This method frequently leads to problems with attachment of the DNA to the slide. This will decrease the amount of DNA that is bound, or lead to a weaker attachment, which could result in DNA washing away during hybridization. This problem also occurs when spotting high concentrations of DNA on slides, further suggesting that there are actually a limited number of attachment sites on glass. To avoid this problem, all DNA is purified before spotting to remove unincorporated nucleotides as well as proteins and partial DNA products. In all cases, these coatings have some amount of background fluorescence.
Silinated slides exhibit low autofluorescence.
Since the quality of the silination can vary dramatically between batches, prescanning each slide is recommended before DNA is spotted onto it. A number of investigators have concluded that it is necessary to prepare arrays in a dedicated cleanroom facility in order to avoid problems with dust particles interfering with the interpretation of slides. While that is a laudable objective, it may not be necessary in all cases. An optional HEPA filtration unit also reduces problems with dust. The robot should be cleaned on a routine basis to remove any dust that may have infiltrated the system.