The structural properties of DNA-linked gold nanoparticle materials were examined using synchrotron smallangle X-ray scattering. The materials are composed of 12 or 19 nm diameter gold particles modified with 3′ or 5′ alkylthiol-capped 12-base oligonucleotides and linked with complementary oligonucleotides. Structure factors were derived from scattering intensities, and nearest-neighbor distances were determined from the primary peak in the pair distance distribution functions. The separation between particles was found to increase linearly with DNA linker length for 24, 48, and 72 base pair linkers. For assemblies formed in 0.3 M NaCl, 10 mM phosphate buffer solution, the increment in the interparticle distance was found to be 2.5 Å per base pair. Particle separations in assemblies at lower electrolyte concentration were larger, indicating that dielectric screening modulates the interactions. The effect of DNA sequence was studied with poly-adenine or polythymine spacer sequences incorporated between the alkylthiol and recognition sequences. The assemblies with poly-adenine spacer sequences showed significantly shorter particle separations than the assemblies involving poly-thymine spacers, a consequence of their different affinities for the gold surface. While the scattering data do not display evidence of long-range order, pair distance distribution functions indicate the presence of short-range order.