Synthesis of solvatofluorochromic 7-arylethynylated 7-deaza-2′-deoxyadenosine derivatives: application to the design of environmentally sensitive fluorescent probes forming stable DNA duplexes

Synthesis and photophysical evaluation of new fluorescent 7-arylethynyl-7-deazaadenosine analogs

Three new fluorescent 7-deaza-2′-deoxyadenosine analogs were synthesized via the Sonogashira cross-coupling reaction of 7-iodo-7-deaza-2′-deoxyadenosine with 1-ethynylpyrene, 2-ethynyl-6-methoxynaphthalene, and 9-ethynylphenanthrene. The spectral properties of these analogs were evaluated in dioxane, EtOH, and H2O to determine their potential for use as environmentally sensitive fluorescent probes. All three analogs displayed large solvatofluorochromicity in H2O, relative to their emission wavelengths in dioxane or EtOH. Moreover, all three analogs exhibited microenvironmental sensitivity of their fluorescence emission intensity, being moderate to high quantum yields in dioxane and EtOH and significantly lower in H2O. Various attempts to perform domino cross-coupling and annuation reactions on 7-deaza-7-alkynyladenine derivatives to form a new fused tricyclic adenine analog were unsuccessful.

A fluorescent 3,7-bis-(naphthalen-1-ylethynylated)-2′-deoxyadenosine analogue reports thymidine in complementary DNA by a large emission Stokes shift

The first example of a fluorescent adenosine analogue possessing simultaneous major- and minor-groove substitution selectively reports base-pairing to thymidine.

Studies of the binding mode of TXNHCH2COOH with calf thymus DNA by spectroscopic methods

In this study, a thioxanthone derivative named 2-(9-oxo-9H-thioxanthen-2ylamino) acetic acid (TX-NHCH2COOH) was used to investigate small molecule and DNA binding interactions. Absorption and fluorescence emission spectroscopy were used and melting studies were used to explain the binding mode of TXNHCH2COOH-DNA. Intrinsic binding constant Kb TXNHCH2COOH was found 6×10(5)M(-1)from UV-Vis absorption spectroscopy. Fluorescence emmision intensity increased by adding ct-DNA to the TXNHCH2COOH and KI quenching experiments resulted with low Ksv value. Additionally, 3.7°C increase for Tm was observed. The observed quenching of EB and ct-DNA complex and increase viscosity values of ct-DNA by addition of TXNHCH2COOH was determined. All those results indicate that TXNHCH2COOH can intercalate into DNA base pairs. Fluorescence microscopy helped to display imaging of the TXNHCH2COOH-DNA solution.

Solvatochromic fluorene-linked nucleoside and DNA as color-changing fluorescent probes for sensing interactions

A nucleoside bearing a solvatochromic push-pull fluorene fluorophore (dCFL ) was designed and synthesized by the Sonogashira coupling of alkyne-linked fluorene 8 with 5-iodo-2'-deoxycytidine. The fluorene building block 8 and labeled nucleoside dCFL exerted bright fluorescence with significant solvatochromic effect providing emission maxima ranging from 421 to 544 nm and high quantum yields even in highly polar solvents, including water. The solvatochromism of 8 was studied by DFT and ADC(2) calculations to show that, depending on the polarity of the solvent, emission either from the planar or the twisted conformation of the excited state can occur. The nucleoside was converted to its triphosphate variant dCFLTP which was found to be a good substrate for DNA polymerases suitable for the enzymatic synthesis of oligonucleotide or DNA probes by primer extension or PCR. The fluorene-linked DNA can be used as fluorescent probes for DNA-protein (p53) or DNA-lipid interactions, exerting significant color changes visible even to the naked eye. They also appear to be suitable for time-dependent fluorescence shift studies on DNA, yielding information on DNA hydration and dynamics.

Development of environmentally sensitive fluorescent and dual emissive deoxyuridine analogues

We designed and developed fluorescent deoxyuridine analogues with strong sensitivity to hydration for the major groove labelling of DNA.

Molecular design of an environmentally sensitive fluorescent nucleoside, 3-deaza-2'-deoxyadenosine derivative: distinguishing thymine by probing the DNA minor groove

An environmentally sensitive fluorescent nucleoside containing a 3-deazaadenine skeleton has been developed, and its photophysical properties were investigated. Newly developed C3-naphthylethynylated 3-deaza-2'-deoxyadenosine ((3nz) A, 1) exhibited dual fluorescence emission from an intramolecular charge-transfer state and a locally excited state, depending upon molecular coplanarity. DNA probes containing 1 clearly discriminated a perfectly matched thymine base on the complementary strand by a distinct change in emission wavelength.

Access to 6-arylpyrrolo[2,3-d]pyrimidines via a palladium-catalyzed direct C–H arylation reaction

A route to 6-arylpyrrolo[2,3-d]pyrimidines via a direct palladium-catalyzed C–H arylation reaction.