It has become industry standard to assign synthesis scales based on the amount of starting material for a synthesis. Of the starting material, a substantial proportion may be unavailable for use due to chemical modification or steric problems. The actual yield should be calculated as described above. The physical appearance of the dried oligonucleotide can differ due to small variations that normally occur in the drying conditions. Oligonucleotide appearance in the sample tubes may range from a small, glassy pellet to a relatively large white, fluffy pellet.
Most samples have a white fluffy pellet.
All sample tubes should be microfuged before opening, to prevent loss of any sample that may have been dispersed in the tube during shipping. Normally, oligonucleotides will go into solution immediately upon addition of water or buffer. Before using, microfuge the solution and determine the A260 of the supernatant. This should give an indication of whether the oligonucleotide has completely dissolved. It looks as if there is something insoluble at the bottom of the sample tube.