Sangita Talukdar

Two giant calix[n]phyrin derivatives namely calix[8]‐ (4) and calix[16]phyrin (5), involving two and four BF₂ units, respectively, were prepared through the condensation of the bis‐naphthobipyrrolylmethene‐BF₂ complex (3) with pentafluorobenzaldehyde. Calix[n]phyrins 4 and 5 display extremely high extinction coefficients (3.67 and 4.82×10⁵ m⁻¹ cm⁻¹, respectively) in the near‐IR region, which was taken as initial evidence for strong excitonic coupling within these cyclic multi‐chromophoric systems. Detailed insights into the effect of excitonic coupling dynamics on the electronic structure and photophysical properties of the macrocycles came from fluorescence, time‐correlated single‐photon counting (TCSPC) and transient absorption (TA) measurements. Support for these experimental findings came from theoretical studies. Theory and experiment confirmed that the coupling between the excitons depends on the specifics of the calix[n]phyrin structure, not just its size.

Two giant calix[n]phyrin derivatives namely calix[8]‐ (4) and calix[16]phyrin (5), involving two and four BF₂ units, respectively, were prepared through the condensation of the bis‐naphthobipyrrolylmethene‐BF₂ complex (3) with pentafluorobenzaldehyde. Calix[n]phyrins 4 and 5 display extremely high extinction coefficients (3.67 and 4.82×10⁵ m⁻¹ cm⁻¹, respectively) in the near‐IR region, which was taken as initial evidence for strong excitonic coupling within these cyclic multi‐chromophoric systems. Detailed insights into the effect of excitonic coupling dynamics on the electronic structure and photophysical properties of the macrocycles came from fluorescence, time‐correlated single‐photon counting (TCSPC) and transient absorption (TA) measurements. Support for these experimental findings came from theoretical studies. Theory and experiment confirmed that the coupling between the excitons depends on the specifics of the calix[n]phyrin structure, not just its size.

Specific sensing of dimeric H45 G-quadruplex DNA using a fluorescence light-up probe, tetrazolylpyrene nucleoside (^TzPyB_Do), is reported.

Much effort has been put forth to develop unnatural, stable, hydrophobic base pairs with orthogonal recognition properties and study their effect on DNA duplex stabilisation. Our continuous efforts on the design of fluorescent unnatural biomolecular building blocks lead us to the synthesis of some triazolyl donor/acceptor unnatural nucleosides via an azide–alkyne 1,3-dipolar cycloaddition reaction as a key step, which we want to report herein. We have studied their photophysical properties and found interesting solvatochromic fluorescence for two of the nucleosides. Photophysical interactions among two donor–acceptor β-nucleosides as well as a pair of α/β-nucleosides have also been evaluated. Furthermore, we have exploited one of the fluorescent nucleosides in studying its interaction with BSA with the help of UV-visible and steady state fluorescence techniques. Our design concept is based on the hypothesis that a pair of such donor/acceptor nucleosides might be involved in π-stacking as well as in photophysical interactions, leading to stabilization of the DNA duplex if such nucleosides can be incorporated into short oligonucleotide sequences. Therefore, the designed bases may find application in biophysical studies in the context of DNA.

In the context of abasic DNA or DNA duplex stabilization, several unnatural nucleosidic/non‐nucleosidic base surrogates have been reported. Toward this end, we have designed and synthesized triazolyl‐aromatic donor chomophores as unnatural nucleoside analogs. These modifications display markedly higher thermal stabilization of abasic DNA duplex in comparison to the stabilization offered by other nucleoside/non‐nucleoside base surrogates reported in the literature. The same oligonucleotide probe containing triazolylphenanthrene nucleotide also offers very good stability of the self‐pair duplex via π‐π stacking interaction and hetero‐pair duplex via charge transfer interaction when paired against triazolyl acceptor aromatic nucleoside. Moreover, the probe in the reverse sequence containing triazolylphenanthrene nucleotide has shown FRET efficiency in a chimeric DNA duplex. The triazolyl nucleotides would expectedly show stability toward exonuclease activity. This unit describes protocols for chemical synthesis of unnatural triazolyl nucleosides and one oligonucleotide probe. The unit also provides a summary of various thermal and photophysical applications of triazolylphenantherene‐containing oligonucleotides. Curr. Protoc. Nucleic Acid Chem. 58:1.32.1‐1.32.27. © 2014 by John Wiley & Sons, Inc.

Dual door entry to exciplex formation was established in a chimeric DNA duplex wherein a fluorescent non-nucleosidic base surrogate (^OxoPyS) is paired against a fluorescent nucleosidic base surrogate (^TPhenB_Do). Packing of the nucleobases via intercalative stacking interactions led to an exciplex emission either via FRET from the donor ^TPhenB_Do or direct excitation of the FRET acceptor ^OxoPyS.

A better than reported abasic duplex stabilization was achieved with the novel triazolylphenanthrene nucleoside ^TPhenB_Do. The large surface area, polarizability and strong stacking propensity of triazolylphenanthrene play a major role in the thermal stabilization of the ^TPhenB_Do–Φ duplex comparable to that of a natural A–T pair via a strong intercalative stacking interaction.

We report the design and synthesis of triazolyl donor/acceptor unnatural nucleosides via click chemistry and studies on the duplex stabilization of DNA containing two such new nucleosides. The observed duplex stabilization among the self-pair/heteropair has been found to be comparable to that of a natural A/T pair. Our observations on the comparable duplex stabilization has been explained on the basis of possible π–π stacking and/or charge transfer interactions between the pairing partners. The evidence of ground-state charge transfer complexation came from the UV–vis spectra and the static quenching of fluorescence in a heteropair. We have also exploited one of our unnatural DNAs in stabilizing abasic DNA.