Synthesis of Caged Nucleosides with Photoremovable Protecting Groups Linked to Intramolecular Antennae

Abstract

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 CÀC 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. Introduction. ± Light-directed, massive parallel combinatorial synthesis with photoremovable protecting groups allows the fabrication of high-density DNA chips [1] [2], i.e., arrays of up to 1 million spots of different oligonucleotides on an area of ca. 1 cm 2 . Such high-density DNA chips represent highly effective diagnostic tools for a variety of genomic applications such as genotyping [3], gene-expression profiling [4], and sequencing by hybridization [5]. Several reviews on DNA chips and their application have been published [6 ± 12].The efficiency of the photolithographic technique for producing high-density DNA chips critically depends on the performance, i.e., the light sensitivity and the uniformity of the photochemical cleavage reaction of the photolabile protecting groups blocking either the terminal 5'-OH or the 3'-OH group in the growing oligonucleotides. Among the photolabile protecting groups currently in use for photolithographic DNA-chip synthesis [13], the [2-(2-nitrophenyl)propoxy]carbonyl (nppoc) group (1) developed by Pfleiderer and co-workers is a prominent example [14] [15]. It reacts in excellent yield and gives rise to a good quantum yield, the only draw-back for a higher light sensitivity being its low absorption coefficient in the near UV, where illumination is usually performed with the 366-nm Hg line. It has been shown that this problem can be overcome by triplet sensitization, e.g., with 9H-thioxanthen-9-one ( thioxanthone ), which has a high absorption coefficient at 366 nm and, on diffusional encounters, transfers its triplet energy to the photoreactive nitrobenzyl chromophore [16]. In O 2 -free solution, the rate of photodeprotection of nppoc-protected thymidine is enhanced by a factor of ca. ten, when thioxanthone is added as a sensitizer. However, since intermolecular energy transfer is rate-limited by diffusion, in the presence of O 2 , the sensitizer is mostly quenched, and the enhancement of the photoreactivity is only weak or even absent. To avoid the diffusional step in energy transfer, we synthesized new

Intramolecular Sensitization of Photocleavage of the Photolabile 2‐(2‐Nitrophenyl)propoxycarbonyl (NPPOC) Protecting Group: Photoproducts and Photokinetics of the Release of Nucleosides

“…Their synthesis and spectroscopic properties are described elsewhere. [29,31] Products after continuous irradiation: For the characterization of the light sensitivity of the new compounds and the distribution of photoproducts, continuous irradiation experiments were carried out with deaerated solutions in methanol by using the lines at 366 and 405 nm, respectively, of a mercury high-pressure light source. At 405 nm, the absorption of the photolabile NPPOC group is practically negligible.…”

“…[26] The enhancement of photolysis of a photolabile protecting group by a covalently linked antenna molecule has been reported by Papageorgiou and coworkers [27,28] and our own group. The syntheses of the compounds shown in Scheme 2 are described in reference [29]. The letter/number code for these compounds is of the general structure TmLn-OR.…”

Highly Efficient Photolabile Protecting Groups with Intramolecular Energy Transfer

“…[15] The syntheses of the compounds shown in Scheme 2 have been described. [16] Except for compound 7, the linkage of the o-nitrophenyl and thioxanthone chromophores at different positions and with different linkers was achieved by C-C coupling reactions (Sonogashira, Heck, Suzuki). For synthesizing the protected thymidines (R = 5'-O-thymidinyl) connected to the protecting group by means of a carbonate bridge, the free alcohols (R = H) were first treated with phosgene or phosgene substitutes and then with thymidine.…”

Photolabile Protecting Groups in Organic Synthesis

“…It has also been used in combination with a nearby strongly absorbing chromophore, playing the role of an antenna in exploiting an efficient energy transfer (Scheme 13.4) [25,26].…”