Covalent incorporation of methyl red dyes into double-stranded DNA for their ordered clustering.
An ordered dye cluster of Methyl Reds was formed in double-stranded DNA by hybridizing two complementary DNA-dye conjugates, each involving a Methyl Red moiety on a threoninol linker and a 1,3-propanediol spacer arranged alternately in the middle of the DNA sequence. In the duplex, Methyl Reds from each strand were axially stacked antiparallel to each other, as determined from NMR analysis. This clustering of Methyl Reds induced distinct changes in both UV/Vis and CD spectra. Single-stranded DNA-Methyl Red conjugates on D-threoninol linkers and (1,3-propanediol) spacers exhibited broad absorption spectra with lambda(max) at around 480 nm, and almost no CD was observed at around the absorption maximum of Methyl Red. However, as Methyl Reds were clustered by hybridization, lambda(max) shifted towards shorter wavelengths with respect to its monomeric transition. This hypsochromic shift increased as the number of Methyl Red molecules increased. Furthermore, a positive couplet was also strongly induced here. These dye clusters are H-aggregates, in which molecular excitons are coupled. The positive couplet demonstrates that the clusters on D-threoninol form a right-handed helix. In contrast, the induced CD became much weaker with Methyl Red on L-threoninol, which intrinsically prefers counterclockwise winding. Thus, mutual orientation of the stacked dye molecules was controlled by the chirality of the linker.
Kashida
Hiromu
H
Research Center for Advanced Science and Technology, The University of Tokyo, Komaba, Meguro-ku, Japan.
Tanaka
Masayuki
M
Baba
Seiki
S
Sakamoto
Taiichi
T
Kawai
Gota
G
Asanuma
Hiroyuki
H
Komiyama
Makoto
M
D001391:Azo Compounds / Q000737:chemistry*; D002942:Circular Dichroism; D004247:DNA / Q000138:chemical synthesis / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D013050:Spectrometry, Fluorescence; D013056:Spectrophotometry, Ultraviolet
D001391:Azo Compounds; C008492:methyl red; D004247:DNA