The present invention provides methods for purifying nucleic acid molecules, wherein each method includes the steps of: (a) synthesizing nucleic acid molecules in a reaction mixture; (b) contacting the nucleic acid molecules with a proteinase for a period of time sufficient to degrade protein in the reaction mixture; (c) applying the nucleic acid molecules treated in accordance with step (b) to a size-limiting filter so that at least some of the nucleic acid molecules are trapped on the filter; and (d) washing the filter with a phosphate buffer having a pH in the range of from about 5.7 to about 8.5.