title: Bulge-like asymmetric heterodye clustering in DNA duplex results in efficient quenching of background emission based on the maximized excitonic interaction.
abstract: Asymmetric dye clusters with a single fluorophore (Cy3) and multiple quenchers (4'-methylthioazobenzene-4-carboxylate, methyl red, and 4'-dimethylamino-2-nitroazobenzene-4-carboxylate) were prepared. The dye and one-to-five quenchers were tethered through D-threoninol to opposite strands of a DNA duplex. NMR analysis revealed that the clusters with a single fluorophore and two quenchers formed a sandwich-like structure (antiparallel H-aggregates). The melting temperatures of all the heteroclusters were almost the same, although structural distortion should become larger, as the number of quenchers increased. An asymmetric heterocluster of a single fluorophore and two quenchers showed larger excitonic interaction (i.e., hypochromicity of Cy3), than did a single Cy3 and a single quencher. Due to the larger exciton coupling between the dyes, the 1:2 heterocluster suppressed the background emission more efficiently than the 1:1 cluster. However, more quenchers did not enhance quenching efficiency due to the saturation of exciton coupling with two quenchers. Finally, this asymmetric 1:2 heterocluster was introduced into the stem region of a molecular beacon (MB; also known as an in-stem MB) targeting the fusion site in the L6 BCR-ABL fusion gene. With this MB design, the signal/background ratio was as high as 68 due to efficient suppression of background emission resulting from the maximized excitonic interaction.
authors: Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya, Japan.
authors: Taiga
authors: T
authors: Fujii
authors: Yuichi
authors: Y
authors: Hara
authors: Takuya
authors: T
authors: Osawa
authors: Hiromu
authors: H
authors: Kashida
authors: Xingguo
authors: X
authors: Liang
authors: Yasuko
authors: Y
authors: Yoshida
authors: Hiroyuki
authors: H
authors: Asanuma
mesh_terms: D000605:Amino Alcohols / Q000737:chemistry; D001391:Azo Compounds; D001483:Base Sequence; D002072:Butylene Glycols / Q000737:chemistry; D002232:Carbocyanines; D002264:Carboxylic Acids / Q000737:chemistry; D004247:DNA / Q000032:analysis*; D005456:Fluorescent Dyes / Q000737:chemistry*; D016313:Genes, abl; D006801:Humans; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008968:Molecular Conformation; D015335:Molecular Probes / Q000737:chemistry*; D008969:Molecular Sequence Data; D009691:Nucleic Acid Denaturation; D009930:Organic Chemicals; D013050:Spectrometry, Fluorescence; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D013696:Temperature
chemical_list: D000605:Amino Alcohols; D001391:Azo Compounds; D002072:Butylene Glycols; D002232:Carbocyanines; D002264:Carboxylic Acids; D005456:Fluorescent Dyes; D015335:Molecular Probes; D009930:Organic Chemicals; C089187:cyanine dye 3; C532652:threoninol; C057718:6-(Dimethylamino)-2-((1E,3E)-4-(4-(dimethylamino)phenyl)-1,3-butadien-1-yl)-1-ethylquinolinium perchlorate; C008492:methyl red; D004247:DNA