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Updated: Mar 13, 2026

Iterative Optimization of DNA Duplexes for Crystallization of SeqA-DNA Complexes
Published on: November 1, 2012
Effect of Methyl Group on Acyclic Serinol Scaffold for Tethering Dyes on the DNA Duplex Stability
Keiji Murayama1, Hiroyuki Asanuma1
1Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.
Abstract:
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.
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