Subhashis Jana

Highly solvatochromic fluorescent naphthalimides: design, synthesis, photophysical properties and fluorescence switch-on sensing of ct-DNA.

We report the design, synthesis and photophysical properties of highly solvatochromic donor/acceptor substituted naphthalimide based fluorophores. The synthesized naphthalimides containing propargyl ends showed highly solvatochromic intramolecular charge transfer (ICT) feature as was revealed from the UV-visible, fluorescence photophysical properties of these fluorophores and DFT/TDDFT calculation. Fluorescence life times for the imide fluorophores were also measured in different solvents. The solid state photophysical property of donor substituted naphthalimide 1 showed promising for future application in material sciences. Furthermore, both the donor/acceptor substituted naphthalimide fluorophores 1-2 were exploited in sensing calf-thymus DNA via switch-on fluorescence response. The propargyl linker containing naphthalimides can further be exploited for the synthesis of labeled biomolecular building blocks.

Synthesis, photophysical properties of triazolyl-donor/acceptor chromophores decorated unnatural amino acids: Incorporation of a pair into Leu-enkephalin peptide and application of triazolylperylene amino acid in sensing BSA.

The research in the field of design and synthesis of unnatural amino acids is growing at a fast space for the increasing demand of proteins of potential therapeutics and many other diversified novel functional applications. Thus, we report herein the design and synthesis of microenvironment sensitive fluorescent triazolyl unnatural amino acids (UNAA) decorated with donor and/or acceptor aromatic chromophores via click chemistry. The synthesized fluorescent amino acids show interesting solvatochromic characteristic and/or intramolecular charge transfer (ICT) feature as is revealed from the UV-visible, fluorescence photophysical properties and DFT/TDDFT calculation. HOMO-LUMO distribution shows that the emissive states of some of the amino acids are characterized with more significant electron redistribution between the triazolyl moiety and the aromatic chromophores linked to it leading to modulated emission property. A pair of donor-acceptor amino acid shows interesting photophysical interaction property indicating a FRET quenching event. Furthermore, one of the amino acid, triazolyl-perylene amino acid, has been exploited for studying interaction with BSA and found that it is able to sense BSA with an enhancement of fluorescence intensity. Finally, we incorporated a pair of donor/acceptor amino acids into a Leu-enkephalin analogue pentapeptide which was found to adopt predominantly type II β-turn conformation. We envisage that our investigation is of importance for the development of new fluorescent donor-acceptor unnatural amino acids a pair of which can be exploited for generating fluorescent peptidomimetic probe of interesting photophysical property for applications in studying peptide-protein interaction.

Solvatochromic fluorescent cyanophenoxazine: design, synthesis, photophysical properties and fluorescence light-up sensing of ct-DNA

We report our new methodology for the Mn2+-catalysed synthesis of donor–acceptor substituted classical fluorescent phenoxazine which showed high solvatochromic emission properties and ct-DNA sensing efficiency via a light-up fluorescence response.

Trichromophoric pentapeptide: impact of β-sheet conformation on dual path to excimer emission and sensing of BSA

We are reporting two mechanisms for excimer emission in a designed trichromophoric pentapeptide wherein the triazolo aromatic amino acid scaffold (ArTAA) nucleates β-sheet conformation. The designed unnatural fluorescent pentapeptide shows an excimer emission either via FRET from the scaffold (ArTAA) acting as a donor or via direct excitation of an acceptor chromophore, TPyAlaDo. Moreover, it serves as an effective fluorescence light-up probe for studying protein–peptide interactions.

Hybridization accompanying FRET event in labeled natural nucleoside-unnatural nucleoside containing chimeric DNA duplexes.

Förster resonance energy transfer (FRET) is a highly efficient strategy in illuminating the structures, structural changes and dynamics of DNA, proteins and other biomolecules and thus is being widely utilized in studying such phenomena, in designing molecular/biomolecular probes for monitoring the hybridization event of two single stranded DNA to form duplex, in gene detection and in many other sensory applications in chemistry, biology and material sciences. Moreover, FRET can give information about the positional status of chromophores within the associated biomolecules with much more accuracy than other methods can yield. Toward this end, we want to report here the ability of fluorescent unnatural nucleoside, triazolylphenanthrene ((TPhen)BDo) to show FRET interaction upon hybridization with fluorescently labeled natural nucleosides, (Per)U or (OxoPy)U or (Per)U, forming two stable chimeric DNA duplexes. The pairing selectivity and the thermal duplex stability of the chimeric duplexes are higher than any of the duplexes with natural nucleoside formed. The hybridization results in a Förster resonance energy transfer (FRET) from donor triazolylphenanthrene of (TPhen)BDo to acceptor oxopyrene of (OxoPy)U and/or to perylene chromophore of (Per)U, respectively, in two chimeric DNA duplexes. Therefore, we have established the FRET process in two chimeric DNA duplexes wherein a fluorescently labeled natural nucleoside ((OxoPy)U or (Per)U) paired against an unnatural nucleoside ((TPhen)BDo) without sacrificing the duplex stability and B-DNA conformation. The hybridization accompanying FRET event in these classes of interacting fluorophores is new. Moreover, there is no report of such designed system of chimeric DNA duplex. Our observed phenomenon and the design can potentially be exploited in designing more of such efficient FRET pairs for useful application in the detection and analysis of biomolecular interactions and in material science application.

Sonogashira Cross-Coupling: Alkyne-Modified Nucleosides and Their Applications

Abstract Ever since the initial report of the Songashira cross-coupling reaction in 1975, researchers from a number of disciplines have been utilizing the method to synthesize conjugated alkynes having wider applications in chemistry, biology, and material sciences. Synthetic chemists and molecular designers have been engaged in modifications of the reaction conditions in an attempt to synthesize alkynylated conjugated molecules/architectures. As a result, the Sonogashira reaction has recently found wide application ranging from the synthesis of natural products and pharmaceuticals, and material science areas such as molecular electronics, dendrimers, and conjugated polymers, to nanoscience. In the generation of modified biomolecular building blocks with new properties and novel functionalities, such as in nucleic acids chemistry, Sonogashira coupling (classical or a modified) has also found widespread application in the generation of modified alkynylated nucleosides. In particular, it is the most powerful tool for installing an improved fluorescence property into natural nucleosides via covalent attachment of a microenvironment-sensitive fluorophore through a rigid acetylenic linker either at C5/C6- of pyrimidine or at C2/C8- of purines or C7- of deaza-purines. Such fluorescently labeled nucleosides and corresponding oligonucleotides are being widely utilized as probes for structural studies of nucleic acids, sequencing, molecular diagnostics, SNP typing, and other applications relating to genomics. Thus, this chapter summarizes classical Sonogashira coupling and its modifications and contributions to the field of nucleic acid chemistry, with particular emphasis on work from our laboratories. Highlights include the synthesis of fluorescently labeled natural nucleosides and their various applications, such as in DNA analysis, monitoring hybridization events, delineating the structure and dynamics of DNA, probing DNA lesions, searching for light-harvesting DNA- based materials, and in other biotechnological and material science applications. Finally, the recent fascinating applications of Sonogashira coupling in the fields of genetic alphabet expansion, DNA-based light-harvesting materials design, double coding nucleosides strategy, and post-synthetic modification of nucleic acids, are discussed.

Axially chiral amino acid scaffolds as efficient fluorescent discriminators of methanol–ethanol

We report a unique fluorescence sensor based on an axially chiral unnatural triazolyl aromatic amino acid scaffold (ArTAA) for discrimination of methanol from ethanol via a switch on fluorescence response. All three sensors, the simple scaffold (ArTAA), and the mono- (PyAm-ArTAA) and bis-pyrenyl- (Py2Am-ArTAA) amides, show similar sensitivity and detection limit ranging from 0.5–2.1 v/v% of ethanol. The solid films of these sensors are also found to be effective in sensing ethanol vapour via generation of a distinct and enhanced fluorescence signal. All our experimental results suggest the role of axial chirality of the hairpin-shaped scaffold in differential solvation guided H-bonding interaction and discriminating between ethanol and methanol with a switch-on fluorescence response.