Self-assembling of metallic nanoparticles to form well-defined nanostructured structures is a field that has been receiving considerable research interest in recent years. In this field, DNA is a commonly used linker molecule to direct the assembly of the nanoscale building blocks because of its unique recognition capabilities, mechanical rigidity, and physicochemical stability. This study reported our novel approach to generate gold nanoparticle-DNA conjugates bearing specially designed DNA linker molecules that can be used as building blocks to construct nanoassemblies with precisely controlled structure or as nanoprobes for quantitative DNA sequence detection analysis. In our approach, gold nanoparticle-DNA conjugates bearing a specific number of long double-stranded DNA strands were prepared by gel electrophoresis. A restriction endonuclease enzyme was then used to manipulate the length of the nanoparticle-bound DNA. This enzymatic cleavage was confirmed by gel electrophoresis, and digestion efficiency of 90% or more was achieved. With this approach, nanoparticle conjugates bearing a specific number of strands of short DNA with less than 20-base can be achieved.