While DNA-directed nano-fabrication enables the high-resolution patterning for conventional electronic materials and devices, the intrinsic self-assembly defects of DNA structures present challenges for further scaling into sub-1 nm technology nodes. The high-dimensional crystallographic defects, including line dislocations and grain boundaries, typically lead to the pattern defects of the DNA lattices. Using periodic line arrays as model systems, we discover that the sequence periodicity mainly determines the formation of line defects, and the defect rate reaches 74% at 8.2-nm line pitch. To suppress high-dimensional defects rate, we develop an effective approach by assigning the orthogonal sequence sets into neighboring unit cells, reducing line defect rate by two orders of magnitude at 7.5-nm line pitch. We further demonstrate densely aligned metal nano-line arrays by depositing metal layers onto the assembled DNA templates. The ultra-scaled critical pitches in the defect-free DNA arrays may further promote the dimension-dependent properties of DNA-templated materials.