The decision trees, based on two or three descriptors, predicted whether an aptamer is likely to have good binding affinity and thus appropriate for synthesis and testing. Analysis of the Nalmefene hydrochloride descriptors that were selected by the QSAR process indicates that the most important descriptors are related to the size of the aptamer, the amount of un-paired nucleotides, the size of the largest internal loop in the 2D structure, the amount of un-paired C GW2580 stretches and the numbers of the conformations generated in the 2D calculation. The size of the better-binding aptamers was relatively large: while the normal size of aptamers is between 15 and 45 nucleotides, our aptamers were larger than 45 nucleotides. The amount of un-paired nucleotides in either external or internal loops strongly contributed to the aptamer activity: on average 61% of the nucleotides were un-paired in all the better-binding aptamers. The C stretches also contributed to the binding affinity, with a minimum of eight C nucleotides, but preferably with twenty or more such nucleotides. These quantitative rules may teach us about the factors governing the interaction between the aptamers and influenza virus. The QSAR approach presented in this study may be less relevant to standard aptamers that show sequence sensitivity; however, it may offer an alternative approach to non-standard cases and lead optimization. Unlike other known aptamers, our oligonucleotides�� binding to hemagglutinin was unexpectedly non-sequence-dependent but rather depended on certain non-specific secondary structures, such as loops and C stretches. Moreover it seems that there is no defined binding site on the aptamer. The aptamers inhibited the first stage of the virus �C cell interaction, as indicated by the experiment in low temperature cell culture. This inhibition could have been the result of different mechanisms, including competitive and non-competitive inhibition of hemagglutinin, and interference with other parts of the virus. For this reason it is less likely that viral resistance due to escape mutants will occur, because the interaction is probably not limited to a single binding site that can be changed by a single point mutation.