Intramolecular Sensitization of Photocleavage of the Photolabile 2-(2-Nitrophenyl)propoxycarbonyl (NPPOC) Protecting Group: Photoproducts and Photokinetics of the Release of Nucleosides
2008, Wöll, Dominik, Smirnova, Julia, Galetskaya, Marina, Prykota, Tamara, Bühler, Jochen, Stengele, Klaus-Peter, Pfleiderer, Wolfgang, Steiner, Ulrich
Novel photolabile protecting groups based on the 2-(2-nitrophenyl)propoxycarbonyl (NPPOC) group with a covalently linked thioxanthone as an intramolecular triplet sensitizer exhibit significantly enhanced light sensitivity under continuous illumination. Herein we present a detailed study of the photokinetics and photoproducts of nucleosides caged with these new protecting groups. Relative to the parent NPPOC group, the light sensitivity of the new photolabile protecting groups is enhanced by up to a factor of 21 at 366 nm and is still quite high at 405 nm, the wavelength at which the sensitivity of the parent compound is practically zero. A new pathway for deprotection of the NPPOC group proceeding through a nitroso benzylalcohol intermediate has been discovered to complement the main mechanism, which involves elimination. Under standard conditions of lithographic DNA-chip synthesis, some of the new compounds, while maintaining the same chip quality, react ten times faster than the unmodified NPPOC-protected nucleosides.
On the Mechanism of Intramolecular Sensitization of Photocleavage of the 2-(2-Nitrophenyl)propoxycarbonyl (NPPOC) Protecting Group
2007, Wöll, Dominik, Laimgruber, Stefan, Galetskaya, Marina, Smirnova, Julia, Pfleiderer, Wolfgang, Heinz, Björn, Gilch, Peter, Steiner, Ulrich
A spectroscopic study of a variety of covalently linked thioxanthone(TX)-linker-2-(2-nitrophenyl)propoxycarbonyl(NPPOC)-substrate conjugates is presented. Herein, the TX chromophore functions as an intramolecular sensitizer to the NPPOC moiety, a photolabile protecting group used in photolithographic DNA chip synthesis. The rate of electronic energy transfer between TX and NPPOC was quantified by means of stationary fluorescence as well as nanosecond and femtosecond time-resolved laser spectroscopy. A dual mechanism of triplet-triplet energy transfer has been observed comprising a slower mechanism involving the T1(*) state of TX with linker-length-dependent time constants longer than 20 ns and a fast mechanism with linker-length-dependent time constants shorter than 3 ns. Evidence is provided that the latter mechanism is due to energy transfer from the T2(n*) state which is in fast equilibrium with the fluorescent S1(*) state. In the case of direct linkage between the aromatic rings of TX and NPPOC, the spectroscopic properties are indicative of one united chromophore which, however, still shows the typical NPPOC cleavage reaction triggered by intramolecular hydrogen atom transfer to the nitro group.
Synthesis of caged nucleosides with photoremovable protecting groups linked to intramolecular antennae
2005, Smirnova, Julia, Wöll, Dominik, Pfleiderer, Wolfgang, Steiner, Ulrich
Based on the [2-(2-nitrophenyl)propoxy]carbonyl (nppoc) group, six new photolabile protecting groups (2, 8, 9b, 16b, 25b, and 26), each covalently linked to a 9H-thioxanthen-9-one (Tx) unit functioning as an intramolecular triplet sensitizer, were synthesized. Linkers were introduced between the Me group or the aromatic ring of nppoc and the 2-position of Tx by means of classical organic synthesis combined with Pd catalyzed CC coupling reactions. The new photolabile protecting groups to be used in light-directed synthesis of DNA chips were attached to the 5-O-atom of thymidine via a carbonate linkage, giving rise to the caged nucleosides 7, 11, 13, 19, 20, and 30.
Photolabile Protecting Groups for Nucleosides : Mechanistic Studies of the 2-(2-Nitrophenyl)ethyl Group
2001, Walbert, Stefan, Pfleiderer, Wolfgang, Steiner, Ulrich
The photochemistry of several 2-(2-nitrophenyl)ethyl-caged compounds including caged thymidine nucleosides was studied by nanosecond laser flash photolysis and stationary illumination experiments with quantitative HPLC analysis for quantum yields and product distribution. Effects of solvent basicity and acidity were investigated by varying the H2O content and HCl concentration, respectively, in MeCN/H2O mixtures. For all compounds 1 - 7 investigated, intramolecular H abstraction by the nitro group from the exocyclic α-position with respect to the aryl moiety was found to be the primary process. The protolytic dissociation equilibrium of the resulting aci-nitro compound was kinetically characterized in the 0.1 - 10 s time region. In general, two reaction channels compete for the aci-nitro compound and its anion: β-elimination of the caged compound occurs from the anion, while from the undissociated aci-nitro compound, a nitrosobenzene derivative is formed with no release of the caged compound. The yield ratio of these two reaction channels can be controlled through shifts in the protolytic dissociation equilibrium of the aci-nitro compound. In solutions with either low basicity (H2O-free MeCN) or high acidity (higher concentration of HCl in H2O/MeCN), two as yet unidentified products are formed, each one specifically for one of the mentioned conditions.
Triplet-Sensitized Photodeprotection of Oligonucleotides in Solution and on Microarray Chips
2004, Wöll, Dominik, Walbert, Stefan, Stengele, Klaus-Peter, Albert, Tom J., Richmond, Todd, Norton, Jason, Singer, Michael, Green, Roland D., Pfleiderer, Wolfgang, Steiner, Ulrich
Conditions and kinetics of triplet sensitization as a method for increasing the light sensitivity of photolabile protecting groups used for the photolithographic synthesis of oligonucleotide microarrays were quantitatively studied with the photolabile 2-(2-nitrophenyl)propyl protecting group in homogeneous solutions and on glass substrates by using laser flash photolysis, continuous illumination with HPLC analysis, fluorescence dye labelling, and hybridization. In terms of efficiency and avoidance of chemical side reactions, 9H-thioxanthen-9-one was the most-suitable sensitizer. Both in solution and on a glass substrate, the photostationary kinetics were quantitatively modelled and the relevant kinetic parameters determined. While the sensitization kinetics was diffusion-controlled both in solution and on the chip, the photostationary kinetics was essentially of zero order only on the chip because here the triplet-quenching effect of the released photoproduct 2-(2-nitrophenyl)propene was suppressed as a consequence of the inhomogeneous reaction that took place in a narrow diffusion zone above the surface from where the photoproducts could quickly escape. The kinetic simulation allowed quantitative estimate of the density of reactive groups on the surface. It was further demonstrated that, with 9H-thioxanthen-9-one as a sensitizer, high-density oligonucleotide microarrays of high quality can be produced with one-third of the normal exposure time.
Anti-pterins as tools to characterize the function of tetrahydrobiopterin in NO synthase
1998, Bömmel, Heike M., Reif, Andreas, Fröhlich, Lothar G., Frey, Armin, Hofmann, Heinrich, Marecak, Dale M., Groehn, Viola, Kotsonis, Peter, La, Mylinh, Köster, Sandra, Meinecke, Matthias, Bernhardt, Manfred, Weeger, Monika, Ghisla, Sandro, Prestwich, Glenn D., Pfleiderer, Wolfgang, Schmidt, Harald H. H. W.
Nitric oxide synthases (NOS) are homodimeric enzymes that NADPH-dependently convert L-arginine to nitric oxide and L-citrulline. Interestingly, all NOS also require (6R)-5,6,7,8-tetrahydro-L-biopterin (H4Bip) for maximal activity although the mechanism is not fully understood. Basal NOS activity, i.e. that in the absence of exogenous H4Bip, has been attributed to enzyme-associated H4Bip. To elucidate further H4Bip function in purified NOS, we developed two types of pterin-based NOS inhibitors, termed anti-pterins. In contrast to type II anti-pterins, type I anti-pterins specifically displaced enzyme-associated H4Bip and inhibited H4Bip-stimulated NOS activity in a fully competitive manner but, surprisingly, had no effect on basal NOS activity. Moreover, for a number of different NOS preparations basal activity (percent of Vmax) was frequently higher than the percentage of pterin saturation and was not affected by preincubation of enzyme with H4Bip. Thus, basal NOS activity appeared to be independent of enzyme-associated H4Bip. The lack of intrinsic 4a-pterincarbinolamine dehydratase activity argued against classical H4Bip redox cycling in NOS. Rather, H4Bip was required for both maximal activity and stability of NOS by binding to the oxygenase/dimerization domain and preventing monomerization and inactivation during L-arginine turnover. Since anti-pterins were also effective in intact cells, they may become useful in modulating states of pathologically high nitric oxide formation.