acids with or without organic or inorganic nanoparticle cores, to enable the synthesis of novel materials and colloidal crystals, the development of high sensitivity probes for chemical and medical diagnostic purposes, and single-entity structures capable of intracellular gene regulation.

SNAs are the cornerstone of Luminex's FDA-cleared Verigene system (now used in over half of the world's top hospitals), EMD Millipore's SmartFlare platform (licensed to AuraSense, Inc.[1] and Holden Pharma), and seven drugs in human clinical trials.

[12] Mirkin is a co-founder of multiple companies, including NanoInk,[13] Nanosphere (acquired by Luminex for $83M in 2016 [14]), Azul 3D,[15] TERA-print,[16] Exicure,[17] and Stoicheia.