We propose a nano-photonic waveguide structure by DNA-directed self-assembled fabrication. In this paper, we focus on the study of quantum dot (QD) behavior under optical stimulation in terms of gain, absorption, and emission characteristics. Both continuous wave (CW) and pulsed operations are considered and the results are compared utilizing the CdSe/ZnS and In0.47Ga0.53As/InP core/shell material systems. Gain coefficients reach optima at pump powers of 0.055 and 0.05 nW for the former and 0.11 and 0.019 μW for the latter in 100 ps pulsed and CW cases, respectively. Due to their unique properties and size, QDs provide a means to create integrated photonic circuits on the nanoscale. Accordingly, the optical propagation of a QD waveguide array in a single line formation is simulated and demonstrates a viable subdiffraction limit optical energy transfer for high coupling coefficient between adjacent QDs. A proposed fabrication process by DNA-directed self-assembly is also described.