Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Photochemical DNA activation.

ABSTRACT: A new photocaged nucleoside was synthesized and incorporated into DNA with the use of standard synthesis conditions. This approach enabled the disruption of specific H-bonds and allowed for the analysis of their contribution to the activity of a DNAzyme. Brief irradiation with nonphotodamaging UV light led to rapid decaging and almost quantitative restoration of DNAzyme activity. The developed strategy has the potential to find widespread application in the light-induced regulation of oligonucleotide function.

SUBMITTER: Lusic H

PROVIDER: S-EPMC2532984 | biostudies-literature | 2007 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Photochemical DNA activation.

Lusic Hrvoje H Young Douglas D DD Lively Mark O MO Deiters Alexander A

Organic letters 20070421 10

A new photocaged nucleoside was synthesized and incorporated into DNA with the use of standard synthesis conditions. This approach enabled the disruption of specific H-bonds and allowed for the analysis of their contribution to the activity of a DNAzyme. Brief irradiation with nonphotodamaging UV light led to rapid decaging and almost quantitative restoration of DNAzyme activity. The developed strategy has the potential to find widespread application in the light-induced regulation of oligonucle ...[more]

PMID: 17447773

Similar Datasets

Photochemical activation of TRPA1 channels in neurons and animals.

Project description:Optogenetics is a powerful research tool because it enables high-resolution optical control of neuronal activity. However, current optogenetic approaches are limited to transgenic systems expressing microbial opsins and other exogenous photoreceptors. Here, we identify optovin, a small molecule that enables repeated photoactivation of motor behaviors in wild-type zebrafish and mice. To our surprise, optovin's behavioral effects are not visually mediated. Rather, photodetection is performed by sensory neurons expressing the cation channel TRPA1. TRPA1 is both necessary and sufficient for the optovin response. Optovin activates human TRPA1 via structure-dependent photochemical reactions with redox-sensitive cysteine residues. In animals with severed spinal cords, optovin treatment enables control of motor activity in the paralyzed extremities by localized illumination. These studies identify a light-based strategy for controlling endogenous TRPA1 receptors in vivo, with potential clinical and research applications in nontransgenic animals, including humans.

| S-EPMC3604056 | biostudies-literature

Photochemical control of DNA structure through radical disproportionation.

Project description:Photolysis of an aryl sulfide-containing 5,6-dihydropyrimidine (1) at 350 nm produces high yields of thymidine and products resulting from trapping of a 5,6-dihydrothymidin-5-yl radical by O? or thiols. Thymidine is believed to result from disproportionation of the radical pair originally generated from C--S bond homolysis of 1 on the microsecond timescale, which is significantly shorter than other photochemical transformations of modified nucleotides into their native forms. Duplex DNA containing 1 is destabilized, presumably due to disruption of ?-stacking. Incorporation of 1 within the binding site of the restriction endonuclease EcoRV provides a photochemical switch for turning on the enzyme's activity. In contrast, 1 is a substrate for endonuclease VIII and serves as a photochemical off switch for this base excision repair enzyme. Modification 1 also modulates the activity of the 10-23 DNAzyme, despite its incorporation into a nonduplex region. Overall, dihydropyrimidine 1 shows promise as a tool to provide spatiotemporal control over DNA structure on the miscrosecond timescale.

| S-EPMC3807129 | biostudies-literature

Photochemical activation of carbon dioxide in Mg+(CO2)(H2O)0,1.

Project description:We combine multi-reference ab initio calculations with UV-VIS action spectroscopy to study photochemical activation of CO2 on a singly charged magnesium ion, [MgCO2(H2O)0,1]+, as a model system for the metal/ligand interactions relevant in CO2 photochemistry. For the non-hydrated species, two separated Mg+ 3s-3p bands are observed within 5.0 eV. The low-energy band splits upon hydration with one water molecule. [Mg(CO2)]+ decomposes highly state-selectively, predominantly via multiphoton processes. Within the low-energy band, CO2 is exclusively lost within the excited state manifold. For the high-energy band, an additional pathway becomes accessible: the CO2 ligand is activated via a charge transfer, with photochemistry taking place on the CO2 - moiety eventually leading to a loss of CO after absorption of a second photon. Upon hydration, already excitation into the first and second excited state leads to CO2 activation in the excited state minimum; however, CO2 predominantly evaporates upon fluorescence or absorption of another photon.

| S-EPMC7335376 | biostudies-literature

Computational studies of CO2 activation via photochemical reactions with reduced sulfur compounds.

Project description:Reactions between CO(2) and reduced sulfur compounds (RSC), H(2)S and CH(3)SH, were investigated using ground and excited state density functional theory (DFT) and coupled cluster (CC) methods to explore possible RSC oxidation mechanisms and CO(2) activation mechanisms in the atmospheric environment. Ground electronic state calculations at the CR-CC(2,3)/6-311+G(2df,2p)//CAM-B3LYP/6-311+G(2df,2p) level show proton transfer as a limiting step in the reduction of CO(2) with activation energies of 49.64 and 47.70 kcal/mol, respectively, for H(2)S and CH(3)SH. On the first excited state surface, CR-EOMCC(2,3)/6-311+G(2df,2p)//CAM-B3LYP/6-311+G(2df,2p) calculations reveal that energies of <250 nm are needed to form H(2)S-CO(2) and CH(3)SH-CO(2) complexes allowing facile hydrogen atom transfer. Once excited, all reaction intermediates and transition states are downhill energetically showing either C-H or C-S bond formation in the excited state whereas only C-S bond formation was found in the ground state. Environmental implications of these data are discussed with a focus on tropospheric reactions between CO(2) and RSC, as well as potential for carbon sequestration using photocatalysis.

| S-EPMC3461351 | biostudies-literature

Cellular delivery and photochemical activation of antisense agents through a nucleobase caging strategy.

Project description:Antisense oligonucleotides are powerful tools to regulate gene expression in cells and model organisms. However, a transfection or microinjection is typically needed for efficient delivery of the antisense agent. We report the conjugation of multiple HIV TAT peptides to a hairpin-protected antisense agent through a light-cleavable nucleobase caging group. This conjugation allows for the facile delivery of the antisense agent without a transfection reagent, and photochemical activation offers precise control over gene expression. The developed approach is highly modular, as demonstrated by the conjugation of folic acid to the caged antisense agent. This enabled targeted cell delivery through cell-surface folate receptors followed by photochemical triggering of antisense activity. Importantly, the presented strategy delivers native oligonucleotides after light-activation, devoid of any delivery functionalities or modifications that could otherwise impair their antisense activity.

| S-EPMC3856437 | biostudies-literature

Photochemical activation of MH3-B1/rGel: a HER2-targeted treatment approach for ovarian cancer.

Project description:HER2-targeted therapy has been shown to have limited efficacy in ovarian cancer despite frequent overexpression of this receptor. Photochemical internalization (PCI) is a modality for cytosolic drug delivery, currently undergoing clinical evaluation. In the present project we studied the application of PCI in combination with the HER2-targeted recombinant fusion toxin, MH3-B1/rGel, for the treatment of ovarian cancer. The SKOV-3 cell line, resistant to trastuzumab- and MH3-B1/rGel- monotherapy, was shown to respond strongly to PCI of MH3-B1/rGel to a similar extent as observed for the treatment-sensitive SK-BR-3 breast cancer cells. Extensive hydrolytic degradation of MH3-B1/rGel in acidic endocytic vesicles was indicated as the mechanism of MH3-B1/rGel resistance in SKOV-3 cells. This was shown by the positive Pearson's correlation coefficient between Alexa488-labeled MH3-B1/rGel and Lysotracker in SKOV-3 cells in contrast to the negative Pearson's correlation coefficient in SK-BR-3 cells. The application of PCI to induce the release of MH3-B1/rGel was also demonstrated to be effective on SKOV-3 xenografts. Application of PCI with MH3-B1/rGel was further found highly effective in the HER2 expressing HOC-7 and NuTu-19 ovarian cancer cell lines. The presented results warrant future development of PCI in combination with MH3-B1/rGel as a novel therapeutic approach in preclinical models of ovarian cancer.

| S-EPMC4494949 | biostudies-literature

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

Project description: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.

| S-EPMC8266620 | biostudies-literature

Photochemical Barcodes.

Project description:A photochemical strategy to encode fluorescence signals in vivo with spatial control was designed around the unique properties of a photoactivatable borondipyrromethene (BODIPY). The photoinduced disconnection of two oxazines, flanking a single BODIPY, in two consecutive steps produces a mixture of three emissive molecules with resolved fluorescence inside polymer beads. The relative amounts and emission intensities of the three fluorophores can be regulated precisely in each bead by adjusting the dose of activating photons to mark individual particles with distinct codes of fluorescence signals. The visible wavelengths and mild illumination sufficient to induce these transformations permit the photochemical barcoding of beads also in living nematodes. Different regions of the same animal can be labeled with distinct barcodes to allow the monitoring of their dynamics for long times with no toxic effects. Thus, our photochemical strategy for the generation of fluorescence barcodes can produce multiple and distinguishable labels in the same biological sample to enable the spatiotemporal tracking of, otherwise indistinguishable, targets.

| S-EPMC6056178 | biostudies-literature

Photochemical Generation of Benzyl Cations That Selectively Cross-Link Guanine and Cytosine in DNA.

Project description:UV irradiation of several aryl boronates efficiently produced bifunctional benzyl cations that selectively form guanine-cytosine cross-links in DNA. Photoinduced homolysis of the C-Br bond took place with the aryl boronate bromides 3a and 4a, generating free radicals that were oxidized to benzyl cations via electron transfer. However, photoirradiation of the quaternary ammonium salts 3b and 4b led to heterolysis of C-N bond, directly producing benzyl cations. The electron-donating group in the aromatic ring greatly enhanced cross-linking efficiency.

| S-EPMC5609456 | biostudies-literature

Photochemical control of DNA decoy function enables precise regulation of nuclear factor ?B activity.

Project description:DNA decoys have been developed for the inhibition of transcriptional regulation of gene expression. However, the present methodology lacks the spatial and temporal control of gene expression that is commonly found in nature. Here, we report the application of photoremovable protecting groups on nucleobases of nuclear factor ?B (NF-?B) DNA decoys to regulate NF-?B-driven transcription of secreted alkaline phosphatase using light as an external control element. The NF-?B family of proteins is comprised of important eukaryotic transcription factors that regulate a wide range of cellular processes and are involved in immune response, development, cellular growth, and cell death. Several diseases, including cancer, arthritis, chronic inflammation, asthma, neurodegenerative diseases, and heart disease, have been linked to constitutively active NF-?B. Through the direct incorporation of caging groups into an NF-?B decoy, we were able to disrupt DNA:DNA hybridization and inhibit the binding of the transcription factor to the DNA decoy until UV irradiation removed the caging groups and restored the activity of the oligonucleotide. Excellent light-switching behavior of transcriptional regulation was observed. This is the first example of a caged DNA decoy for the photochemical regulation of gene expression in mammalian cells and represents an important addition to the toolbox of light-controlled gene regulatory agents.

| S-EPMC3157586 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data