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Results
In vitro selection and sequence analysis of Asp f 1 decapeptide-binding aptamers
Thirteen rounds of in vitro selection were used to isolate aptamers that show favorable binding properties to the Asp f 1 IgE-binding decapeptide. Thirty-three clones derived from aptamers remaining in the final round were sequenced. Sequence alignment using the ClustalX software program revealed no single consensus sequence that is conserved among the entire Rapamycin of sequenced clones ( Supplementary Table S1). Examination of the sequences reveals a strong tendency towards C-richness, with most clones containing close to or above 50% cytosine residues. Secondary structural prediction using mfold did not reveal any two aptamers that share an exact similar structural folding.
Binding studies
Ten clones randomly selected from the 33 sequenced aptamers, together with a control random aptamer, were tested for their individual abilities to bind immobilized Asp f 1 decapeptide. The results of the binding assays are shown in Fig. 1.