The structure of plastid DNA (ptDNA) provides insight concerning its replication, repair, maintenance, and stability. We are studying DNA molecules and their association with proteins in plastid nucleoids as maize seedlings develop from the newest cells in the basal meristem to the oldest in the leaf tip. When observing unbound ptDNA from light-grown seedlings, we have found that ptDNA copy number and molecular integrity decline from complex-branched forms (Type I) in the meristem, to a mixture of smaller complex and simple forms (Type II) in the stalk, and small simple forms (Type III) in the leaf blade. In contrast, preliminary examination of unbound stalk ptDNA showed that for the dark-grown seedlings ptDNA is maintained at high copy numbers, with large complex forms. Furthermore, DNA fibers connected to these complexes were longer in dark-grown than light-grown stalk. We will now continue to examine unbound ptDNA in the meristem and leaf blade from dark-grown seedlings. Once finished examining all samples of unbound dark-grown ptDNA, we will analyze nucleoid-associated ptDNA and deproteinized ptDNA of dark- and light-grown seedlings by gel electrophoresis and fluorescence microscopy. For the basal meristem of light- and dark-grown seedlings, in nucleoid-associated ptDNA, we expect similar high-integrity Type I ptDNA, since this is where replication is highest. In contrast, we expect major structural differences in the nucleoid-associated leaf blade ptDNA, with small Type III in light-grown and high-integrity complex Type I forms in dark-grown plants. We propose that replication and repair occurs exclusively on nucleoid-associated ptDNA and that unbound ptDNA is susceptible to nuclease degradation. Therefore, we expect complex forms for nucleoid-associated ptDNA and small, degraded molecules for the non-nucleoid fraction. On a larger scale, this research will be important for genetically modifying maize tissue, because we will know more about the structural integrity of the DNA we are targeting.