<title>Abstract</title>
Xeno nucleic acids, which are synthetic analogues of natural nucleic acids, have potential for use in nucleic acid drugs and as orthogonal genetic biopolymers and prebiotic precursors. Although few acyclic nucleic acids can stably bind to RNA and DNA, serinol nucleic acid (SNA) and L-threoninol nucleic acid (L-<italic>a</italic>TNA) stably bind to them. Here we disclose crystal structures of RNA hybridizing with SNA and with L-<italic>a</italic>TNA. The heteroduplexes show unwound right-handed helical structures. Unlike canonical A-type duplexes, the base pairs in the heteroduplexes align perpendicularly to the helical axes, and consequently helical pitches are large. The unwound helical structures originate from interactions between nucleobases and neighbouring backbones of L-<italic>a</italic>TNA and SNA through CH–O bonds. In addition, SNA and L-<italic>a</italic>TNA form a triplex structure via C:G*G parallel Hoogsteen interactions with RNA. The unique structural features of the RNA-recognizing mode of L-<italic>a</italic>TNA and SNA should prove useful in nanotechnology, biotechnology, and basic research into prebiotic chemistry.