The ability to place DNA on surfaces with increased and controllable reactivity is of fundamental importance in the development of next-generation DNA and protein biochips. The present work demonstrates the ability to control both the localization of the DNA on a surface and its reactivity by a self-assembly approach that is dependent on two variables: DNA structure and surface environment. Here we utilize a two-step adsorption scheme to control the adsorption and reactivity of DNA embedded within two types of alkyl thiol monolayers (either methyl-terminated or hydroxyl-terminated). In addition, by changing the structure of the chemisorbed DNA from fully single stranded to a 50% double stranded at its side adjacent to the surface, we were able to observe a clear dependence of DNA reactivity on both the DNA structure and the type of alkyl thiol monolayer covering the surface. The adsorption and the reactivity yield of the DNA were monitored either by its ability to hybridize to a complementary target molecule or by an enzymatic reaction involving DNA phosphorylation catalyzed by the enzyme T4 polynucleotide kinase.