There are three main analytical methods for determining nucleotide sequences in oligodeoxyribonucleotides. In two of the methods. Mobility Shift Analysis (1 ,2 ) and Chemical Cleavage Analysis (4 ,5 ), sequences are inferred by visualizing patterns of fragments derived from the oligomer by enzymatic or chemical cleavage, whereas the third, Nested Set Analysis (6 ), involves the direct determination of the terminal nucleotide for each member of a nested set of oligomer subfragments. For analytical work on chemically-synthesized oligomers, the direct nested set method has some advantage over the other two, especially in cases involving oligomers whose purity might be in question or in analyses requiring assignments of identities and locations of modified or unusual bases. Brief summaries of the experimental procedures used in the three methods, together with a detailed description of all the steps involved in the Nested Set Analysis, are given below.