What is desalting?
When used with respect to purification of an oligo, the term “desalting” refers to the removal of small molecule organic impurities that result as by-products of synthesis. The only salt present is the DNA itself. The negative charge of the phosphate backbone of the oligo is balanced by a positively charged counter-ion to maintain electroneutrality (typically with ammonium ions). Oligonucleotide post-synthesis involves the removal of protecting groups from the individual bases by incubation in ammonia or another basic reagent. The product can be purified to remove the cleaved base protecting groups and other synthesis by-products. This process is commonly referred to as “desalting”. If you are simply running PCR reactions, your oligos do not need to be desalted. If you are running a kinase reaction, you will want your oligos desalted.
