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Recombination is a significant source of genetic variation amongst RNA viruses and may occur even in the absence of enzymes (Chetverina et al., 1999). Non-enzymatic recombination remains more enigmatic than its enzymemediated counterpart and the structural rules by which it occurs are still largely unknown. Recent studies of nonenzymatic recombination, between fragments of human immunodeficiency virus 1 (HIV-1) RNA and human influenza A virus RNA (M2-RNA)(Nechaev et al., 2009), have indicated patterns in the sequences of recombinants, alluding to particular secondary structural motifs. The 3D structural arrangements of such motifs may provide clues which will help to elucidate the mechanisms of non-enzymatic RNA recombination. Here we aim to investigate the 3D structures of recombinant RNA molecules in an attempt to uncover some of the structural rules underpinning non-enzymatic …