The amplification of genomic Alu elements by retroposition, i.e. by 
reintegration of reverse-transcribed RNA, suggests that Alu RNA plays an 
important role in this process. We report enzymatic studies of the secondary 
structure of Alu RNAs transcribed in vitro from two recently retroposed Alu 
elements. These experiments show that the dimeric organization of an Alu 
sequence is reflected in its RNA folding. Alu subunits fold independently, 
conserving secondary structure motifs of their progenitor 7 SL RNA molecule. 
Energy minimization analysis indicates that this folding pattern is also 
characteristic of different Alu and Alu-like sequences and has been conserved 
since primate divergence. By analogy to 7 SL RNA, the Alu RNA folding may be 
important for specific interactions with proteins. This could indicate a 
physiological function for Alu transcripts. However, this can be also seen as a 
structural adaptation leading to efficient retroposition of these sequence 
elements.