Transformation of COUPY Fluorophores into a Novel Class of Visible-Light-Cleavable Photolabile Protecting Groups

Although photolabile protecting groups (PPGs) have found widespread applications in several fields of chemistry, biology and materials science, there is a growing interest in expanding the photochemical toolbox to overcome some of the limitations of classical caging groups. In this work, the synthesis of a new class of visible-light-sensitive PPGs based on low-molecular weight COUPY fluorophores with several attractive properties, including long-wavelength absorption, is reported. Besides being stable to spontaneous hydrolysis in the dark, COUPY-based PPGs can be efficiently photoactivated with yellow (560 nm) and red light (620 nm) under physiological-like conditions, thereby offering the possibility of unmasking functional groups from COUPY photocages under irradiation conditions in which other PPGs remain stable. Additionally, COUPY photocages exhibit excellent cellular uptake and accumulate selectively in mitochondria, opening the door to the delivery of caged analogues of biologically active compounds into these organelles.     

Computational design of improved two‐photon active caging compounds based on nitrodibenzofuran

Nitrodibenzofuran (NDBF) has recently been established as photolabile protecting group and efficiently used as two‐photon active cage. In this work, a computational approach is exploited to rationally design improved two‐photon active caging groups based on this NDBF chromophore. For this objective, first the two‐photon absorption (TPA) properties of NDBF are investigated in detail and a suitable theoretical approach for the reliable simulation of TPA spectra of this class of compounds is identified. Then, virtual chemical modifications are performed by introduction of substituents at the chromophore and replacement of the central furan ring by pyrolle, thiophene, and borrole heterocycles. Subsequently, the TPA properties of the resulting compounds are computed, and the influences of the chemical modifications on TPA properties investigated in detail. The most promising candidates with largely increased two‐photon uncaging efficiencies are dimethylamino‐substituted derivatives of NDBF, nitrodibenzopyrrol, and nitrodibenzothiophene. © 2012 Wiley Periodicals, Inc.     

Thiocoumarin Caged Nucleotides: Synthetic Access and Their Photophysical Properties

Photocages have been successfully applied in cellular signaling studies for the controlled release of metabolites with high spatio-temporal resolution. Commonly, coumarin photocages are activated by UV light and the quantum yields of uncaging are relatively low, which can limit their applications in vivo. Here, syntheses, the determination of the photophysical properties, and quantum chemical calculations of 7-diethylamino-4-hydroxymethyl-thiocoumarin (thio-DEACM) and caged adenine nucleotides are reported and compared to the widely used 7-diethylamino-4-hydroxymethyl-coumarin (DEACM) caging group. In this comparison, thio-DEACM stands out as a phosphate cage with improved photophysical properties, such as red-shifted absorption and significantly faster photolysis kinetics.     

Toward the development of new photolabile protecting groups that can rapidly release bioactive compounds upon photolysis with visible light

The synthesis and characterization of a new photolabile protecting group (caging group) for carboxylic acids, the 2-(dimethylamino)-5-nitrophenyl (DANP) group, is described. This compound has a major absorption band in the visible wavelength region with a maximum near 400 nm (epsilon400 = 9077 M(-1) cm(-1) at pH 7.4 and 21 degrees C). The caging group is attached through an ester linkage to the carboxyl functionality of beta-alanine, which activates the inhibitory glycine receptor in the mammalian central nervous system. Such caged compounds play an important role in transient kinetic investigations of fast cellular processes. Upon photolysis of DANP-caged beta-alanine, the caging group is released within 5 micros. Quantum yields of 0.03 and 0.002 were obtained in the UV region (308 and 360 nm) and the visible region (450 nm), respectively. Laser-pulse photolysis experiments, using 337 or 360 nm light, were performed with the caged compound equilibrated with HEK 293 cells transiently transfected with cDNA encoding the alpha1 homomeric, wild-type glycine receptor. The experiments demonstrated that neither DANP-caged beta-alanine nor its byproducts inhibit or activate the glycine receptors on the cell surface. Under physiological conditions, the DANP-caged beta-alanine is water-soluble and stable and can be used for transient kinetic measurements.     

Phototriggers for nucleobases with improved photochemical properties

Synthesis and photochemical properties of new photoremovable protecting groups for nucleobases are described. Four caged 2'-deoxycytidines (dCs) were synthesized, and their photochemical properties were measured under simulated physiological conditions. Two new coumarin-caged dCs show better photochemical and photophysical properties than those of the caged dCs having previously reported caging groups.     

The α,5-dicarboxy-2-nitrobenzyl caging group, a tool for biophysical applications with improved hydrophilicity: synthesis, photochemical properties and biological characterization

Earlier we reported on the synthesis of α,4-dicarboxy-2-nitrobenyzl caged compounds (Schaper, K. et al. [2002] Eur. J. Org. Chem., 1037–1046). These compounds have the advantage of an increased hydrophilicity compared with the well-established α-carboxy-2-nitrobenzyl caged compounds; however, the release of the active compound becomes slower due to the introduction of the additional carboxy group. Based upon theoretical calculations we predicted that the release would become faster when the additional carboxy group is moved to the 5-position. Here we describe the synthesis and the photochemical and biological characterization of an α,5-dicarboxy-2-nitrobenyzl caged compound. The high hydrophilicity of the new caging group is maintained due to the fact that the additional carboxy moiety is preserved, while the release of the active species from the new derivative is even faster than for the reference, an α-CNB caged compound.     

3-Nitro-2-naphthalenemethanol: a photocleavable protecting group for carboxylic acids

Photocleavable protecting groups are important in synthesis and caging. Among many such groups, 2-nitrobenzyl and related groups have been found useful in many applications. However, most of the known 2-nitrobenzyl-based caging chromophores show either low quantum yield or the photolysis wavelength is not suitable for various applications. In this paper, we report 2-nitro-3-naphthalenemethanol (NNM) as an efficient photocleavable protecting group for molecules containing a carboxylic function. NNM possesses photochemical properties better than the 2-nitrobenzyl chromophores as it is photoactivatable at 380 nm in aqueous medium (CH₃CN/H₂O, 3:2 v/v) showing the desired photochemistry. The carboxylic acids are efficiently photoreleased from NNM-based esters in almost quantitative yield.     

A photolabile ligand for light-activated release of caged copper

A photosensitive caged copper complex has been prepared from a tetradentate ligand (H2cage) composed of two pyridyl-amide arms connected by a photoreactive nitrophenyl group. H2cage binds Cu2+ in aqueous solution with a stability constant (log beta) of 10.8, which corresponds to a KD of 16 pM at pH 7.4. The neutral Cu2+ complex, [Cu(OH2)(cage)], crystallizes as a distorted trigonal bipyramid coordinated by two amide and two pyridyl N atoms, with a water molecule bound in the trigonal plane. Photolysis with 350 nm UV light cleaves the ligand backbone to release photoproducts with significantly diminished affinity for Cu2+, thereby uncaging the metal ion. When coordinated as the caged complex, copper has diminished reactivity to produce hydroxyl radicals from Fenton-like reaction mixtures containing hydrogen peroxide and ascorbic acid. Postphotolysis, uncaged copper promotes hydroxyl radical formation under the same conditions. The strategy of caging copper is promising for applications where light could be used to trigger release of copper as a pro-oxidant to increase oxidative stress or as a tool to release copper intracellularly to study mechanisms of copper trafficking.     

Synthesis of Site‐Specifically Phosphate‐Caged siRNAs and Evaluation of Their RNAi Activity and Stability

A complete set of new photolabile nucleoside phosphoramidites were synthesized, then site‐specifically incorporated into sense or antisense strands of siRNA for phosphate caging. Single caging modification was made along siRNA strands and their photomodulation of gene silencing were examined by using the firefly luciferase reporter gene. Several key phosphate positions were then identified. Furthermore, multiple caging modifications at these key positions led to significantly enhanced photomodulation of gene silencing activity, suggesting a synergistic effect. The caging group on both the terminally phosphate‐caged siRNA and the single‐stranded caged RNA has comparatively high stability, whereas hydrolysis of the caged group from the internally caged siRNA was observed, irrespective of the presence of Mg²⁺. Molecular dynamic simulations demonstrated that enhanced hydrolysis of the caging group on internally phosphate‐caged siRNAs was due to easy fragmentation of the caging group upon formation of the pentavalent intermediate of the phosphotriester with attack by water. The caging group in the terminally phosphate‐caged siRNA or single‐stranded caged RNA prefers to form π–π stacks with nearby nucleobases. In addition to providing explanations for previous observations, this study sheds further light on the design of caged oligonucleotides and indicates the direction of future development of nucleic acid drugs with phosphate modifications.     

Selective Modification for Red-Shifted Excitability: A Small Change in Structure,a Huge Change in Photochemistry

We developed three bathochromic, green-light activatable, photolabile protecting groups based on a nitrodibenzofuran (NDBF) core with D-π-A push–pull structures. Variation of donor substituents (D) at the favored ring position enabled us to observe their impact on the photolysis quantum yields. Comparing our new azetidinyl-NDBF (Az-NDBF) photolabile protecting group with our earlier published DMA-NDBF, we obtained insight into its excitation-specific photochemistry. While the “two-photon-only” cage DMA-NDBF was inert against one-photon excitation (1PE) in the visible spectral range, we were able to efficiently release glutamic acid from azetidinyl-NDBF with irradiation at 420 and 530 nm. Thus, a minimal change (a cyclization adding only one carbon atom) resulted in a drastically changed photochemical behavior, which enables photolysis in the green part of the spectrum.     

Wavelength-selective uncaging of dA and dC residues

Nitrodibenzofuran (NDBF) groups are used as photolabile "caging" groups to temporarily mask the Watson-Crick interaction of dA and dC residues. They show improved masking capabilities and are photodeprotected 12 times more efficiently than 1-(o-nitrophenyl)-ethyl (NPE) caging groups in these positions. Furthermore, NDBF groups can be removed wavelength-selectively in the presence of NPE groups. This will allow more complex (un)caging strategies of oligonucleotides--beyond the usual irreversible triggering.     

Time-resolved spectroscopic studies of B(12) coenzymes: a comparison of the primary photolysis mechanism in methyl-, ethyl-, n-propyl-, and 5'-deoxyadenosylcobalamin.

An ultrafast transient absorption study of the primary photolysis of ethyl- and n-propylcobalamin in water is presented. Data have been obtained for two distinct excitation wavelengths, 400 nm at the edge of the UV gamma-band absorption, and 520 nm in the strong visible alphabeta-band absorption. These data are compared with results reported earlier for the B(12) coenzymes, methyl- and adenosylcobalamin. The data obtained for ethylcobalamin and n-propylcobalamin following excitation at 400 nm demonstrate the formation of one major photoproduct on a picosecond time scale. This photoproduct is spectroscopically identifiable as a cob(II)alamin species. Excitation of methyl-, ethyl-, and n-propylcobalamin at 520 nm in the low-lying alphabeta absorption band results in bond homolysis proceeding via a bound cob(III)alamin MLCT state. For all of the cobalamins studied here competition between geminate recombination of caged radical pairs and cage escape occurs on a time scale of 500 to 700 ps. The rate constants for geminate recombination in aqueous solution fall within a factor of 2 between 0.76 and 1.4 ns(-1). Intrinsic cage escape occurs on time scales ranging from 相似文献   

Masked Rhodamine Dyes of Five Principal Colors Revealed by Photolysis of a 2‐Diazo‐1‐Indanone Caging Group: Synthesis,Photophysics, and Light Microscopy Applications

Caged rhodamine dyes (Rhodamines NN) of five basic colors were synthesized and used as “hidden” markers in subdiffractional and conventional light microscopy. These masked fluorophores with a 2‐diazo‐1‐indanone group can be irreversibly photoactivated, either by irradiation with UV‐ or violet light (one‐photon process), or by exposure to intense red light (λ～750 nm; two‐photon mode). All dyes possess a very small 2‐diazoketone caging group incorporated into the 2‐diazo‐1‐indanone residue with a quaternary carbon atom (C‐3) and a spiro‐9H‐xanthene fragment. Initially they are non‐colored (pale yellow), non‐fluorescent, and absorb at λ=330–350 nm (molar extinction coefficient (ε)≈10⁴ M^?1 cm^?1) with a band edge that extends to about λ=440 nm. The absorption and emission bands of the uncaged derivatives are tunable over a wide range (λ=511–633 and 525–653 nm, respectively). The unmasked dyes are highly colored and fluorescent (ε= 3–8×10⁴ M^?1 cm^?1 and fluorescence quantum yields (?)=40–85 % in the unbound state and in methanol). By stepwise and orthogonal protection of carboxylic and sulfonic acid groups a highly water‐soluble caged red‐emitting dye with two sulfonic acid residues was prepared. Rhodamines NN were decorated with amino‐reactive N‐hydroxysuccinimidyl ester groups, applied in aqueous buffers, easily conjugated with proteins, and readily photoactivated (uncaged) with λ=375–420 nm light or intense red light (λ=775 nm). Protein conjugates with optimal degrees of labeling (3–6) were prepared and uncaged with λ=405 nm light in aqueous buffer solutions (?=20–38 %). The photochemical cleavage of the masking group generates only molecular nitrogen. Some 10–40 % of the non‐fluorescent (dark) byproducts are also formed. However, they have low absorbance and do not quench the fluorescence of the uncaged dyes. Photoactivation of the individual molecules of Rhodamines NN (e.g., due to reversible or irreversible transition to a “dark” non‐emitting state or photobleaching) provides multicolor images with subdiffractional optical resolution. The applicability of these novel caged fluorophores in super‐resolution optical microscopy is exemplified.     

Inactivation of Competitive Decay Channels Leads to Enhanced Coumarin Photochemistry

In the development of photolabile protecting groups, it is of high interest to selectively modify photochemical properties with structural changes as simple as possible. In this work, knowledge of fluorophore optimization was adopted and used to design new coumarin- based photocages. Photolysis efficiency was selectively modulated by inactivating competitive decay channels, such as twisted intramolecular charge transfer (TICT) or hydrogen-bonding, and the photolytic release of the neurotransmitter serotonin was demonstrated. Structural modifications inspired by the fluorophore ATTO 390 led to a significant increase in the uncaging cross section that can be further improved by the simple addition of a double bond. Ultrafast transient absorption spectroscopy gave insights into the underlying solvent-dependent photophysical dynamics. The chromophores presented here are excellently suited as new photocages in the visible wavelength range due to their simple synthesis and their superior photochemical properties.     

Styryl conjugated coumarin caged alcohol: efficient photorelease by either one-photon long wavelength or two-photon NIR excitation

The synthesis and photorelease properties of a new phototrigger for alcohols are described. Compared to ester 4 caged by the reported [7-(diethylamino)coumarin-4-yl]methoxycarbonyl (DEACM) phototrigger, the caged ester 3 shows an efficient single-photon photolysis efficiency upon irradiation of long wavelength light (λ = 475 nm) and a stronger two-photon photolysis sensitivity with 800 nm laser light. Its promising properties and the efficient photorelease of adenosine make it very useful as a caging group for biological applications.     

Rethinking Uncaging: A New Antiaromatic Photocage Driven by a Gain of Resonance Energy

Photoactivatable compounds for example photoswitches or photolabile protecting groups (PPGs, photocages) for spatiotemporal light control, play a crucial role in different areas of research. For each application, parameters such as the absorption spectrum, solubility in the respective media and/or photochemical quantum yields for several competing processes need to be optimized. The design of new photochemical tools therefore remains an important task. In this study, we exploited the concept of excited-state-aromaticity, first described by N. Colin Baird in 1971, to investigate a new class of photocages, based on cyclic, ground-state-antiaromatic systems. Several thio- and nitrogen-functionalized compounds were synthesized, photochemically characterized and further optimized, supported by quantum chemical calculations. After choosing the optimal scaffold, which shows an excellent uncaging quantum yield of 28 %, we achieved a bathochromic shift of over 100 nm, resulting in a robust, well accessible, visible light absorbing, compact new photocage with a clean photoreaction and a high quantum product (ϵ⋅Φ) of 893 M⁻¹ cm⁻¹ at 405 nm.     

核酸光化学生物学

光敏感基团作为光化学开关被广泛应用于各种生物过程的光调控中。特别是过去十几年内,核苷酸、寡聚核苷酸和DNA/RNA的光敏修饰策略得到了长足的发展,并在细胞信号传导和靶基因的功能调控等诸多生物学研究中发挥重要的作用。本文主要针对常用的光敏感基团、光敏感核酸及其化学生物学研究进展进行简要综述,并对未来核酸光化学生物学的研究进行了展望。     

Photodissociation and caging of HBr and HI molecules on the surface of large rare gas clusters

Photodissociation experiments were carried out at a wavelength of 243 nm for single HBr and HI molecules adsorbed on the surface of large Nen, Arn, Krn and Xen clusters. The average size is about = 130; the size ranges = 62-139 for the system HBr-Arn and = 110-830 for HI-Xen were covered. In this way the dependence of the photodissociation dynamics on both the size and the rare gas host cluster was investigated. The main observable is the kinetic energy distribution of the outgoing H atoms. The key results are that we do not find any size dependence for either system but that we observe a strong dependence on the rare gas clusters. All systems exhibit H atoms with no energy loss that indicate direct cage exit and those with nearly zero energy that are an indication of complete caging. The intensity ratio of caged to uncaged H atoms is largest for Nen, decreases with increasing mass of the cage atoms, and is weakest for Xen. On the basis of accompanying calculations this behaviour is attributed to the large amplitude motion of the light H atom. This leads to direct cage exit and penetration of the atom through the cluster with different energy transfer per collision depending on the rare gas atoms. The differences between HBr and HI molecules are attributed to different surface states, a flat and an encapsulated site.     

Design, synthesis, and biological evaluation of platensimycin analogues with varying degrees of molecular complexity

The molecular design, chemical synthesis, and biological evaluation of two distinct series of platensimycin analogues with varying degrees of complexity are described. The first series of compounds probes the biological importance of the benzoic acid subunit of the molecule, while the second series explores the tetracyclic cage domain. The biological data obtained reveal that, while the substituted benzoic acid domain of platensimycin is a highly conserved structural motif within the active compounds with strict functional group requirements, the cage domain of the molecule can tolerate considerable structural modifications without losing biological action. These findings refine our present understanding of the platensimycin pharmacophore and establish certain structure-activity relationships from which the next generation of designed analogues of this new antibiotic may emerge.