Functional molecules such as
dyes (
Methyl Red,
azobenzene, and
Naphthyl Red) were tethered on D-
threoninol as base surrogates (
threoninol-
nucleotide), which were consecutively incorporated at the center of natural
oligodeoxyribonucleotides (ODNs). Hybridization of two ODNs involving
threoninol-
nucleotides allowed interstrand clustering of the
dyes on D-
threoninol and greatly stabilized the duplex. When two complementary ODNs, both of which had tethered Methyl Reds on consecutive D-threoninols, were hybridized, the melting temperature increased proportionally to the number of Methyl Reds, due to stacking interactions. Clustering of Methyl Reds induced both hypsochromicity and narrowing of the band, demonstrating that Methyl Reds were axially stacked relative to each other (H-aggregation). Since hybridization lowered the intensity of circular dichroism peaks at the pi-pi* transition region of
Methyl Red (300-500 nm), clustered Methyl Reds were scarcely
wound in the duplex. Alternate hetero
dye clusters could also be prepared only by hybridization of two ODNs with different
threoninol-
nucleotides, such as
Methyl Red-
azobenzene and
Methyl Red-
Naphthyl Red combinations. A combination of
Methyl Red and
azobenzene induced bathochromic shift and broadening of the band at the
Methyl Red region due to the disturbance of exciton interaction among Methyl Reds. But interestingly, the
Methyl Red and
Naphthyl Red combination induced merging of each absorption band to give a single sharp band, indicating that exciton interaction occurred among the different
dyes. Thus, D-
threoninol can be a versatile scaffold for introducing functional molecules into
DNA for their ordered clustering.