Sorry, it's short for basepair (bp) of DNA (eg a, c, t, or g). Currently it costs about ten cents a bp to synthesize a particular stretch of sequence from one of the companies in the article (dime a base). An average protein can be encoded by 1 kilo basepair, a small bacterial genome by 1 mega basepair, and a human genome by 6 giga basepair.
Maybe the confusion here is that prices are sometimes spoken of as 'a [currency unit] a [item]' which can be understood as 'one [currency unit] per [item]'.
EDIT: I know what's a base pair. I didn't understand the "penny" and "dime" in this context.