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We have synthesized acyclicallo-threoninol nucleic acids (allo-aTNAs), artificial xeno-nucleic acids (XNAs) that are diastereomers of acyclic threoninol nucleic acids (aTNAs), and have investigated their supramolecular properties. Theallo-aTNAs formed homo-duplexes in an antiparallel manner but with lower thermal stability than DNA, whereasaTNAs formed extremely stable homo-duplexes. Theallo-aTNAs formed duplexes with complementaryaTNAs and serinol nucleic acid (SNA). The affinities ofL-allo-aTNA were the highest forL-aTNA and the lowest forD-aTNA, with SNA being intermediate. The affinities ofD-allo-aTNA were the reverse. Circular dichroism measurements revealed thatL- andD-allo-aTNAs had weak right-handed and left-handed helicities, respectively. The weak helicity ofallo-aTNAs likely explains the poor chiral discrimination of these XNAs, which is in contrast toaTNAs that have strong helical orthogonality. Energy-minimized structures ofL-allo-aTNA/RNA andL-allo-aTNA/L-allo-aTNA indicated that the methyl group on theallo-aTNA strand is unfavourable for duplex formation. In contrast, the methyl group onL-aTNA likely stabilizes the duplex structurevia hydrophobic effects and van der Waals interactions. Thus, the configuration of the methyl group on the XNA scaffold had an unexpectedly large impact on the hybridization ability and structure.