title: Reversed assembly of dyes in an RNA duplex compared with those in DNA.
abstract: We prepared reversed dye clusters by hybridizing two RNA oligomers, each of which tethered dyes (Methyl Red, 4'-methylthioazobenzene, and thiazole orange) on D-threoninols (threoninol nucleotides) at the center of their strands. NMR spectroscopic analyses revealed that two dyes from each strand were axially stacked in an antiparallel manner to each other in the duplex, and were located adjacent to the 3'-side of a natural nucleobase. Interestingly, this positional relationship of the dyes was completely the opposite of that assembled in DNA that we reported previously: dyes in DNA were located adjacent to the 5'-side of a natural nucleobase. This observation was also consistent with the circular dichroism of dimerized dyes in which the Cotton effect of the dyes (i.e., the winding properties of two dyes) was inverted in RNA relative to that in DNA. Further spectroscopic analyses revealed that clustering of the dyes on RNA duplexes induced distinct hypsochromicity and narrowing of the band, thus demonstrating that the dyes were axially stacked (i.e., H-aggregates) even on an A-type helix. On the basis of these results, we also prepared heterodimers of a fluorophore (thiazole orange) and quencher (Methyl Red) in an RNA duplex. Fluorescence from thiazole orange was found to be strongly quenched by Methyl Red due to the excitonic interaction, so that the ratio of fluorescent intensities of the RNA-thiazole orange conjugate with and without its complementary strand carrying a quencher became as high as 27. We believe that these RNA-dye conjugates are potentially useful probes for real-time monitoring of RNA interference (RNAi) mechanisms.
authors.affiliation: Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
authors.forename: Taiga
authors.initials: T
authors.lastname: Fujii
authors.forename: Masaaki
authors.initials: M
authors.lastname: Urushihara
authors.forename: Hiromu
authors.initials: H
authors.lastname: Kashida
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Ito
authors.forename: Xingguo
authors.initials: X
authors.lastname: Liang
authors.forename: Maho
authors.initials: M
authors.lastname: Yagi-Utsumi
authors.forename: Koichi
authors.initials: K
authors.lastname: Kato
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Asanuma
mesh_terms: D000605:Amino Alcohols / Q000737:chemistry; D001391:Azo Compounds / Q000737:chemistry; D052160:Benzothiazoles / Q000737:chemistry; D002072:Butylene Glycols / Q000737:chemistry; D004396:Coloring Agents / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D009690:Nucleic Acid Conformation; D011804:Quinolines / Q000737:chemistry; D012313:RNA / Q000737:chemistry*; D034622:RNA Interference
chemical_list: D000605:Amino Alcohols; D001391:Azo Compounds; D052160:Benzothiazoles; D002072:Butylene Glycols; D004396:Coloring Agents; D011804:Quinolines; C532652:threoninol; C051000:thiazole orange; D012313:RNA; C008492:methyl red; D004247:DNA