A minimum of three nucleotides in the loop are necessary for p-RNA oligomers to assume a hairpin rather than a duplex structure. Such hairpin structures form with comparable ease, as they do in RNA, in spite of the (conjectured) higher rigidity of the p-RNA backbone. Base stacking in p-RNA duplexes is interstrand rather than intrastrand; therefore, dangling bases enhance duplex stability when they are at the 2′-end (and not at the 4′-end).
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Micura et al. (1997) studied this question.
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