The use of direct-write dip-pen nanolithography (DPN) to generate covalently anchored, nanoscale patterns of oligonucleotides on both metallic and insulating substrates is described. Modification of DNA with hexanethiol groups allowed patterning on gold, and oligonucleotides bearing 5'-terminal acrylamide groups could be patterned on derivatized silica. Feature sizes ranging from many micrometers to less than 100 nanometers were achieved, and the resulting patterns exhibited the sequence-specific binding properties of the DNA from which they were composed. The patterns can be used to direct the assembly of individual oligonucleotide-modified particles on a surface, and the deposition of multiple DNA sequences in a single array is demonstrated.