Tuning Exciton Coupling of Merocyanine Nucleoside Dimers by RNA, DNA and GNA Double Helix Conformations

Abstract

Exciton coupling between two or more chromophores in a specific environment is a key mechanism associated with color tuning and modulation of absorption energies. This concept is well exemplified by natural photosynthetic proteins, and can also be achieved in synthetic nucleic acid nanostructures. Here we report the coupling of barbituric acid merocyanine (BAM) nucleoside analogues and show that exciton coupling can be tuned by the double helix conformation. BAM is a nucleobase mimic that was incorporated in the phosphodiester backbone of RNA, DNA and GNA oligonucleotides. Duplexes with different backbone constitutions and geometries afforded different mutual dye arrangements, leading to distinct optical signatures due to competing modes of chromophore organization via electrostatic, dipolar, π-π-stacking and hydrogen-bonding interactions. The realized supramolecular motifs include hydrogenbonded BAM-adenine base pairs and antiparallel as well as rotationally stacked BAM dimer aggregates with distinct absorption, CD and fluorescence properties.

Rhodium(III)-Catalyzed Synthesis of Diverse Fluorescent Polycyclic Purinium Salts from 6-Arylpurine Nucleosides and Alkynes

“…Fluorescent nucleoside analogs and modified nucleobases can function as natural nucleobases that not only retain their biochemical functionalities, such as hydrogen bonding, base pairing, enzyme incorporation, and π–π-stacking, but also provide enhanced fluorescence properties. They can be incorporated into DNA and RNA with only minimal effects on biochemical function.…”

Solvophobically‐Driven Merocyanine Dye Assembly: Predominant Dipole‐Dipole Interactions Over Hydrogen‐Bonding

“…In summary, we have demonstrated the self‐assembly of a merocyanine dye ( MC−OH ) in its crystal structure and in aqueous solvent (with 10% dioxane), which is still less familiar [14d] in small molecule‐based building blocks. In the present work we demonstrate that solvophobically‐assisted dipole‐dipole interactions can produce stable larger aggregates of MC−OH in water, resulting in the formation of stable core‐shell nanodiscs by antiparallel π‐stacking even at a very low CAC (∼1.1 x10 −5 M), which is rarely reported for merocyanine dye assembly in polar solvent.…”

“…Previously reported molecular designs for organized merocyanine dye assembly have been majorly executed in organic less polar solvents that are known to increase the binding strength of the dipole‐dipole interactions of the dye [8,16] . In a slightly different approach, we herein studied the self‐assembly of MC−OH (equipped with a free hydroxy‐group) in highly polar aqueous environment, [14d] as we envisaged that larger aggregates from antiparallel dimers of merocyanine can be achieved through increased dispersion forces in water between the exposed hydrophobic π‐faces. Our results reveal that under specific conditions, where there is a possibility of intermolecular H‐bonding, the dye stacks in a manner so as to satisfy the H‐bonding, predominantly.…”

Modification at the C2′-O-Position with 2-Methylbenzothiophene Induces Unique Structural Changes and Thermal Transitions on Duplexes of RNA and DNA

“…This was supported via modeling, where increasing the number of sodium atoms led to structural changes on the duplex, overall (Table ). The fact that the T m values at 235 and 260 nm are the same indicates a high degree of cooperativity among the BT-units and nucleobases ) into a more thermodynamically stable structure, resulting in optimal nucleobase interactions; and (4) increased temperatures lead to denaturation of the duplex.…”