Figure 1.

Rational modular design of composite RNA aptamers. (A) Depiction of the general scheme. Functional ‘loops’ are combined and organized with the help of structural elements. All elements are connected via double-stranded stems into a putative composite molecule. In the assembled product of the hypothetical example, thick black lines represent double-stranded stems; solid red dots represent individual aptamers. (B) Predicted most stable secondary structure of the Aptabody Sa-B52 by mfold (35). This molecule comprises six parts, including four aptamers and two three-way junctions. Each part is indicated. The thick bar in the middle signifies the sequence corresponding to the BamHI site on the template. (C) Predicted most stable secondary structure of the Aptabodies R06-B52 (upper left) and Sa-TAR (lower right) by mfold, annotated as in (B).