Preparation of supramolecular chromophoric assemblies using a DNA duplex

Abstract

Organization of supramolecular assemblies of chromophores with precisely-controlled orientation and sequence remains challenging. Nucleic acids with complementary base sequences spontaneously form double-helical structures. Therefore, covalent attachment of chromophores to DNA or RNA can be used to control assembly and orientation of chromophores. In this perspective, we first review our recent work on the assemblies of fluorophores (pyrene and perylene) by using natural base pairs. The interaction between dyes can be strictly controlled by means of cluster and interstrand wedge motifs. We then discuss novel artificial base pairs that can suppress the interaction between fluorophores and nucleobases. We incorporated a cyclohexane moiety into DNA, and showed that these artificial base pairs suppressed the electron-hole transfer between fluorophores and nucleobases and enhanced the quantum yields of fluorophores. These base pairs can potentially be used to accumulate fluorophores inside DNA duplexes without decreasing quantum yields.

Recognition of mixed-sequence DNA using double-stranded probes with interstrand zipper arrangements of O2′-triphenylene- and coronene-functionalized RNA monomers

“…45 However, the overlap between the absorption maxima of the triphenylene and nucleobase moieties in the 250–270 nm region precluded a detailed binding mode analysis by UV/Vis signals (results not shown). Steady-state fluorescence emission spectra of X -modified ONs and the corresponding duplexes with cDNA/cRNA ( λ ex = 260 nm, T = 5 °C) exhibit broad and unstructured emission between 350–450 nm (Figure 2 and Figure S2†).…”

Pyrene-modified PNAs: Stacking interactions and selective excimer emission in PNA2DNA triplexes

“…The DNA-induced formation or enhancement of these excimer bands can be explained if a PNA 2 DNA triplex is formed, favoured by the prevalence of pyrimidines in the PNA [22–23]. The PNA 2 DNA triplex, in this sequence, is destabilized by the presence of a pyrimidine base (T) in the 5’-end of the DNA; thus this sequence represents a good model for evaluating the stabilization/destabilization effects due to the presence of pyrene units.…”

Simultaneous binding of a cyclophane and classical intercalators to DNA: observation of FRET-mediated white light emission

“…1,2 FRET based fluorescence colour tuning, with fluorophores incorporated into various scaffolds including polymers, biomolecules, micelles, supramolecular assemblies and nanoparticles, is a widely investigated approach for white light generation. 5,[25][26][27][28] A key component of developing DNA based energy transfer systems is the control of distances between the bound molecules, which has an important role in the DNA mediated energy transfer process. [18][19][20][21][22][23][24] Moreover, the predictable secondary structure, unique binding sites for small molecules and the ability to control the spatial arrangement of chromophores with nanoscale precision make DNA an excellent scaffold for related applications in optoelectronic devices and sensors.…”

“…[3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18] Among these scaffolds, DNA-cationic surfactant complexes have emerged as intriguing candidates for optoelectronic applications in recent years because of their unique material properties, including solubility in organic solvents and the ability to form thermally stable, transparent films. 27,[29][30][31][32][33] This in turn is regulated by apparent binding constants and allosteric factors when multiple chromophores are involved. 5,[25][26][27][28] A key component of developing DNA based energy transfer systems is the control of distances between the bound molecules, which has an important role in the DNA mediated energy transfer process.…”