DNA−Dye Conjugates for Controllable H* Aggregation¹

Abstract

Methyl Red H aggregate of predetermined size is successfully synthesized from the DNA conjugate involving multiple Methyl Red moieties in sequence. In the single stranded state, hypsochromicity monotonically increases with the number of incorporated dyes: the peak maximum of the conjugate involving six Methyl Reds appears at 415 nm, and the shift is as great as 69 nm (3435 cm(-)(1)) with respect to the monomeric transition. This large hypsochromicity accompanied by the narrowing of the band clearly demonstrates that H aggregate is formed in the single strand. H aggregation is further promoted at higher ionic strength. Upon addition of complementary DNA below the T(m), however, this H band disappears and a new peak appears at 448 nm, indicating that aggregated structure is changed by the duplex formation. This spectral change is completely reversible so that the H band at 415 nm appears again above T(m). Thus, aggregated structure can be reversibly controlled by the formation and dissociation of the DNA duplex.

H-Aggregation of Azobenzene-Substituted Amphiphiles in Vesicular Membranes

“…In more detail, going from 10 to 66 mol % a total shift of 8 nm was observed and then from 66 to 75 mol % a shift of 12 nm was reported. By contrast, a gradual increase in H-aggregation was reported recently for a DNA strand, 37 the effect increasing with an increasing number of azobenzene units.…”

Non‐covalent Versus Covalent Control of Self‐Assembly and Chirality of Nile Red‐modified Nucleoside and DNA

“…[14] Similarly, DNA has also been used as the structural scaffold for the helical organization of a series of chromophores including pyrene, [15][16][17][18][19] porphyrin, [20] biphenyl, [21] oligo(p-phenylenevinylene)s [22] etc. and dyes including azobenzene derived dyes, [23] perylene bisimide [24][25][26] etc. It is important to point out that, even though nucleobases and DNA have been independently exploited as the structural scaffold for the guided organization of chromophores and dyes, a direct comparison is elusive.…”

Synthesis and structural properties of oligonucleotides covalently linked to acridine and quindoline derivatives through a threoninol linker

“…In this paper we present the synthesis and the structural properties of oligonucleotides linked to one or several acridine and/or quindoline molecules using the threoninol backbone [10]. The presence of the DNA-intercalating unit at the 3'-end of the oligonucleotides induce a strong stabilization of duplex and quadruplex structures.…”

“…Threoninol has been used to introduce several units of Methyl Red moieties [10], photoactive azobenzenes [11,12], acridine [13], pyrene and perylene [14], tetrathiofulvalene [15] and DNA-binding drugs [8,9] in oligonucleotides. This compound can be obtained enantiomerically pure from commercial sources and have two hydroxyl groups (one primary and one secondary) and one amino group.…”