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Effect of Methyl Group on Acyclic Serinol Scaffold for Tethering Dyes on the DNA Duplex Stability

Acyclic serinol derivatives are useful scaffolds for tethering dyes within DNA duplexes. Here we synthesised an inverse l‐threoninol (il‐threoninol) scaffold and compared its effect on DNA duplex stability to other acyclic artificial nucleic acid scaffolds that are based on d‐threoninol, l‐threoninol, and serinol. When planar trans‐azobenzene was incorporated into the DNA duplex through a single bulge‐like motif (the wedge), the il‐threoninol scaffold stabilised the duplex most efficiently. When scaffolds were incorporated in complementary positions (dimer motif) or in three adjacent positions (cluster motif), d‐threoninol was the most stabilising. CD spectra indicated that the effect of scaffold on the duplex stability was closely related to the winding induced by each scaffold. When trans‐azobenzene was photo‐isomerised to non‐planar cis‐azobenzene, il‐threoninol destabilised the duplex most strongly, irrespective of the number of artificial residues incorporated. The properties of the il‐threoninol scaffold make it a useful tether for dyes or other functionalities.