Abstract: The present invention provides methods and apparatus for the optical fingerprinting of nucleic acid molecules. In certain embodiments, the invention provides methods for labeling nucleic acid molecules using-site-specific nucleic acid binding partners that bind to nucleic acids without cleaving the molecule. The nucleic acid binding partners can be labeled directly with a fluorophore, such as a quantum dot (QD), or indirectly. Examples of suitable binding partners include cut-deficient restriction endonucleases (cdREs), transcription factors, the binding domains of nucleic acid polymerases, antibodies and the like. The methods disclosed make the assembly of fingerprint contigs easier and allows for digitizing the results so as to provide for easier computer manipulation and assembly. The invention also includes a microarray, the microarray designed to provide for easy deposition and high-throughput fingerprinting. The invention also provides for methods of using the microarrays.