title: Effect of Methyl Group on Acyclic Serinol Scaffold for Tethering Dyes on the DNA Duplex Stability.
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.
authors: Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.
authors: Keiji
authors: K
authors: Murayama
authors: Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.
authors: Hiroyuki
authors: H
authors: Asanuma
mesh_terms: D001391:Azo Compounds / Q000737:chemistry; D001483:Base Sequence; D002942:Circular Dichroism; D004396:Coloring Agents / Q000737:chemistry*; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D007536:Isomerism; D009690:Nucleic Acid Conformation; D011412:Propanolamines / Q000737:chemistry*; D011409:Propylene Glycols / Q000737:chemistry*; D013056:Spectrophotometry, Ultraviolet; D013816:Thermodynamics
chemical_list: D001391:Azo Compounds; D004396:Coloring Agents; D011412:Propanolamines; D011409:Propylene Glycols; D004247:DNA; C009850:azobenzene; C072422:serinol
keywords: Azo compounds; DNA; UV/Vis spectroscopy; oligonucleotides; photochromism