DNA linkers with different bending angles were employed to mediate the conversion between the 2D hexagonal close-packed (hcp) and square architectures in the aggregates of 13 nm Au nanoparticles directed by oligo-DNA. For terminus thiol-modified (TM) oligo-DNA oriented almost perpendicularly on the particle surface, the architecture is converted from hcp to square with increased bending angle of the linker molecules as a result of increased steric effect. For phosphate backbone sulfur modified (PM) oligo-DNA loaded approximately parallel on the particle surface, the architecture is converted from square to hcp with increased bending angle of the linkers as a result of the decreased steric effect.