Developed at Harvard Medical School, this invention provides nucleic acid arrays specifically designed for the assay of DNA-dependent protein:protein binding and/or physical interactions between proteins and nucleic acid molecules. Intermolecular analyses enabled by this technology are advantageously performed in massively-parallel fashion under uniform reaction conditions. This technology enables researchers to:

- Screen for polypeptides that bind nucleic acid sequences of interest.

- Highlight potential gene regulatory elements.

- Identify candidate co-regulated genes based upon their affinity for a given trans-regulator.

- Identify nucleotides or amino acids that mediate specific DNA:protein or protein:protein interactions.