The transmission electron microscopy (TEM) is used for taking images of the nanodiamonds and/or the resulting DNA-origami structures. As the TEM offers nanometer resolution the nanodiamonds can be easily resolved. However the contrast of DNA structures is too low. In order to make them visible, one has to stain the samples with uranyl acetate.
An AFM (Atomic Force Microscope) is a type of scanning probe microscope which can have a sub-nanometer resolution. We used it to survey our origami-structures and its modifications.
Nanodrop is a spectrophotometer. One can measure the absorption spectra of any solution in the visible and near UV-range. Many materials have a characterisitc absorption spectrum. We used this fact to check which chemicals are left after purification of a sample. Furthermore one can determine the nucleid acid concentration of a sample.
FluoroLog (Fluorescence spectrometer)
FluoroLog is a fluorescence spectrometer which is able to measure both the emission and excitation spectra. It was used to roughly determine the optical properties of the NV centers of the used nanodiamonds. A detailed documentary of FluoroLog can be found at: http://loci.wisc.edu/files/loci/FL3manual.PDF
In order to purify and/or wash our samples we had to centrifuge them. We used it frequently in order to remove free material after functionlizing the nanodiamonds.
Gel electrophoresis is a method to seperate DNA-structures by their size and charge. Depending on the size of the DNA-structures we had to use two different types of gel. As polyacrylamide gel has typically a comparatively small pore size it is ideally suited to seperate small DNA fragments or molecules. In contrast to that, we had to use agarose gel to analyze our origami structures.
caDNAano is 3D design tool for DNA origami. We used it for designing our origami structures.