Lighting Up DNA with the Environment-Sensitive Bright Adenine Analogue qAN4

The fluorescent adenine analogue qAN4 was recently shown to possess promising photophysical properties, including a high brightness as a monomer. Here we report the synthesis of the phosphoramidite of qAN4 and its successful incorporation into DNA oligonucleotides using standard solid-phase synthesis. Circular dichroism and thermal melting studies indicate that the qAN4-modification has a stabilizing effect on the B-form of DNA. Moreover, qAN4 base-pairs selectively with thymine with mismatch penalties similar to those of mismatches of adenine. The low energy absorption band of qAN4 inside DNA has its peak around 358 nm and the emission in duplex DNA is partly quenched and blue-shifted (ca. 410 nm), compared to the monomeric form. The spectral properties of the fluorophore also show sensitivity to pH; a property that may find biological applications. Quantum yields in single-stranded DNA range from 1-29 % and in duplex DNA from 1-7 %. In combination with the absorptive properties, this gives an average brightness inside duplex DNA of 275 M-1  cm-1 , more than five times higher than the most used environment-sensitive fluorescent base analogue, 2-aminopurine. Finally, we show that qAN4 can be used to advantage as a donor for interbase FRET applications in combination with adenine analogue qAnitro as an acceptor

Synthesis, oligonucleotide incorporation and fluorescence properties in DNA of a bicyclic thymine analogue

Fluorescent base analogues (FBAs) have emerged as a powerful class of molecular reporters of location and environment for nucleic acids. In our overall mission to develop bright and useful FBAs for all natural nucleobases, herein we describe the synthesis and thorough characterization of bicyclic thymidine (bT), both as a monomer and when incorporated into DNA. We have developed a robust synthetic route for the preparation of the bT DNA monomer and the corresponding protected phosphoramidite for solid-phase DNA synthesis. The bT deoxyribonucleoside has a brightness value of 790 M−1cm−1in water, which is comparable or higher than most fluorescent thymine analogues reported. When incorporated into DNA, bT pairs selectively with adenine without perturbing the B-form structure, keeping the melting thermodynamics of the B-form duplex DNA virtually unchanged. As for most fluorescent base analogues, the emission of bT is reduced inside DNA (4.5- and 13-fold in single- and double-stranded DNA, respectively). Overall, these properties make bT an interesting thymine analogue for studying DNA and an excellent starting point for the development of brighter bT derivatives

Iron Carbonyl Mediated Parallel Synthesis

This thesis describes the examination and development of cationic iron carbonyl complexes for use in parallel synthesis both in solution phase and on solid phase. A solution phase methodology for carbon-carbon and carbon-heteroatom formation, utilizing polymer bound reagents and scavengers and amenable for automation has been successfully developed. Ten different nucleophiles (carbon, nitrogen, oxygen, and sulfur) were used, giving the targeted cyclohexadienoic amides in good yields and excellent purities. The solution phase methodology was transferred to a solid phase protocol, generating a diverse set of eighteen cyclohexadienoic amides of excellent purities and in good yields using nine different nucleophiles (carbon, nitrogen, oxygen, and phosphorous). Both methods use the same reaction conditions for all nucleophiles demonstrating the versatility of these methods in generating compound libraries of high diversity. Even sterically hindered nucleophiles like tert-butanol gave good results. Activated esters were also investigated as potential linkers for iron carbonyl mediated chemistry on solid phase, and a tetrafluorophenol linkage was found to be the most suitable for this purpose. Synthesis of oseltamivir analogues and galectin inhibitors based on cationic iron carbonyl chemistry has been undertaken and work is currently in progress to finalize these projects. This thesis also describes the investigation of a phosphate based linker for cationic iron carbonyl chemistry on solid phase. In solution phase, palladium and nickel catalyzed cross-coupling reaction cleaved the investigated enyl and dienyl phosphates to give the targeted olefins. However, when transferring to a solid phase protocol only traces of the desired olefin were detected. In summary, this thesis shows that cationic iron carbonyl chemistry is amenable for parallel synthesis both in solution and on solid phase using the same reaction conditions for a wide range of nucleophiles.Keywords: solid phase, parallel synthesis, scavenger, polymer bound reagent, iron carbonyl complex, cation, dienyl, active ester, linker, oseltamivir, galectin inhibito

Iron Carbonyl Mediated Parallel Synthesis

This thesis describes the examination and development of cationic iron carbonyl complexes for use in parallel synthesis both in solution phase and on solid phase. A solution phase methodology for carbon-carbon and carbon-heteroatom formation, utilizing polymer bound reagents and scavengers and amenable for automation has been successfully developed. Ten different nucleophiles (carbon, nitrogen, oxygen, and sulfur) were used, giving the targeted cyclohexadienoic amides in good yields and excellent purities. The solution phase methodology was transferred to a solid phase protocol, generating a diverse set of eighteen cyclohexadienoic amides of excellent purities and in good yields using nine different nucleophiles (carbon, nitrogen, oxygen, and phosphorous). Both methods use the same reaction conditions for all nucleophiles demonstrating the versatility of these methods in generating compound libraries of high diversity. Even sterically hindered nucleophiles like tert-butanol gave good results. Activated esters were also investigated as potential linkers for iron carbonyl mediated chemistry on solid phase, and a tetrafluorophenol linkage was found to be the most suitable for this purpose. Synthesis of oseltamivir analogues and galectin inhibitors based on cationic iron carbonyl chemistry has been undertaken and work is currently in progress to finalize these projects. This thesis also describes the investigation of a phosphate based linker for cationic iron carbonyl chemistry on solid phase. In solution phase, palladium and nickel catalyzed cross-coupling reaction cleaved the investigated enyl and dienyl phosphates to give the targeted olefins. However, when transferring to a solid phase protocol only traces of the desired olefin were detected. In summary, this thesis shows that cationic iron carbonyl chemistry is amenable for parallel synthesis both in solution and on solid phase using the same reaction conditions for a wide range of nucleophiles.Keywords: solid phase, parallel synthesis, scavenger, polymer bound reagent, iron carbonyl complex, cation, dienyl, active ester, linker, oseltamivir, galectin inhibito

Carbon-carbon and carbon-heteroatom bond formation on solid phase using cationic iron carbonyl complexes

Iron-mediated methodology for the formation of carbon-carbon and carbon-heteroatom sp(3) bonds on solid phase has been developed. Treatment of a polymer-bound cationic iron cyclohexadienyl complex with carbon, oxygen, nitrogen, and phosphorus nucleophiles, followed by cleavage with amines and subsequent decomplexation, yielded 18 different cyclohexadienoic acid amides of high purity

Synthetic applications of cationic iron and cobalt carbonyl complexes

Metal carbonyl stabilized cationic species react with a wide range of nucleophiles under mild conditions, and have thus found many synthetic applications. In this Perspective, we describe the utility of iron carbonyl dienyl cations in solution and solid phase parallel synthesis, and in the development of a new synthetic route towards oseltamivir phosphate (Tamiflu). We also discuss the solid phase version of the Nicholas reaction, employing cobalt carbonyl stabilized propargylic cations, and giving access to substituted alkynes

Synthetic applications of cationic iron and cobalt carbonyl complexes

Metal carbonyl stabilized cationic species react with a wide range of nucleophiles under mild conditions, and have thus found many synthetic applications. In this Perspective, we describe the utility of iron carbonyl dienyl cations in solution and solid phase parallel synthesis, and in the development of a new synthetic route towards oseltamivir phosphate (Tamiflu). We also discuss the solid phase version of the Nicholas reaction, employing cobalt carbonyl stabilized propargylic cations, and giving access to substituted alkynes