It was successful to pattern a Au substrate with DNAs that were fed through a NFP chip. Nine dots in a 3x3 array were deposited. The imaging was done with a commercial tip since the NFP did not produce good imaging.
Single-strand DNAs were diluted in PBS (phosphate buffered saline) to have a concentration of ~10 nM. The DNA was provided by Dr. Sergey Rozhok of Mirkin group. The single-strand DNA has a sulfur group on one end so that it can be immobilized on a Au substrate.
The holding times for each row were 32 s, 16 s, and 8 s (from the top). However, it was observed that the size of dots does not distinguishably vary. Dr. Yu-Hsu Chang, a post-doc in Mirkin group, who observed our experiments, mentioned that he had also difficulties in controlling the size of DNA dots when he did his own experiments with DNAs. More experiments will be pursued regarding this issue.
According to Dr. Chang, although it is most likely that the deposited materials are DNA, it may be still possible that the materials consist of not only DNA, but also salt from the saline, or even only solidified salt without DNAs. He suggested scanning the substrate after rinsing with DI water to remove any deposited salt mixed with the DNA.
We tried to follow his suggestion to confirm that the deposited materials contain DNA. For such a trial, scratches were needed as a reference on the surface because it initially did not have any; Dirt on the surface was used as a reference. The substrate was taken out for scratches, and also the reservoir of the NFP chip was refilled. However, we could not reproduce the patterning. Because of that, it was not possible to check the existence of salt. It was speculated that the channel was clogged when the solution dried. More experiments will follow next week.
For activities with Raymond next week, single-strand DNA with sulfur group on one end and fluorescence tag on the other end will be tried. The existence of DNA in the patters can be readily confirmed by fluorescence microscopy. With that verified, single-strand DNA will be pattered for hybridization with a complementary strand tagged with fluorescence. Abigail Lytton-Jean, a grad student in Mirkin group, is an expert in DNA, and she promised to supply aforementioned DNAs.
Raymond and I also worked together last week for DNA patterning. The DNA was diluted in DMF (dymethyl formamide) mixed with MgCl2, which is the same type of solution used in a paper on DNA patterning from Mirkin group (Demers et al., Science 296, 1836 (2002)). Since we ended up with making puddles, Raymond suggested to use PBS this time. However, a couple of post-docs in Minkin group including Dr. Chang suggested that it would the best to stick to the recipe reported in the paper by Demers because it is verified and practiced many times since then. Accordingly, two types of solution will be used next week: DMF+MgCl2 and PBS.
The NFP chip used last week was inspected using SEM to show molecules deposited in the cavities of the volcano tips.
