Sometimes I notice that the dried oligos have a brown color when they have dried. Is this the natural color of DNA or is the brown color a sign of contamination?

Synthetic oligos can appear brownish, white, or clear depending on the prep.  A brownish color is caused by the oxidizer used during the synthesis and is usually most apparent in large scale oligos.  Fortunately, the oligo still functions well in the assay they are used for.

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