Photolabile Linker Research Articles

Photocleavable Guide crRNAs for a Light-Controllable CRISPR/Cas9 System.

The design of controllable and precise RNA-targeted CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats) systems is an important problem of modern molecular biology and genetic technology. Herein, we have designed a series of photocleavable guide CRISPR RNAs (crRNA) and their 2'-modified (2'-fluoro and locked nucleic acid) analogs containing one or two 1-(2-nitrophenyl)-1,2-ethanediol photolabile linkers (PL). We have demonstrated that these crRNAs can be destroyed by relatively mild UVA irradiation with the rate constants 0.24-0.77 min-1 and that the photocleavage markedly slows down the action of Cas9 nuclease in the model in vitro system. Two PLs provide more rapid crRNA destruction than a single linker. PLs in the crRNA structure improve the specificity of DNA cleavage by Cas9 nuclease for the fully complementary target. The application of photocleavable crRNA in CRISPR/Cas9 genome editing permits the system to be switched off in a spatiotemporally controlled manner, thus alleviating its off-target effects.

Coumarin-Based Photodegradable Hydrogels Enable Two-Photon Subtractive Biofabrication at 300 mm s-1.

Spatiotemporally controlled two-photon photodegradation of hydrogels has gained increasing attention for high-precision subtractive tissue engineering. However, conventional photolabile hydrogels often have poor efficiency upon two-photon excitation in the near-infrared (NIR) region and thus require high laser dosage that may compromise cell activity. As a result, high-speed two-photon hydrogel erosion in the presence of cells remains challenging. Here we introduce the design and synthesis of efficient coumarin-based photodegradable hydrogels to overcome these limitations. A set of photolabile coumarin-functionalized polyethylene glycol linkers are synthesized through a Passerini multicomponent reaction. After mixing these linkers with thiolated hyaluronic acid, semi-synthetic photodegradable hydrogels are formed in situ via Michael addition crosslinking. The efficiency of photodegradation in these hydrogels is significantly higher than that in nitrobenzyl counterparts upon two-photon irradiation at 780 nm. A complex microfluidic network mimicking the bone microarchitecture is successfully fabricated in preformed coumarin hydrogels at high speeds of up to 300 mm s-1 and low laser dosage down to 10 mW. Further, we demonstrate fast two-photon printing of hollow microchannels inside a hydrogel to spatiotemporally direct cell migration in 3D. Collectively, these hydrogels may open new avenues for fast laser-guided tissue fabrication at high spatial resolution.

Single drop analysis of mercury ions by rational design of peptide coated gold nanoparticles integrated with MALDI-MS measurement

In this study, a novel and rapid method for specific identification and accurate quantification of Hg2+ in environmental water was developed by using laser cleavable cysteine containing peptides modified gold nanoparticles coupled with high resolution matrix-assisted laser desorption ionization time-of-flight mass spectrometer (MALDI-TOF MS) measurement. First, gold nanoparticles were prepared by the reduction of tetrachloroauric (III) acid (HAuCl4) solution. Various cysteine containing peptides, photolabile linkers, including mercury ion binding motif with a proper molecular mass and amino acids were synthesized by solid phase peptide synthesis (SPPS). Subsequently, thiol-containing peptides were coated onto the surface of gold nanoparticles via the formation of gold-thiol (Au–S) bond. The resulting cysteine containing peptides modified gold nanoparticles were designed to specifically capture Hg2+ in water samples. After conjugated complex formation, ions of Hg2+–peptide complex were directly liberated by ultraviolet laser radiation by way of MALDI-MS using α-Cyano-4-hydroxycinnamic acid (CHCA) as matrix. The linear dynamic range of Hg2+ concentration in this study was 1–100 pmol/μL with coefficient of determination 0.9987. The limit of detection (LOD) and limit of quantification (LOQ) were 0.19 and 0.63 pmol/μL, respectively. Notably, the developed method allows rapid quantification of Hg2+ in 5 min and the desired sample volume was down to few μL.

Engineering Enzyme-Cleavable Oligonucleotides by Automated Solid-Phase Incorporation of Cathepsin B Sensitive Dipeptide Linkers.

Oligonucleotides containing cleavable linkers have emerged as versatile tools to achieve stimulus‐responsive and site‐specific cleavage of DNA. However, the limitations of previously reported cleavable linkers including photolabile and disulfide linkers have restricted their applications in vivo. Inspired by the cathepsin B‐sensitive dipeptide linkers in antibody–drug conjugates (ADCs) such as Adcetris, we have developed Val‐Ala‐02 and Val‐Ala‐Chalcone phosphoramidites for the automated synthesis of enzyme‐cleavable oligonucleotides. Cathepsin B digests Val‐Ala‐02 and Val‐Ala‐Chalcone linkers efficiently, enabling cleavage of oligonucleotides into two components or release of small‐molecule payloads. Based on the prior success of dipeptide linkers in ADCs, we believe that these dipeptide linker phosphoramidites will promote new clinical applications of therapeutic oligonucleotides.

Engineering Enzyme-Cleavable Oligonucleotides by Automated Solid-Phase Incorporation of Cathepsin B Sensitive Dipeptide Linkers.

Oligonucleotides containing cleavable linkers have emerged as versatile tools to achieve stimulus-responsive and site-specific cleavage of DNA. However, the limitations of previously reported cleavable linkers including photolabile and disulfide linkers have restricted their applications in vivo. Inspired by the cathepsin B-sensitive dipeptide linkers in antibody-drug conjugates (ADCs) such as Adcetris, we have developed Val-Ala-02 and Val-Ala-Chalcone phosphoramidites for the automated synthesis of enzyme-cleavable oligonucleotides. Cathepsin B digests Val-Ala-02 and Val-Ala-Chalcone linkers efficiently, enabling cleavage of oligonucleotides into two components or release of small-molecule payloads. Based on the prior success of dipeptide linkers in ADCs, we believe that these dipeptide linker phosphoramidites will promote new clinical applications of therapeutic oligonucleotides.

Synthesis of a Lewis b hexasaccharide thioglycoside donor and its use towards an extended mucin core Tn heptasaccharide structure and a photoreactive biotinylated serine linked hexasaccharide.

Investigation into Heliobacter pylori binding to Lewis b (Leb) antigens through the blood group antigen binding adhesion protein (BabA) requires structurally well-defined tools. A Leb hexasaccharide thioglycoside donor was chemically prepared through a linear approach starting from D-lactose. This donor can be used to attach reducing end linkers providing a range of options for conjugation techniques or to further extend the oligosaccharide structure. To evaluate its efficiency as a donor, it was coupled to a 6-OH GalNAc acceptor, producing an extended Leb-containing Tn mucin core structure in 84% yield, and to L-serine in 72% yield. The latter compound was subsequently functionalized with a photolabile diazirine linker and biotin, creating a Leb hexasaccharide structure-function tool suitable for lectin tagging interaction studies. This donor opens a wide range of possibilities for conjugation of Leb structures to produce a variety of chemical biology tools to assist in the study of these interactions.

Automated Synthesis of Chondroitin Sulfate Oligosaccharides.

Glycosaminoglycans (GAGs) are important sulfated carbohydrates prevalently found in the extracellular matrix that serve many biological functions. The synthesis of structurally diverse but defined GAGs is extremely challenging as one has to account for the various sulfation patterns. Described is the automated synthesis of chondroitin sulfate hexasaccharides on a solid support equipped with a photolabile linker. The linker cleavage from the resin is performed in a continuous-flow photoreactor under chemically mild conditions. This approach serves as a general scheme to access oligosaccharides of all GAG families.

Synchronization of Nanoparticle Sensitization and Radiosensitizing Chemotherapy through Cell Cycle Arrest Achieving Ultralow X-ray Dose Delivery to Pancreatic Tumors.

Pancreatic cancer is among the leading causes of cancer-related death and remains a formidable therapeutic challenge. To date, surgical resection and chemotherapy have been the standards of care. Methotrexate (MTX), which is recognized as a refractory drug for pancreatic cells, was conjugated to the surface of LiYF4:Ce3+ nanoparticles (NP-MTX) through a photocleavable linker molecule. When LiYF4:Ce3+ NPs are stimulated by X-rays, they emit light, which induces the photocleavage of the photolabile linker molecule to release MTX. MTX can target pancreatic tumors, which overexpress folic acid (FA) receptors and are internalized into the cell through receptor-mediated endocytosis. The synergistic effect of the NP-MTX treatment initiated by X-ray irradiation occurs due to the combination of nanoparticle sensitization and the radiosensitizing chemotherapy of the photocleaved MTX molecule. This dual sensitization effect mediated by NP-MTX enabled 40% dose enhancement, which corresponded with an increase in the generation of cytotoxic cellular reactive oxygen species (ROS) and enhanced S phase arrest within the cell cycle. The delivery of an ultralow radiation dose of 0.1 Gy resulted in the photocleavage of MTX from NP-MTX, and this strategy demonstrated in vivo efficacy against AsPC-1 and PANC-1 xenografted pancreatic tumors.

Vitamin B12 Derivatives Suitably Tailored for the Synthesis of Photolabile Conjugates.

Vitamin B12 conjugates are broadly studied in biological sciences. As light offers spatiotemporal control, we decided to develop a method for the preparation of vitamin B12 conjugates that release tethered molecules upon exposure to light. Herein, we report vitamin B12 derivatives possessing a photolabile linker suitable for conjugation with amines, azides, and alkynes. The potential applications of such conjugates are broad and include the delivery of drugs, labels, and imaging agents to their place of action and spatiotemporal release.

Red Light-Triggered Polyethylene Glycol Deshielding from Photolabile Cyanine-Modified Mesoporous Silica Nanoparticles for On-Demand Drug Release.

PEGylation of drug delivery systems (DDSs) provides a promising approach to overcome the side effect of traditional chemotherapy via the enhanced permeability and retention (EPR) effect, although it further inhibits the internalization behavior of nanocarriers. PEGylation/dePEGylation of the nanocarriers at the desired site exhibits great advantages for nanocarrier-based on-demand drug release. Here, we reported a photoinduced polyethylene glycol (PEG) deshielding nanocarrier, SiO2@DOX-Cy-PEG, for on-demand drug release in an acidic tumor microenvironment. SiO2@DOX nanoparticles were functionalized with PEG-alkyne chains by click reaction with the photolabile cyanine-azide linkers. Under red light irradiation (650 nm), doxorubicin (DOX) can be effectively released from mesoporous silica nanoparticles (MSNs) due to the photolysis of Cy, resulting in the cleavage of the linkers and PEG deshielding in cancer cells. Therefore, SiO2@DOX-Cy-PEG nanoparticles with irradiation arouse a higher cell apoptosis and death ratio, further proving that dePEGylation of MSNs accelerates the release of DOX. In addition, the experiment of the antitumor effect in vivo demonstrated that dePEGylation of the SiO2@DOX-Cy-PEG could effectively promote the therapeutic effect on xenografted 4T1 tumor-bearing BALB/c mice. The results suggested that SiO2@DOX-Cy-PEG was a precisely and remotely on-demand drug delivery system controlled by red light.

On-demand and tunable dual wavelength release of antibody using light-responsive hydrogels.

There has been an increased interest in the use of protein therapeutics, especially antibodies, for the treatment of a variety of diseases due to their high specificity to tissues and biological pathways of interest. However, the use of antibodies can be hindered by physical aggregation, degradation, and diffusion when injected in vivo leading to the need for antibody-releasing depots for the controlled and localized delivery within tissues of interest. Here, we investigated photolabile hydrogel chemistries for creating on-demand and tunable antibody release profiles. Innovative, scalable synthetic procedures were established and applied for fabricating hydrogels with nitrobenzyl (NB) and coumarin (CMR) photolabile crosslinks that responded to clinically relevant doses of long-wavelength UV and short-wavelength visible light. This synthetic procedure includes a route to make a CMR linker possessing two functional handles at the same ring position with water-stable bonds. The photocleavage properties of NB and CMR crosslinked hydrogels were characterized, as well as their potential for translational studies by degradation through pig skin, a good human skin mimic. The mechanism of hydrogel degradation, bulk versus surface eroding, was determined to be dependent on the wavelength of light utilized and the molar absorptivity of the different photolabile linkers, providing a facile means for altering protein release upon hydrogel degradation. Further, the encapsulation and on-demand release of a model monoclonal antibody was demonstrated, highlighting the ability to control antibody release from these hydrogels through the application of light while retaining its bioactivity. In particular, the newly designed CMR hydrogels undergo surface erosion-based protein release using visible light, which is more commonly used clinically. Overall, this work establishes scalable syntheses and relevant pairings of formulation-irradiation conditions for designing on-demand and light-responsive material systems that provide controlled, tunable release of bioactive proteins toward addressing barriers to preclinical translation of light-based materials and ultimately improving therapeutic regimens.

Optical Control of a CRISPR/Cas9 System for Gene Editing by Using Photolabile crRNA

AbstractCurrently CRISPR/Cas9 is a widely used efficient tool for gene editing. Precise control over the CRISPR/Cas9 system with high temporal and spatial resolution is essential for studying gene regulation and editing. Here, we synthesized a novel light‐controlled crRNA by coupling vitamin E and a photolabile linker at the 5′ terminus to inactivate the CRISPR/Cas9 system. The vitamin E modification did not affect ribonucleoprotein (RNP) formation of Cas9/crRNA/tracrRNA complexes but did inhibit the association of RNP with the target DNA. Upon light irradiation, vitamin E‐caged crRNA was successfully activated to achieve light‐induced genome editing of vascular endothelial cell‐growth factor A (VEGFA) in human cells through a T7E1 assay and Sanger sequencing as well as gene knockdown of EGFP expression in EGFP stably expressing cells. This new caging strategy for crRNA could provide new methods for spatiotemporal photoregulation of CRISPR/Cas9‐mediated gene editing.

Optical Control of a CRISPR/Cas9 System for Gene Editing by Using Photolabile crRNA.

Currently CRISPR/Cas9 is a widely used efficient tool for gene editing. Precise control over the CRISPR/Cas9 system with high temporal and spatial resolution is essential for studying gene regulation and editing. Here, we synthesized a novel light-controlled crRNA by coupling vitamin E and a photolabile linker at the 5' terminus to inactivate the CRISPR/Cas9 system. The vitamin E modification did not affect ribonucleoprotein (RNP) formation of Cas9/crRNA/tracrRNA complexes but did inhibit the association of RNP with the target DNA. Upon light irradiation, vitamin E-caged crRNA was successfully activated to achieve light-induced genome editing of vascular endothelial cell-growth factor A (VEGFA) in human cells through a T7E1 assay and Sanger sequencing as well as gene knockdown of EGFP expression in EGFP stably expressing cells. This new caging strategy for crRNA could provide new methods for spatiotemporal photoregulation of CRISPR/Cas9-mediated gene editing.

Flow Photocleavage for Automated Glycan Assembly (AGA)

Automated glycan assembly (AGA) is contingent on the development of simple, efficient cleavage strategies to liberate complex, high value products from a solid support resin. Given the rapid advances in the structural complexity of carbohydrates that can be constructed via this enabling technology, effective cleavage is a persistent challenge. Photolabile linkers have a venerable history in AGA and mitigate potential complications arising from chemically induced release protocols. However, photochemical cleavage strategies have traditionally relied upon mercury vapor lamps, which present challenges in establishing well-defined, reproducible, and nonhazardous conditions for this ultimate step of the AGA sequence. To complement the existing batch strategies, a safe and sustainable approach for the continuous flow photocleavage from solid support using LEDs has been developed. By employing a custom-built LED flow reactor, photocleavage yields of up to 80% were achieved in less than 1 h. Efficiency could be further improved by merging flow photochemistry with pregrinding. Validation of this strategy is showcased in a proof of concept AGA synthesis of a model dimannoside.

Rapid Generation of Hierarchically Porous Metal–Organic Frameworks through Laser Photolysis

Hierarchically porous metal-organic frameworks (HP-MOFs) facilitate mass transfer due to mesoporosity while preserving the advantage of microporosity. This unique feature endows HP-MOFs with remarkable application potential in multiple fields. Recently, new methods such as linker labilization for the construction of HP-MOFs have emerged. To further enrich the synthetic toolkit of MOFs, we report a controlled photolytic removal of linkers to create mesopores within microporous MOFs at tens of milliseconds. Ultraviolet (UV) laser has been applied to eliminate "photolabile" linkers without affecting the overall crystallinity and integrity of the original framework. Presumably, the creation of mesopores can be attributed to the missing-cluster defects, which can be tuned through varying the time of laser exposure and ratio of photolabile/robust linkers. Upon laser exposure, MOF crystals shrank while metal oxide nanoparticles formed giving rise to the HP-MOFs. In addition, photolysis can also be utilized for the fabrication of complicated patterns with high precision, paving the way towards MOF lithography, which has enormous potential in sensing and catalysis.

Photolabile Linkers: Exploiting Labile Bond Chemistry to Control Mode and Rate of Hydrogel Degradation and Protein Release.

Photolabile moieties have been utilized in applications ranging from peptide synthesis and controlled protein activation to tunable and dynamic materials. The photochromic properties of nitrobenzyl (NB) based linkers are readily tuned to respond to cytocompatible light doses and are widely utilized in cell culture and otherbiological applications. While widely utilized, little is known about how the microenvironment, particularly confined aqueous environments (e.g., hydrogels), affects both the mode and rate of cleavage of NB moieties, leading to unpredictable limitations in control over system properties (e.g., rapid hydrolysis or slow photolysis). To address these challenges, we synthesized and characterized the photolysis and hydrolysis of NB moieties containing different labile bonds (i.e., ester, amide, carbonate, or carbamate) that served as labile crosslinkswithin step-growth hydrogels. We observed that NB ester bond exhibited significant rates of both photolysis and hydrolysis, whereas, importantly, the NB carbamate bond had superior light responsiveness and resistance to hydrolysis within the hydrogel microenvironment. Exploiting this synergy and orthogonality of photolytic and hydrolytic degradation, we designed concentric cylinder hydrogels loaded with different cargoes (e.g., model protein with different fluorophores) for either combinatorial or sequential release, respectively. Overall, this work provides new facile chemical approaches for tuning the degradability of NB linkers and an innovative strategy for the construction of multimodal degradable hydrogels, which can be utilized to guide the design of not only tunable materials platforms but also controlled synthetic protocols or surface modification strategies.

Synthesis and Evaluation of Caged siRNAs with Single cRGD Modification for Photoregulating RNA Interference.

We designed and synthesized caged siRNAs with photolabile linker and single cRGD peptide modifications for the photoregulation of gene expression. Photolabile linker and cRGD were inserted at 5' terminus of siRNAs to obtain cRGD-modified caged siRNAs. All these caged siRNAs could be activated through light activation to release the native siRNAs and further achieve the photoregulation of gene silencing of two exogenous reporter genes (firefly luciferase and green fluorescent protein, GFP) and one endogenous gene (the mitosis motor protein, Eg5). The intracellular distribution and cellular uptake pathways of these caged siRNAs were also investigated. Tumor-bearing mice were further used to demonstrate the photoregulation of gene silencing with cRGD-modified caged siRNAs in vivo. Overall, the data support the use of this new generation of caged siRNAs in cancer therapy.

The breaking beads approach for photocleavage from solid support.

Photocleavage from polystyrene beads is a pivotal reaction for solid phase synthesis that relies on photolabile linkers. Photocleavage from intact porous polystyrene beads is not optimal because light cannot penetrate into the beads and the surface area exposed to irradiation is limited. Thus, hazardous, technically challenging and expensive setups are used for photocleavage from intact beads. We developed a new concept in which grinding the beads during or prior to irradiation is employed as an essential part of the photocleavage process. By grinding the beads we are exposing more surface area to the light source, hence, photocleavage can be performed even using a simple benchtop LED setup. This approach proved very efficient for photocleavage of various model compounds including fully protected oligosaccharides.

Cellular expression through morphogen delivery by light activated magnetic microrobots

Microrobots have many potential uses in microbiology since they can be remotely actuated and precisely manipulated in biochemical fluids. Cellular function and response depends on biochemicals. Therefore, various delivery methods have been developed for delivering biologically relevant cargo using microrobots. However, localized targeting without payload leakage during transport is challenging. Here, we design a microrobotic platform capable of on-demand delivery of signaling molecules in biological systems. The on-demand delivery method is based on a light-responsive photolabile linker which releases a cell-to-cell signaling molecule when exposed to light, integrated on the surface of microrobots. Successful delivery of the signaling molecules and subsequent gene regulation is also demonstrated. This proposed method can be used for multiple applications, especially in biology, engineering, and medicine where on-demand delivery of chemical cargo at targeted locations is important.

Traceless Photolabile Linker Expedites the Chemical Synthesis of Complex Oligosaccharides by Automated Glycan Assembly.

Automated glycan assembly (AGA) aims at accelerating access to synthetic oligosaccharides to meet the demand for defined glycans as tools for molecular glycobiology. The linkers used to connect the growing glycan chain to the solid support play a pivotal role in the synthesis strategy as they determine all chemical conditions used during the synthesis and the form of the glycan obtained at the end of it. Here, we describe a traceless photolabile linker used to prepare carbohydrates with a free reducing end. Modification of the o-nitrobenzyl scaffold of the linker is key to high yields and compatibility with the AGA workflow. The assembly of an asymmetrical biantennary N-glycan from oligosaccharide fragments prepared by AGA and linear as well as branched β-oligoglucans is described to illustrate the power of the method. These substrates will serve as standards and biomarkers to examine the unique specificity of glycosyl hydrolases.