Next-Generation o-Nitrobenzyl Photolabile Groups for Light-Directed Chemistry and Microarray Synthesis

Recent progress in DNA data storage based on high-throughput DNA synthesis

DNA data storage has emerged as a solution for storing massive volumes of data by utilizing nucleic acids as a digital information medium. DNA offers exceptionally high storage density, long durability, and low maintenance costs compared to conventional storage media such as flash memory and hard disk drives. DNA data storage consists of the following steps: encoding, DNA synthesis (i.e., writing), preservation, retrieval, DNA sequencing (i.e., reading), and decoding. Out of these steps, DNA synthesis presents a bottleneck due to imperfect coupling efficiency, low throughput, and excessive use of organic solvents. Overcoming these challenges is essential to establish DNA as a viable data storage medium. In this review, we provide the overall process of DNA data storage, presenting the recent progress of each step. Next, we examine a detailed overview of DNA synthesis methods with an emphasis on their limitations. Lastly, we discuss the efforts to overcome the constraints of each method and their prospects.

Accelerated, high-quality photolithographic synthesis of RNA microarrays in situ

Nucleic acid photolithography is the only microarray fabrication process that has demonstrated chemical versatility accommodating any type of nucleic acid. The current approach to RNA microarray synthesis requires long coupling and photolysis times and suffers from unavoidable degradation postsynthesis. In this study, we developed a series of RNA phosphoramidites with improved chemical and photochemical protection of the 2'- and 5'-OH functions. In so doing, we reduced the coupling time by more than half and the photolysis time by a factor of 4. Sequence libraries that would otherwise take over 6 hours to synthesize can now be prepared in half the time. Degradation is substantially lowered, and concomitantly, hybridization signals can reach over seven times those of the previous state of the art. Under those conditions, high-density RNA microarrays and RNA libraries can now be synthesized at greatly accelerated rates. We also synthesized fluorogenic RNA Mango aptamers on microarrays and investigated the effect of sequence mutations on their fluorogenic properties.

High-throughput DNA synthesis for data storage

With the explosion of digital world, the dramatically increasing data volume is expected to reach 175 ZB (1 ZB = 1012 GB) in 2025. Storing such huge global data would consume tons of resources. Fortunately, it has been found that the deoxyribonucleic acid (DNA) molecule is the most compact and durable information storage medium in the world so far. Its high coding density and long-term preservation properties make itself one of the best data storage carriers for the future. High-throughput DNA synthesis is a key technology for "DNA data storage", which encodes binary data stream (0/1) into quaternary long DNA sequences consisting of four bases (A/G/C/T). In this review, the workflow of DNA data storage and the basic methods of artificial DNA synthesis technology are outlined first. Then, the technical characteristics of different synthesis methods and the state-of-the-art of representative commercial companies, with a primary focus on silicon chip microarray-based synthesis and novel enzymatic DNA synthesis are presented. Finally, the recent status of DNA storage and new opportunities for future development in the field of high-throughput, large-scale DNA synthesis technology are summarized.

The effects of photoactivated ciprofloxacin and bile acids on biofilms on bile duct catheters

OBJECTIVES

This study examined the potential of a novel photoactivatable ciprofloxacin to act against bacterial infections and microbiomes related to biliary diseases. It also evaluated treatment by combining the impact of bile acids and antibiotics on biofilms. Innovative strategies were evaluated to address the elusive bile duct microbiome resulting in biofilm-related infections linked to biliary catheters. The healthy biliary system is considered sterile, but bile microbiomes can occur in disease, and these correlate with hepatobiliary diseases. Causes include biofilms that form on internal-external biliary drainage catheters. These biliary catheters were used to noninvasively study the otherwise elusive bile microbiome for a pilot study.

METHODS

A new photoactivatable antibiotic was tested for efficacy against human-derived pathogenic bacterial isolates - Salmonella enterica and Escherichia coli - and catheter-derived bile duct microbiomes. In addition, the effect of bile acids on the antibiotic treatment of biofilms was quantified using crystal violet staining, confocal laser scanning microscopy, and biofilm image analysis. Two novel approaches for targeting biliary biofilms were tested.

RESULTS

A photoactivated antibiotic based on ciprofloxacin showed efficacy in preventing biofilm formation and reducing bacterial viability without harming eukaryotic cells. Furthermore, combination treatment of antibiotics with bile acids, such as ursodesoxycholic acid, mildly influenced biofilm biomass but reduced bacterial survival within biofilms.

CONCLUSION

Bile acids, in addition to their endocrine and paracrine functions, may enhance antibiotic killing of bacterial biofilms compared with antibiotics alone. These approaches hold promise for treating biliary infections such as cholangitis.

An Update on Protection of 5'-Hydroxyl Functions of Nucleosides and Oligonucleotides

The synthesis of natural and chemically modified nucleosides and oligonucleotides is in great demand due to its increasing number of applications in diverse areas of research. These include tools for diagnostics and proteomics, research reagents for molecular biology, probes for functional genomics, and the design, discovery, development, and manufacture of new therapeutics. The likelihood of success in synthesizing these molecules is often dependent on the correct choice of a protection strategy to block the 5'-hydroxyl group of a carbohydrate moiety, nucleoside, or oligonucleotide. This topic was reviewed extensively in the year 2000. The purpose of this article is to complement and update the original review with recently published methodologies recommended for the protection and deprotection of the 5'-hydroxyl group. © 2024 Wiley Periodicals LLC.

Nonaqueous Oxidation in DNA Microarray Synthesis Improves the Oligonucleotide Quality and Preserves Surface Integrity on Gold and Indium Tin Oxide Substrates

Nucleic acids attached to electrically conductive surfaces are very frequently used platforms for sensing and analyte detection as well as for imaging. Synthesizing DNA on these uncommon substrates and preserving the conductive layer is challenging as this coating tends to be damaged by the repeated use of iodine and water, which is the standard oxidizing medium following phosphoramidite coupling. Here, we thoroughly investigate the use of camphorsulfonyl oxaziridine (CSO), a nonaqueous alternative to I2/H2O, for the synthesis of DNA microarrays in situ. We find that CSO performs equally well in producing high hybridization signals on glass microscope slides, and CSO also protects the conductive layer on gold and indium tin oxide (ITO)-coated slides. DNA synthesis on conductive substrates with CSO oxidation yields microarrays of quality approaching that of conventional glass with intact physicochemical properties.

Dipodal Silanes Greatly Stabilize Glass Surface Functionalization for DNA Microarray Synthesis and High-Throughput Biological Assays

Glass is by far the most common substrate for biomolecular arrays, including high-throughput sequencing flow cells and microarrays. The native glass hydroxyl surface is modified by using silane chemistry to provide appropriate functional groups and reactivities for either in situ synthesis or surface immobilization of biologically or chemically synthesized biomolecules. These arrays, typically of oligonucleotides or peptides, are then subjected to long incubation times in warm aqueous buffers prior to fluorescence readout. Under these conditions, the siloxy bonds to the glass are susceptible to hydrolysis, resulting in significant loss of biomolecules and concomitant loss of signal from the assay. Here, we demonstrate that functionalization of glass surfaces with dipodal silanes results in greatly improved stability compared to equivalent functionalization with standard monopodal silanes. Using photolithographic in situ synthesis of DNA, we show that dipodal silanes are compatible with phosphoramidite chemistry and that hybridization performed on the resulting arrays provides greatly improved signal and signal-to-noise ratios compared with surfaces functionalized with monopodal silanes.

An 8-bit monochrome palette of fluorescent nucleic acid sequences for DNA-based painting

The ability to regulate, maintain and reproduce fluorogenic properties is a fundamental prerequisite of modern molecular diagnostics, nanotechnology and bioimaging. The sequence-dependence of the fluorescence properties in fluorophores commonly used in nucleic acid labelling is here being exploited to assemble a color scale in 256 shades of green Cy3 fluorescence. Using photolithography, we synthesize microarrays of labeled nucleic acids that can accurately reproduce 8-bit monochrome graphics by mapping color to fluorescence intensity and sequence. This DNA-based painting approach paves the way for a full RGB scale array fabrication process.

Efficiency of Functional Group Caging with Second-Generation Green- and Red-Light-Labile BODIPY Photoremovable Protecting Groups

BODIPY-based photocages release substrates by excitation with wavelengths in the visible to near-IR regions. The recent development of more efficient BODIPY photocages spurred us to evaluate the scope and efficiency of these second-generation boron-methylated green-light and red-light-absorbing BODIPY photocages. Here, we show that these more photosensitive photocages release amine, alcohol, phenol, phosphate, halides, and carboxylic acid derivatives with much higher quantum yields than first-generation BODIPY photocages and excellent chemical yields. Chemical yields are near-quantitative for the release of all functional groups except the photorelease of amines, which react with concomitantly photogenerated singlet oxygen. In these cases, high chemical yields for photoreleased amines are restored by irradiation under an inert atmosphere. The photorelease quantum yield has a weak relationship with the leaving group pK_a of the green-absorbing BODIPY photocages but little relationship with the red-absorbing derivatives, suggesting that factors other than leaving group quality impact the quantum yield. For the photorelease of alcohols, in all cases a carbonate linker (that loses CO₂ upon photorelease) significantly increases both the quantum yield and the chemical yield compared to those for direct photorelease via the ether.

Spotting Trends in Organocatalyzed and Other Organomediated (De)polymerizations and Polymer Functionalizations

Organocatalysis has evolved into an effective complement to metal- or enzyme-based catalysis in polymerization, polymer functionalization, and depolymerization. The ease of removal and greater sustainability of organocatalysts relative to transition-metal-based ones has spurred development in specialty applications, e.g., medical devices, drug delivery, optoelectronics. Despite this, the use of organocatalysis and other organomediated reactions in polymer chemistry is still rapidly developing, and we envisage their rapidly growing application in nascent areas such as controlled radical polymerization, additive manufacturing, and chemical recycling in the coming years. In this Review, we describe ten trending areas where we anticipate paradigm shifts resulting from novel organocatalysts and other transition-metal-free conditions. We highlight opportunities and challenges and detail how new discoveries could lead to previously inaccessible functional materials and a potentially circular plastics economy.

Sequence-dependence of Cy3 and Cy5 dyes in 3' terminally-labeled single-stranded DNA

Fluorescence is an ideal tool to see and manipulate nucleic acids, and engage in their rich and complex biophysical properties. Labeling is the preferred approach to track and quantify fluorescence with nucleic acids and cyanine dyes are emblematic in this context. The fluorescent properties of cyanine dyes are known to be sequence-dependent, with purines in the immediate vicinity increasing the fluorescence intensity of Cy3 and Cy5 dyes, and the ability of nucleobases to modulate the photophysical properties of common fluorophores may influence fluorescence measurements in critical assays such as FISH, qPCR or high-throughput sequencing. In this paper, we comprehensively map the sequence-dependence of Cy3 and Cy5 dyes in 3'-fluorescently labeled single-stranded DNA by preparing the complete permutation library of the 5 consecutive nucleotides immediately adjacent to the dye, or 1024 sequences. G-rich motifs dominate the high fluorescence range, while C-rich motifs lead to significant quenching, an observation consistent with 5'-labeled systems. We also uncover GCGC patterns in the extreme top range of fluorescence, a feature specific to 3'-Cy3 and Cy5 oligonucleotides. This study represents the final piece in linking nucleotide identity to fluorescence changes for Cy3, Cy5 and fluorescein in all 3', 5', single-stranded and double-stranded DNA formats.

Simple synthesis of massively parallel RNA microarrays via enzymatic conversion from DNA microarrays

RNA catalytic and binding interactions with proteins and small molecules are fundamental elements of cellular life processes as well as the basis for RNA therapeutics and molecular engineering. In the absence of quantitative predictive capacity for such bioaffinity interactions, high throughput experimental approaches are needed to sufficiently sample RNA sequence space. Here we report on a simple and highly accessible approach to convert commercially available customized DNA microarrays of any complexity and density to RNA microarrays via a T7 RNA polymerase-mediated extension of photocrosslinked methyl RNA primers and subsequent degradation of the DNA templates.

Blue or Near-Infrared Light-Triggered Release of Halogens via Blebbistatin Photocage

Photocages can provide spatial and temporal control to accurately release the various chemicals and bioactive groups when excited by light. Although the absorption spectra of most photocages are in the ultraviolet absorption region, only a few absorb in the visible or near-infrared region. Blebbistatin (Bleb) would release a hydroxyl radical under blue one-photon or two-photon near-infrared light (800 nm) irradiation. In this work, typical chlorine and bromine as leaving groups substituted hydroxyl compounds (Bleb-Cl, Bleb-Br) are synthesized to evaluate the photocage's capability of Bleb's platform. Driven by the excited-state charge transfer, Bleb-Cl and Bleb-Br show good photolysis quantum yield to uncage the halogen anion and the uncaging process would be accelerated in water solution. The photochemical reaction, final product's analysis, and femtosecond transient absorption studies on Bleb-Cl/Bleb-Br demonstrate that Bleb can act as a photocage platform to release the halogen ion via heterolytic reaction when irradiated by blue or near-infrared light. Therefore, Bleb can be a new generation of visible or near-infrared light-triggered photocage.

Synthesis of Cyclic Peptides in SPPS with Npb-OH Photolabile Protecting Group

Significant efforts have been made in recent years to identify more environmentally benign and safe alternatives to side-chain protection and deprotection in solid-phase peptide synthesis (SPPS). Several protecting groups have been endorsed as suitable candidates, but finding a greener protecting group in SPPS has been challenging. Here, based on the 2-(o-nitrophenyl) propan-1-ol (Npp-OH) photolabile protecting group, a structural modification was carried out to synthesize a series of derivatives. Through experimental verification, we found that 3-(o-Nitrophenyl) butan-2-ol (Npb-OH) had a high photo-release rate, high tolerance to the key conditions of Fmoc-SPPS (20% piperidine DMF alkaline solution, and pure TFA acidic solution), and applicability as a carboxyl-protective group in aliphatic and aromatic carboxyl groups. Finally, Npb-OH was successfully applied to the synthesis of head–tail cyclic peptides and side-chain–tail cyclic peptides. Moreover, we found that Npb-OH could effectively resist diketopiperazines (DKP). The α-H of Npb-OH was found to be necessary for its photosensitivity in comparison to 3-(o-Nitrophenyl)but-3-en-2-ol (Npbe-OH) during photolysis-rate verification.

A disulfide-based linker for thiol-norbornene conjugation: formation and cleavage of hydrogels by the use of light

Photolabile groups are the key components of photo-responsive polymers, dynamically tunable materials with multiple applications in materials and life sciences. They usually consist of a chromophore and a labile bond and are inherently light sensitive. An exception are disulfides, simple reversible linkages, which become photocleavable upon addition of a photoinitiator. Despite their practical features, disulfides are rarely utilized due to their impractical formation. Here, we report a disulfide-based linker series bearing norbornene terminals for facile crosslinking of thiol-functionalized macromers via light-triggered thiol-ene conjugation (TEC). Besides finding a highly reactive lead compound, we also identify an unexpected TEC-retardation, strongly dependent on the molecular linker structure and affecting hydrogel stability. Finally, we present a useful method for localized disulfide cleavage by two-photon irradiation permitting micropatterning of disulfide-crosslinked networks.

Photolabile 2-(2-Nitrophenyl)-propyloxycarbonyl (NPPOC) for Stereoselective Glycosylation and Its Application in Consecutive Assembly of Oligosaccharides

A photolabile protecting group (PPG) 2-(2-nitrophenyl)-propyloxycarbonyl (NPPOC) was explored in glycosylation and applied in the consecutive synthesis of oligosaccharides. NPPOC displays a strong neighboring group participation (NGP) effect to facilitate the construction of 1,2-trans glycosides in excellent yield. Notably, NPPOC could be efficiently removed by photolysis, and the deprotection conditions are friendly to typical protecting groups. A branched and asymmetric oligomannose Man6 was rapidly prepared, and the consecutive assembly of oligosaccharides without intermediate purification was further investigated owing to the compatibility conditions between NPPPOC's photolysis and glycosylation.

Sequence-dependent quenching of fluorescein fluorescence on single-stranded and double-stranded DNA

Fluorescein is commonly used to label macromolecules, particularly proteins and nucleic acids, but its fluorescence is known to be strongly dependent on its direct chemical environment.

Exploring the Potential of 2-(2-Nitrophenyl)ethyl-Caged N-Hydroxysulfonamides for the Photoactivated Release of Nitroxyl (HNO)

The emergence of nitroxyl (HNO) as a biological signaling molecule is attracting increasing attention. HNO-based prodrugs show considerable potential in treating congestive heart failure, with HNO reacting rapidly with metal centers and protein-bound and free thiols. A new class of 2-(2-nitrophenyl)ethyl (2-NPE)-photocaged N-hydroxysulfonamides has been developed, and the mechanisms of photodecomposition have been investigated. Three photodecomposition pathways are observed: the desired concomitant C-O/N-S bond cleavage to generate HNO, sulfinate, and 2-nitrostyrene, C-O bond cleavage to give the parent sulfohydroxamic acid and 2-nitrostyrene, and O-N bond cleavage to release a sulfonamide and 2-nitrophenylacetaldehyde. Laser flash photolysis experiments provide support for a Norrish type II mechanism involving 1,5-hydrogen atom abstraction to generate an aci-nitro species. A mechanism is proposed in which the (Z)-aci-nitro intermediate undergoes either C-O bond cleavage to release RSO₂NHO(H), concerted C-O/N-S bond cleavage to generate sulfinate and HNO, or isomerization to the (E)-isomer prior to O-N bond cleavage. The pK_a of the N(H) of the N-hydroxysulfonamide plays a key role in determining whether C-O or concerted C-O/N-S bond cleavage occurs. Deprotonating this site favors the desired C-O/N-S bond cleavage at the expense of an increased level of undesired O-N bond cleavage. Triplet state quenchers have no effect on the observed photoproducts.

Bitter Sensing TAS2R50 Mediates the trans-Resveratrol-Induced Anti-inflammatory Effect on Interleukin 6 Release in HGF-1 Cells in Culture

Recent data have shown anti-inflammatory effects for trans-resveratrol (RSV) and rosmarinic acid (RA) in various immune-competent cell models through reduction of lipopolysaccharide (LPS)-induced interleukin 6 (IL-6) release. Because both compounds have been reported to taste bitter, we hypothesized an involvement of human bitter taste sensing receptors (TAS2Rs) on IL-6 release in LPS-treated human gingival fibroblasts (HGF-1). First, the bitter taste intensity of RSV and RA was compared in a sensory trial with 10 untrained panelists, of whom 90% rated a 50 ppm of RSV in water solution more bitter than 50 ppm of RA. A mean 19 ± 6% reduction of the RSV-induced bitter taste intensity was achieved by co-administration of 50 ppm of the bitter-masking, TAS2R43 antagonist homoeriodictyol (HED). Mechanistic experiments in a stably CRISPR-Cas9-edited TAS2R43ko gastric cell model revealed involvement of TAS2R43 in the HED-evoked effect on RSV-induced proton secretion, whereas the cellular response to RSV did not depend upon TAS2R43. Next, the IL-6 modulatory effect of 100 μM RSV was studied in LPS-treated immune-competent HGF-1 cells. After 6 h of treatment, RSV reduced the LPS-induced IL-6 gene expression and protein release by -46.2 ± 12.7 and -73.9 ± 2.99%, respectively. This RSV-evoked effect was abolished by co-administration of HED. Because real-time quantitative polymerase chain reaction analyses revealed a regulation of TAS2R50 in RSV with or without HED-treated HGF-1 cells, an siRNA knockdown approach of TAS2R50 was applied to verify TAS2R50 involvement in the RSV-induced reduction of the LPS-evoked IL-6 release in HGT-1 cells.

Luminescence switching in polymerically confined carbon nanoparticles triggered by UV-light

Photo-caged carbon nanoparticles (CNPs) that are non-luminescent under typical microscopic illumination but can be activated by UV light have been synthesized in this work. Negatively charged "bare" CNPs with high luminescence can lose their photoluminescence (PL) when they are chemically crosslinked to a monomer and subsequently polymerized to form an intra-particulate "caged" network at the nanoscale surface. These caged particles could regain their PL emission upon UV irradiation for a sustained period (∼24 h) resulting in the photolytic cleavage of the polymer network, thus, freeing the nanoscale surface of CNPs, ultimately resulting in six-fold emission enhancement. This reversible "on-off-on" PL switching process was verified by spectroscopic techniques. We successfully demonstrated in this work that CNPs can be switched reversibly between fluorescent and non-fluorescent states by irradiation with light. These results further substantiate that the origin of PL in CNPs is a surface phenomenon and highly dependent on their nanoscale coverage.

Chemical and photochemical error rates in light-directed synthesis of complex DNA libraries

Nucleic acid microarrays are the only tools that can supply very large oligonucleotide libraries, cornerstones of the nascent fields of de novo gene assembly and DNA data storage. Although the chemical synthesis of oligonucleotides is highly developed and robust, it is not error free, requiring the design of methods that can correct or compensate for errors, or select for high-fidelity oligomers. However, outside the realm of array manufacturers, little is known about the sources of errors and their extent. In this study, we look at the error rate of DNA libraries synthesized by photolithography and dissect the proportion of deletion, insertion and substitution errors. We find that the deletion rate is governed by the photolysis yield. We identify the most important substitution error and correlate it to phosphoramidite coupling. Besides synthetic failures originating from the coupling cycle, we uncover the role of imperfections and limitations related to optics, highlight the importance of absorbing UV light to avoid internal reflections and chart the dependence of error rate on both position on the array and position within individual oligonucleotides. Being able to precisely quantify all types of errors will allow for optimal choice of fabrication parameters and array design.

Sequence Preference and Initiator Promiscuity for De Novo DNA Synthesis by Terminal Deoxynucleotidyl Transferase

The untemplated activity of terminal deoxynucleotidyl transferase (TdT) represents its most appealing feature. Its use is well established in applications aiming for extension of a DNA initiator strand, but a more recent focus points to its potential in enzymatic de novo synthesis of DNA. Whereas its low substrate specificity for nucleoside triphosphates has been studied extensively, here we interrogate how the activity of TdT is modulated by the nature of the initiating strands, in particular their length, chemistry, and nucleotide composition. Investigation of full permutational libraries of mono- to pentamers of d-DNA, l-DNA, and 2′O-methyl-RNA of differing directionality immobilized to glass surfaces, and generated via photolithographic in situ synthesis, shows that the efficiency of extension strongly depends on the nucleobase sequence. We also show TdT being catalytically active on a non-nucleosidic substrate, hexaethylene glycol. These results offer new perspectives on constraints and strategies for de novo synthesis of DNA using TdT regarding the requirements for initiation of enzymatic generation of DNA.

Multiwavelength Control of Mixtures Using Visible Light-Absorbing Photocages

Selective deprotection of functional groups using different wavelengths of light is attractive for materials synthesis as well as for achieving independent photocontrol over substrates in biological systems. Here, we show that mixtures of recently developed visible light-absorbing BODIPY-derived photoremovable protecting groups (PRPGs) and a coumarin-derived PRPG can undergo wavelength-selective activation, giving independent optical control over a mixture of photocaged substrates using biologically benign long-wavelength light.

Synthesis and Characterisation of Photolabile SPhNPPOC-Protected (R)-MiniPEG Containing Chiral γ-Peptide Nucleic Acid Monomers

Peptide nucleic acid (PNA) microarrays are expected to be developed as a new generation of gene detection tools. However, poor water solubility and the limitation of the sequence design of achiral PNA probes mainly hinder their application. Accordingly, (R)-diethylene glycol containing a chiral PNA (miniPEG-γPNA) has been developed to solve these problems. Light-directed synthesis is an effective method to fabricate high-density microarrays. Thiophenyl-2-(2-nitrophenyl)propoxycarbonyl (SPhNPPOC) is a newly synthesised photolabile protective group with high photolytic efficiency. Protecting the PNA monomers with SPhNPPOC may improve the preparation process of PNA microarrays by light-directed synthesis in terms of shortening the deprotection time and restraining side reactions. In this article, SPhNPPOC/carbobenzoxy (Cbz)-protected chiral miniPEG-γPNA monomers are synthesised, and the photo-deprotection rate is approximately twice that of a 2-(2-nitrophenyl)propyloxycarbonyl (NPPOC)-protected monomer. The monomers are expected to be used for the efficient and rapid fabrication of chiral miniPEG-γPNA microarrays through a photolithographic strategy.

Recent progress in non-native nucleic acid modifications

While Nature harnesses RNA and DNA to store, read and write genetic information, the inherent programmability, synthetic accessibility and wide functionality of these nucleic acids make them attractive tools for use in a vast array of applications.

Visible-to-NIR-Light Activated Release: From Small Molecules to Nanomaterials

Photoactivatable (alternatively, photoremovable, photoreleasable, or photocleavable) protecting groups (PPGs), also known as caged or photocaged compounds, are used to enable non-invasive spatiotemporal photochemical control over the release of species of interest. Recent years have seen the development of PPGs activatable by biologically and chemically benign visible and near-infrared (NIR) light. These long-wavelength-absorbing moieties expand the applicability of this powerful method and its accessibility to non-specialist users. This review comprehensively covers organic and transition metal-containing photoactivatable compounds (complexes) that absorb in the visible- and NIR-range to release various leaving groups and gasotransmitters (carbon monoxide, nitric oxide, and hydrogen sulfide). The text also covers visible- and NIR-light-induced photosensitized release using molecular sensitizers, quantum dots, and upconversion and second-harmonic nanoparticles, as well as release via photodynamic (photooxygenation by singlet oxygen) and photothermal effects. Release from photoactivatable polymers, micelles, vesicles, and photoswitches, along with the related emerging field of photopharmacology, is discussed at the end of the review.

l-DNA Duplex Formation as a Bioorthogonal Information Channel in Nucleic Acid-Based Surface Patterning

Photolithographic in situ synthesis of nucleic acids enables extremely high oligonucleotide sequence density as well as complex surface patterning and combined spatial and molecular information encoding. No longer limited to DNA synthesis, the technique allows for total control of both chemical and Cartesian space organization on surfaces, suggesting that hybridization patterns can be used to encode, display or encrypt informative signals on multiple chemically orthogonal levels. Nevertheless, cross-hybridization reduces the available sequence space and limits information density. Here we introduce an additional, fully independent information channel in surface patterning with in situ l-DNA synthesis. The bioorthogonality of mirror-image DNA duplex formation prevents both cross-hybridization on chimeric l-/d-DNA microarrays and also results in enzymatic orthogonality, such as nuclease-proof DNA-based signatures on the surface. We show how chimeric l-/d-DNA hybridization can be used to create informative surface patterns including QR codes, highly counterfeiting resistant authenticity watermarks, and concealed messages within high-density d-DNA microarrays.

Low cost DNA data storage using photolithographic synthesis and advanced information reconstruction and error correction

Due to its longevity and enormous information density, DNA is an attractive medium for archival storage. The current hamstring of DNA data storage systems-both in cost and speed-is synthesis. The key idea for breaking this bottleneck pursued in this work is to move beyond the low-error and expensive synthesis employed almost exclusively in today's systems, towards cheaper, potentially faster, but high-error synthesis technologies. Here, we demonstrate a DNA storage system that relies on massively parallel light-directed synthesis, which is considerably cheaper than conventional solid-phase synthesis. However, this technology has a high sequence error rate when optimized for speed. We demonstrate that even in this high-error regime, reliable storage of information is possible, by developing a pipeline of algorithms for encoding and reconstruction of the information. In our experiments, we store a file containing sheet music of Mozart, and show perfect data recovery from low synthesis fidelity DNA.

Recent progress in creating complex and multiplexed surface-grafted macromolecular architectures

Surface-grafted macromolecules, including polymers, DNA, peptides, etc., are versatile modifications to tailor the interfacial functions in a wide range of fields. In this review, we aim to provide an overview of the most recent progress in engineering surface-grafted chains for the creation of complex and multiplexed surface architectures over micro- to macro-scopic areas. A brief introduction to surface grafting is given first. Then the fabrication of complex surface architectures is summarized with a focus on controlled chain conformations, grafting densities and three-dimensional structures. Furthermore, recent advances are highlighted for the generation of multiplexed arrays with designed chemical composition in both horizontal and vertical dimensions. The applications of such complicated macromolecular architectures are then briefly discussed. Finally, some perspective outlooks for future studies and challenges are suggested. We hope that this review will be helpful to those just entering this field and those in the field requiring quick access to useful reference information about the progress in the properties, processing, performance, and applications of functional surface-grafted architectures.

Efficient Far-Red/Near-IR Absorbing BODIPY Photocages by Blocking Unproductive Conical Intersections

Photocages are light-sensitive chemical protecting groups that give investigators control over activation of biomolecules using targeted light irradiation. A compelling application of far-red/near-IR absorbing photocages is their potential for deep tissue activation of biomolecules and phototherapeutics. Toward this goal, we recently reported BODIPY photocages that absorb near-IR light. However, these photocages have reduced photorelease efficiencies compared to shorter-wavelength absorbing photocages, which has hindered their application. Because photochemistry is a zero-sum competition of rates, improvement of the quantum yield of a photoreaction can be achieved either by making the desired photoreaction more efficient or by hobbling competitive decay channels. This latter strategy of inhibiting unproductive decay channels was pursued to improve the release efficiency of long-wavelength absorbing BODIPY photocages by synthesizing structures that block access to unproductive singlet internal conversion conical intersections, which have recently been located for simple BODIPY structures from excited state dynamic simulations. This strategy led to the synthesis of new conformationally restrained boron-methylated BODIPY photocages that absorb light strongly around 700 nm. In the best case, a photocage was identified with an extinction coefficient of 124000 M^-1 cm^-1, a quantum yield of photorelease of 3.8%, and an overall quantum efficiency of 4650 M^-1 cm^-1 at 680 nm. This derivative has a quantum efficiency that is 50-fold higher than the best known BODIPY photocages absorbing >600 nm, validating the effectiveness of a strategy for designing efficient photoreactions by thwarting competitive excited state decay channels. Furthermore, 1,7-diaryl substitutions were found to improve the quantum yields of photorelease by excited state participation and blocking ion pair recombination by internal nucleophilic trapping. No cellular toxicity (trypan blue exclusion) was observed at 20 μM, and photoactivation was demonstrated in HeLa cells using red light.

Recent Trends in Applying Rrtho-Nitrobenzyl Esters for the Design of Photo-Responsive Polymer Networks

Polymers with light-responsive groups have gained increased attention in the design of functional materials, as they allow changes in polymers properties, on demand, and simply by light exposure. For the synthesis of polymers and polymer networks with photolabile properties, the introduction o-nitrobenzyl alcohol (o-NB) derivatives as light-responsive chromophores has become a convenient and powerful route. Although o-NB groups were successfully exploited in numerous applications, this review pays particular attention to the studies in which they were included as photo-responsive moieties in thin polymer films and functional polymer coatings. The review is divided into four different sections according to the chemical structure of the polymer networks: (i) acrylate and methacrylate; (ii) thiol-click; (iii) epoxy; and (iv) polydimethylsiloxane. We conclude with an outlook of the present challenges and future perspectives of the versatile and unique features of o-NB chemistry.

Specificity and Efficiency of the Uracil DNA Glycosylase-Mediated Strand Cleavage Surveyed on Large Sequence Libraries

Uracil-DNA glycosylase (UDG) is a critical DNA repair enzyme that is well conserved and ubiquitous in nearly all life forms. UDG protects genomic information integrity by catalyzing the excision from DNA of uracil nucleobases resulting from misincorporation or spontaneous cytosine deamination. UDG-mediated strand cleavage is also an important tool in molecular biotechnology, allowing for controlled and location-specific cleavage of single- and double DNA chemically or enzymatically synthesized with single or multiple incorporations of deoxyuridine. Although the cleavage mechanism is well-understood, detailed knowledge of efficiency and sequence specificity, in both single and double-stranded DNA contexts, has so far remained incomplete. Here we use an experimental approach based on the large-scale photolithographic synthesis of uracil-containing DNA oligonucleotides to comprehensively probe the context-dependent uracil excision efficiency of UDG.

Large-Scale Photolithographic Synthesis of Chimeric DNA/RNA Hairpin Microarrays To Explore Sequence Specificity Landscapes of RNase HII Cleavage

Ribonuclease HII (RNase HII) is an essential endoribonuclease that binds to double-stranded DNA with RNA nucleotide incorporations and cleaves 5' of the ribonucleotide at RNA-DNA junctions. Thought to be present in all domains of life, RNase HII protects genomic integrity by initiating excision repair pathways that protect the encoded information from rapid degradation. There is sparse evidence that the enzyme cleaves some substrates better than others, but a large-scale study is missing. Such large-scale studies can be carried out on microarrays, and we employ chemical photolithography to synthesize very large combinatorial libraries of fluorescently labeled DNA/RNA chimeric sequences that self-anneal to form hairpin structures that are substrates for Escherichia coli RNase HII. The relative activity is determined by the loss of fluorescence upon cleavage. Each substrate includes a double-stranded 5 bp variable region with one to five consecutive ribonucleotide substitutions. We also examined the effect of all possible single and double mismatches, for a total of >9500 unique structures. Differences in cleavage efficiency indicate some level of substrate preference, and we identified the 5'-dC/rC-rA-dX-3' motif in well-cleaved substrates. The results significantly extend known patterns of RNase HII sequence specificity and serve as a template using large-scale photolithographic synthesis to comprehensively map landscapes of substrate specificity of nucleic acid-processing enzymes.

Multi-level patterning nucleic acid photolithography

The versatile and tunable self-assembly properties of nucleic acids and engineered nucleic acid constructs make them invaluable in constructing microscale and nanoscale devices, structures and circuits. Increasing the complexity, functionality and ease of assembly of such constructs, as well as interfacing them to the macroscopic world requires a multifaceted and programmable fabrication approach that combines efficient and spatially resolved nucleic acid synthesis with multiple post-synthetic chemical and enzymatic modifications. Here we demonstrate a multi-level photolithographic patterning approach that starts with large-scale in situ surface synthesis of natural, modified or chimeric nucleic acid molecular structures and is followed by chemical and enzymatic nucleic acid modifications and processing. The resulting high-complexity, micrometer-resolution nucleic acid surface patterns include linear and branched structures, multi-color fluorophore labeling and programmable targeted oligonucleotide immobilization and cleavage.

Encrypted Oligonucleotide Arrays for Molecular Authentication

Counterfeiting is an incredibly widespread problem, with some estimates placing its economic impact above 2% of worldwide GDP. The scale of the issue suggests that current preventive measures are either technologically insufficient or too impractical and costly to be widely adopted. High-density arrays of biomolecules are explored here as security devices that can be coupled to a valuable commodity as proof of its authenticity. Light-directed DNA array fabrication technology is used to synthesize arrays that are designed to resist analysis with sequencing-by-hybridization approaches. A relatively simple sequence design strategy forces a counterfeiter to undertake a prohibitively high number of complex experiments to decipher the array sequences employed.

Chip-SIP: Stable Isotope Probing Analyzed with rRNA-Targeted Microarrays and NanoSIMS

Chip-SIP is a stable isotope probing (SIP) method for linking microbial identity and function in mixed communities and is capable of analyzing multiple isotopes (¹³C, ¹⁵N, and ¹⁸O) simultaneously. This method uses a high-density microarray to separate taxon-specific 16S (or 18S) rRNA genes and a high sensitivity magnetic sector secondary ion mass spectrometer (SIMS) to determine the relative isotope incorporation of the rRNA at each probe location. Using a maskless array synthesizer (MAS), we synthesize multiple unique sequences to target hundreds of taxa at the ribosomal operational taxonomic unit (OTU) level on an array surface, and then analyze it with a NanoSIMS 50, using its high-spatial resolution imaging capability to generate isotope ratios for individual probes. The Chip-SIP method has been used in diverse systems, including surface marine and estuarine water, rhizosphere, and peat soils, to quantify taxon-specific relative incorporation of different substrates in complex microbial communities. Depending on the hypothesis and experimental design, Chip-SIP allows the user to compare the same community incorporating different substrates, different communities incorporating the same substrate(s), or quantify how a community responds to treatment effects, such as temperature or nutrient concentrations.

Photo-triggered polymer nanomedicines: From molecular mechanisms to therapeutic applications

The use of nanotechnology to improve treatment efficacy and reduce side effects is central to nanomedicine. In this context, stimuli-responsive drug delivery systems (DDS) such as chemical/physical gels or nanoparticles such as polymersomes, micelles or nanogels are particularly promising and are the focus of this review. Several stimuli have been considered but light as an exogenous trigger presents many advantages that are pertinent for clinical applications such as high spatial and temporal control and low cost. Underlying mechanisms required for the release of therapeutic agents in vitro and in vivo range from the molecular scale, namely photoisomerization, hydrophobicity photoswitching, photocleavage or heat generation via nanoheaters, through to the macromolecular scale. As well as these approaches, DDS destabilization, DDS permeation pore unblocking and formation are discussed.

High-Density RNA Microarrays Synthesized In Situ by Photolithography

While high-density DNA microarrays have been available for over three decades, the synthesis of equivalent RNA microarrays has proven intractable until now. Herein we describe the first in situ synthesis of mixed-based, high-density RNA microarrays using photolithography and light-sensitive RNA phosphoramidites. With coupling efficiencies comparable to those of DNA monomers, RNA oligonucleotides at least 30 nucleotides long can now efficiently be prepared using modified phosphoramidite chemistry. A two-step deprotection route unmasks the phosphodiester, the exocyclic amines and the 2' hydroxyl. Hybridization and enzymatic assays validate the quality and the identity of the surface-bound RNA. We show that high-density is feasible by synthesizing a complex RNA permutation library with 262144 unique sequences. We also introduce DNA/RNA chimeric microarrays and explore their applications by mapping the sequence specificity of RNase HII.

High-Efficiency Reverse (5'→3') Synthesis of Complex DNA Microarrays

DNA microarrays are important analytical tools in genetics and have recently found multiple new biotechnological roles in applications requiring free 3' terminal hydroxyl groups, particularly as a starting point for enzymatic extension via DNA or RNA polymerases. Here we demonstrate the highly efficient reverse synthesis of complex DNA arrays using a photolithographic approach. The method is analogous to conventional solid phase synthesis but makes use of phosphoramidites with the benzoyl-2-(2-nitrophenyl)-propoxycarbonyl (BzNPPOC) photolabile protecting group on the 3'-hydroxyl group. The use of BzNPPOC, with more than twice the photolytic efficiency of the 2-(2-nitrophenyl)-propoxycarbonyl (NPPOC) previously used for 5'→3' synthesis, combined with additional optimizations to the coupling and oxidation reactions results in an approximately 3-fold improvement in the reverse synthesis efficiency of complex arrays of DNA oligonucleotides. The coupling efficiencies of the reverse phosphoramidites are as good as those of regular phosphoramidites, resulting in comparable yields. Microarrays of DNA surface tethered on the 5' end and with free 3' hydroxyl termini can be synthesized quickly and with similarly high stepwise coupling efficiency as microarrays using conventional 3'→5' synthesis.

o-Nitrobenzyl-Based Photobase Generators: Efficient Photoinitiators for Visible-Light Induced Thiol-Michael Addition Photopolymerization

In this contribution, three o-nitrobenzyl-based photobase systems were synthesized and evaluated for visible light initiated thiol-Michael addition polymerizations. With a modified structure, the (3,4-methylenedioxy-6-nitrophenyl)-propyloxycarbonyl (MNPPOC) protected base performance exceeds that of the nonsubstituted 2-(2-nitrophenyl)-propyloxycarbonyl (NPPOC) protected base and an ITX sensitized photobase system, with respect to both long-wavelength light sensitivity and photolytic efficiency. In material synthesis, MNPPOC-TMG is capable of initiating photo thiol-Michael polymerization efficiently and orthogonally with only limited visible light exposure and generating a highly homogeneous cross-linked polymer network. This approach enables the thiol-Michael "click" reaction to be conducted with a low-energy, visible light irradiation and, thus, expands its applications in biocompatible and UV sensitive materials.

Family of BODIPY Photocages Cleaved by Single Photons of Visible/Near-Infrared Light

Photocages are light-sensitive chemical protecting groups that provide external control over when, where, and how much of a biological substrate is activated in cells using targeted light irradiation. Regrettably, most popular photocages (e.g., o-nitrobenzyl groups) absorb cell-damaging ultraviolet wavelengths. A challenge with achieving longer wavelength bond-breaking photochemistry is that long-wavelength-absorbing chromophores have shorter excited-state lifetimes and diminished excited-state energies. However, here we report the synthesis of a family of BODIPY-derived photocages with tunable absorptions across the visible/near-infrared that release chemical cargo under irradiation. Derivatives with appended styryl groups feature absorptions above 700 nm, yielding photocages cleaved with the highest known wavelengths of light via a direct single-photon-release mechanism. Photorelease with red light is demonstrated in living HeLa cells, Drosophila S2 cells, and bovine GM07373 cells upon ∼5 min irradiation. No cytotoxicity is observed at 20 μM photocage concentration using the trypan blue exclusion assay. Improved B-alkylated derivatives feature improved quantum efficiencies of photorelease ∼20-fold larger, on par with the popular o-nitrobenzyl photocages (εΦ = 50-100 M^-1 cm^-1), but absorbing red/near-IR light in the biological window instead of UV light.