DNA　base　pairing　has　been　used　for　many　years　to　direct　the　arrangement　of　inorganic　nanocrystals　into　small　groupings　and　arrays　with　tailored　optical　and　electrical　properties.　The　control　of　DNA-mediated　assembly　depends　crucially　on　a　better　understanding　of　three-dimensional　structure　of　DNA-nanocrystal-hybridized　building　blocks.　Existing　techniques　do　not　allow　for　structural　determination　of　these　flexible　and　heterogeneous　samples.　Here　we　report　cryo-electron　microscopy　and　negative-staining　electron　tomography　approaches　to　image,　and　three-dimensionally　reconstruct　a　single　DNA-nanogold　conjugate,　an　84-bp　double-stranded　DNA　with　two　5-nm　nanogold　particles　for　potential　substrates　in　plasmon-coupling　experiments.　By　individual-particle　electron　tomography　reconstruction,　we　obtain　14　density　maps　at　similar　to　2-nm　resolution.　Using　these　maps　as　constraints,　we　derive　14　conformations　of　dsDNA　by　molecular　dynamics　simulations.　The　conformational　variation　is　consistent　with　that　from　liquid　solution,　suggesting　that　individual-particle　electron　tomography　could　be　an　expected　approach　to　study　DNA-assembling　and　flexible　protein　structure　and　dynamics.