To determine the substrate specificity of A3A, we systematically quantified the affinity of A3A for nucleic acid substrates as a function of substrate sequence, length, secondary structure, and solution pH. We identified the A3A preferred ssDNA binding motif, (T/C)TC(A/G) and found binding correlated with enzymatic activity. Also, we determined that A3A can bind RNA in a sequence specific manner. Surprisingly, A3A’s signature sequence was necessary but not sufficient to account for A3A’s high affinity for ssDNA. Significantly, A3A bound more tightly to the motif in longer oligonucleotides, and in the context of a hairpin loop. Using recently published structures of A3As complexed with ssDNA from our lab and others, we propose a structural model for the molecular mechanism for this enhanced affinity where inter-DNA interactions contribute to A3A recognition of the cognate sequence. This model provides insights into how the nucleotides flanking the canonical TC sequence may contribute to substrate sequence preference of A3A.