We describe the synthesis of small (2-nm diameter) gold nanoparticles densely functionalized with thiolated DNA (DNA-Au NPs) and a method to separate these particles from excess free DNA after synthesis. The separation method utilizes the thermodynamically enhanced binding properties of 2-nm DNA-Au NPs, compared to free excess DNA, to selectively hybridize these small particles to larger (15-nm diameter) DNA-Au NPs and form aggregates that can be isolated by simple centrifugation. These 2-nm DNA-Au NPs are obtained in a 46% overall yield, have a high surface coverage of DNA (64.8 +/- 6.4 pmol/cm(2)), and as a result, exhibit increased melting temperatures and cooperative melting properties.