p-Hydroxyphenacyl bromide as photoremoveable thiol label: a potential phototrigger for thiol-containing biomolecules

Photochemical modifications for DNA/RNA oligonucleotides

Light-triggered chemical reactions can provide excellent tools to investigate the fundamental mechanisms important in biology. Light is easily applicable and orthogonal to most cellular events, and its dose and locality can be controlled in tissues and cells. Light-induced conversion of photochemical groups installed on small molecules, proteins, and oligonucleotides can alter their functional states and thus the ensuing biological events. Recently, photochemical control of DNA/RNA structure and function has garnered attention thanks to the rapidly expanding photochemistry used in diverse biological applications. Photoconvertible groups can be incorporated in the backbone, ribose, and nucleobase of an oligonucleotide to undergo various irreversible and reversible light-induced reactions such as cleavage, crosslinking, isomerization, and intramolecular cyclization reactions. In this review, we gather a list of photoconvertible groups used in oligonucleotides and summarize their reaction characteristics, impacts on DNA/RNA thermal stability and structure, as well as their biological applications.

Light sensitive phenacyl crosslinked dextran hydrogels for controlled delivery

Stimuli‐responsive soft materials enable controlled release of loaded drug molecules and biomolecules. Controlled release of potent chemotherapeutic or immunotherapeutic agents is crucial to reduce unwanted side effects. In an effort to develop controlled release strategies that can be triggered by using Cerenkov luminescence, we have developed polymer hydrogels that can release bovine serum albumin and immunoglobulin G by using light (254 nm–375 nm) as a trigger. We describe the synthesis and photochemical characterization of two light sensitive phenacyl bis‐azide crosslinkers that are used to prepare transparent self‐supporting hydrogel patches. One crosslinker was designed to optimize the overlap with the Cerenkov luminescence emission window, bearing an π‐extended phenacyl core, resulting in a high quantum yield (14 %) of photocleavage when irradiated with 375 nm light. We used the extended phenacyl crosslinker for the preparation of protein‐loaded dextran hydrogel patches, which showed efficient and selective dosed release of bovine serum albumin or immunoglobulin G after irradiation with 375 nm light. Cerenkov‐triggered release is as yet inconclusive due to unexpected side‐reactivity. Based on the high quantum yield, efficient release and large overlap with the Cerenkov window, we envision application of these photosensitive soft materials in radiation targeted drug release.

Postsynthetic Modification of DNA Phosphodiester Backbone for Photocaged DNAzyme

Photocaged (photoactivatable) biomolecules are powerful tools for noninvasive control of biochemical activities by light irradiation. DNAzymes (deoxyribozymes) are single-stranded oligonucleotides with a broad range of enzymatic activities. In this work, to construct photocaged DNAzymes, we developed a facile and mild postsynthetic method to incorporate an interesting photolabile modification (thioether-enol phosphate, phenol substituted, TEEP-OH) into readily available phosphorothioate DNA. Upon light irradiation, TEEP-OH transformed into a native DNA phosphodiester, and accordingly the DNAzymes with RNA-cleaving activities were turned "on" from its inactive and caged form. Activation of the TEEP-OH-caged DNAzyme by light was also successful inside live cells.

Stereochemically probing the photo-Favorskii rearrangement: a mechanistic investigation

Using model (R)-2-acetyl-2-phenyl acetate esters of (S)- or (R)-α-substituted-p-hydroxybutyrophenones (S,R)-12a and (R,R)-12b, we have shown that a highly efficient photo-Favorskii rearrangement proceeds through a series of intermediates to form racemic rearrangement products. The stereogenic methine on the photoproduct, rac-2-(p-hydroxyphenyl)propanoic acid (rac-9), is formed by closure of a phenoxy-allyloxy intermediate 17 collapsing to a cyclopropanone, the "Favorskii" intermediate 18. These results quantify the intermediacy of a racemized triplet biradical (3)16 on the major rearrangement pathway elusively to the intermediate 18. Thus, intersystem crossing from the triplet biradical surface to the ground state generates a planar zwitterion prior to formation of a Favorskii cyclopropanone that retains no memory of its stereochemical origin. These results parallel the mechanism of Dewar and Bordwell for the ground state formation of cyclopropanone 3 that proceeds through an oxyallyl zwitterionic intermediate. The results are not consistent with the stereospecific S(N)2 ground state Favorskii mechanism observed by Stork, House, and Bernetti. Interconversion of the diastereomeric starting esters of (S,R)-12a and (R,R)-12b during photolysis did not occur, thus ruling out leaving group return prior to rearrangement.

Photoinduced Polymer Chain Scission of Alkoxyphenacyl Based Polycarbonates

We report the design and development of a new class of alkoxyphenacyl based photodegradable polycarbonates. These polymers incorporate the photoactive moiety in the backbone and, when irradiated at 300 nm, undergo controlled chain scission. Micropatterned thin films of these polymers were fabricated by photolithographic techniques. The use of these photodegradable polymers for controlled release applications was demonstrated by the release of Nile Red from polymeric nanoparticles. In addition, these polymers are mechanically robust, thermally stable, and hydrolytically degradable.

Preparation and photophysical properties of a caged kynurenine

We have prepared l-kyurenine 4-hydroxyphenacyl ester, a caged derivative of L-kynurenine. N(α)-tBOC-L-tryptophan was reacted with 4-hydroxyphenacyl bromide in DMF with K(2)CO(3) as the base to give the N(α)-tBOC 4-hydroxyphenacyl ester. The ester was then treated with O(3) in MeOH at -20°C, followed by trifluoroacetic acid in CH(2)Cl(2), then aqueous HCl to obtain the caged kynurenine as the dihydrochloride salt. The caged kynurenine is stable as a dry solid in the dark at -78°C, but in aqueous solutions in phosphate buffer at pH 7-8 hydrolyzes rapidly (t(1/2) ∼5 min). Solutions in Tris at pH 7 are more stable (t(1/2) >30 min), and solutions in 1mM HCl are stable for several hours. As expected, the ester is cleaved in microseconds with laser pulses at 355 nm. The caged kynurenine may be useful for preparation of substrate complexes for crystallography or in biological studies on kynurenine.

Applications of p-hydroxyphenacyl (pHP) and coumarin-4-ylmethyl photoremovable protecting groups

Most applications of photoremovable protecting groups have used o-nitrobenzyl compounds and their (often commercially available) derivatives that, however, have several disadvantages. The focus of this review is on applications of the more recently developed title compounds, which are especially well suited for time-resolved biochemical and physiological investigations, because they release the caged substrates in high yield within a few nanoseconds or less. Together, these two chromophores cover the action spectrum for photorelease from >700 nm to 250 nm.

p-Hydroxyphenacyl photoremovable protecting groups - Robust photochemistry despite substituent diversity

A broadly based investigation of the effects of a diverse array of substituents on the photochemical rearrangement of p-hydroxyphenacyl esters has demonstrated that common substituents such as F, MeO, CN, CO2R, CONH2, and CH3 have little effect on the rate and quantum efficiencies for the photo-Favorskii rearrangement and the release of the acid leaving group or on the lifetimes of the reactive triplet state. A decrease in the quantum yields across all substituents was observed for the release and rearrangement when the photolyses were carried out in buffered aqueous media at pHs that exceeded the ground-state pKa of the chromophore where the conjugate base is the predominant form. Otherwise, substituents have only a very modest effect on the photoreaction of these robust chromophores.

Competing pathways in the photo-Favorskii rearrangement and release of esters: studies on fluorinated p-hydroxyphenacyl-caged GABA and glutamate phototriggers

Three new trifluoromethylated p-hydroxyphenacyl (pHP)-caged gamma-aminobutyric acid (GABA) and glutamate (Glu) derivatives have been examined for their efficacy as photoremovable protecting groups in aqueous solution. Through the replacement of hydrogen with fluorine, e.g., a m-trifluoromethyl or a m-trifluoromethoxy versus m-methoxy substituents on the pHP chromophore, modest increases in the quantum yields for the release of amino acids GABA and glutamate as well as improved lipophilicity were realized. The pHP triplet undergoes a photo-Favorskii rearrangement with concomitant release of the amino acid substrate. Deprotonation competes with the rearrangement from the triplet excited state and yields the pHP conjugate base that, upon reprotonation, regenerates the starting ketoester, a chemically unproductive or "energy-wasting" process. When picosecond pump-probe spectroscopy is employed, GABA derivatives 2-5 are characterized by short triplet lifetimes, a manifestation of their rapid release of GABA. The bioavailability of released GABA at the GABA(A) receptor improved when the release took place from m-OCF3 (2) but decreased for m-CF3 (3) when compared with the parent pHP derivative. These studies demonstrate that pKa and lipophilicity exert significant but sometimes opposing influences on the photochemistry and biological activity of pHP phototriggers.

A Theoretical Investigation of P-Hydroxyphenacyl Caged Phototrigger Compounds: How Water Induces the Photodeprotection and Subsequent Rearrangement Reactions

Complete active-space self-consistent field (CASSCF) calculations with a (14,11) active space and density functional theory calculations followed by Car-Parrinello molecular dynamic simulations are reported for the p-hydroxyphenacyl acetate, diethyl phosphate, and diphenyl phosphate phototrigger compounds. These calculations considered the explicit hydrogen bonding of water molecules to the phototrigger compound and help reveal the role of water in promoting the photodeprotection and subsequent rearrangement reactions for the p-hydroxyphenacyl caged phototrigger compounds experimentally observed in the presence of appreciable amounts of water but not observed in neat nonproton solvents like acetonitrile. The 267 nm excitation of the phototrigger compounds leads to an instantaneous population of the S3(1pipi*) state Franck-Condon region, which is followed by an internal conversion deactivation route to the S1(1npi*) state via a 1pipi*/1npi* vibronic coupling. The shorter lifetime of the S1(1npi*) state (approximately 1 ps) starting from the FC geometry is terminated by a fast intersystem crossing at a 3pipi*/3npi* intersection with a structure of mixed pipi*/npi* excitation in the triplet state. The deprotection reaction is triggered by a proton (or hydrogen atom) transfer assisted by water bridges and emanates from this pipi*/npi* triplet state intersection. With the departure of the leaving group, the reaction evolves into a water-mediated post-deprotection phase where the spin inversion of pQM (X, 3A) leads to a spiroketone in the ground state by a cyclization process that is followed by an attack of water to produce a 1,1'-di-hydroxyl-spiroketone. Finally, the H atom of the hydroxyl in 1,1'-di-hydroxyl-spiroketon transfers back to the p-O atom aided by water molecules to generate the p-hydroxyphenyl-acetic acid final rearrangement product.

Femtosecond Transient Absorption and Nanosecond Time-Resolved Resonance Raman Study of the Solvent-Dependent Photo-Deprotection Reaction of Benzoin Diethyl Phosphate

A combined femtosecond transient absorption (fs-TA) and nanosecond time-resolved resonance Raman (ns-TR3) study was performed to directly detect the dynamics and elucidate the mechanism of the excited state deactivation and solvent-dependent photo-deprotection pathways for benzoin diethyl phosphate (BDP) in neat acetonitrile (MeCN) and 75 % H2O/25 % MeCN. Comparison of the TA spectral evolution observed in the two solvents provides explicit evidence that the photophysical deactivation of the BDP singlet excited state has little solvent dependence. The TA spectra also indicate the related internal conversion (IC) and intersystem crossing (ISC) processes occur rapidly on hundreds of femtoseconds and approximately 2-3 ps time scales, respectively. From this and in conjunction with a photochemistry study and ground state resonance Raman (RR) measurements, the TA results reveal that the phenacyl localized BDP triplet state (that is mainly npi* nature) is the common and immediate precursor to the photo-deprotection reaction in both solvents. However, the triplet deprotection follows different pathways in neat MeCN versus the largely water containing solvent. The deprotection reaction in MeCN was determined to occur with a approximately 11 ns time constant and the reaction was found to be an unimolecular process leading to elimination of the diethyl phosphoric acid apparently concurrent with cyclization to yield the benzofuran product. In the water mixed solvent, the triplet reaction was observed to proceed with a approximately 15 ns time constant and the reaction leads to not only the deprotection-cyclization but also a heterolytic dissociation to release the diethyl phosphate anion through a branching and competing mechanism. The ns-TR3 spectra combined with relevant DFT calculations have been used to characterize the dynamics, structure and vibrational frequencies to help identify the important intermediates as well as to explore the reaction pathway leading to formation of the solvolysis product in the largely water solvent. A consecutive mechanism has been revealed for the heterolysis-solvolysis reaction in the water mixed solvent. The present work provides direct and irrevocable evidence for the dynamics and mechanistic description of the overall photophysics and deprotection related photochemistry for BDP.

Efficient Synthesis of 2‘,3‘-Dideoxy-2‘-amino-3‘-thiouridine

[reaction: see text] Metal ion rescue experiments provide a powerful approach to establish the presence and role of divalent metal ions in the biological function of RNA. The utility of this approach depends on the availability of suitable nucleoside analogues. To expand the range of this experimental strategy, we describe the first synthesis of 2',3'-dideoxy-2'-amino-3'-thiouridine (12) in 19.5% overall yield starting from 2,2'-anhydrouridine (1).