title: De novo design of functional oligonucleotides with acyclic scaffolds.
abstract: In this account, we demonstrate a new methodology for the de novo design of functional oligonucleotides with the acyclic scaffolds threoninol and serinol. Four functional motifs-wedge, interstrand-wedge, dimer, and cluster-have been prepared from natural DNA or RNA and functional base surrogates prepared from d-threoninol. The following applications of these motifs are described: (1) photoregulation of formation and dissociation of a DNA duplex modified with azobenzene, (2) sequence-specific detection of DNA using a fluorescent probe, (3) formation of fluorophore assemblies that mimic quantum dots, (4) improved strand selectivity of siRNA modified with a base surrogate, and (5) in vivo tracing of the RNAi pathway. Finally, we introduce artificial nucleic acids (XNAs) prepared from d-threoninol and serinol functionalized with each of the four nucleobases, which have unique properties compared with other acyclic XNAs. Functional oligonucleotides designed from acyclic scaffolds will be powerful tools for both DNA nanotechnology and biotechnology.
authors.affiliation: Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan. asanuma@nubio.nagoya-u.ac.jp.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Asanuma
authors.forename: Hiromu
authors.initials: H
authors.lastname: Kashida
authors.forename: Yukiko
authors.initials: Y
authors.lastname: Kamiya
mesh_terms: D004247:DNA / Q000032:analysis; D005456:Fluorescent Dyes / Q000737:chemistry; D015394:Molecular Structure; D009841:Oligonucleotides / Q000737:chemistry*; D010777:Photochemistry; D045663:Quantum Dots
chemical_list: D005456:Fluorescent Dyes; D009841:Oligonucleotides; D004247:DNA
keywords: fluorescent probes; helical structures; nucleic acids; oligonucleotides; photochemistry