| Size | Price | Stock | Qty |
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| 5mg |
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| 10mg |
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| Other Sizes |
| Targets |
DMNB-caged-Serine does not have a defined biological target in its caged form; it is a synthetic amino acid analog designed for light-induced uncaging. Upon exposure to UV or visible blue light, the DMNB caging group is photolyzed, releasing free L-serine. The released serine then targets its natural biological receptors and enzymes, including serine transporters, serine hydroxymethyltransferase (SHMT), and incorporation into proteins by the cellular translation machinery as a catalytic residue, hydrogen bonding partner, or site of post-translational modification. DMNB-caged-Serine can be used as a catalytic residue, hydrogen bonding partner or site of post-translational modification.
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| ln Vitro |
DMNB-caged-Serine prevents phosphorylation and the consequent export of the receptor Msn5 when it is replaced at the phosphorylated serine site that regulates Pho4 nuclear export [1].
In vitro studies demonstrate that DMNB-caged-Serine is stable in the dark and does not interfere with normal cellular processes until photolysis. When incorporated into proteins in Saccharomyces cerevisiae in response to the amber nonsense codon (TAG) by being introduced into growth medium at millimolar concentrations, it facilitates control over the chemical composition of mammalian proteins. Upon exposure to visible blue light (405 nm) in cells, the caging group is removed, releasing the native serine residue and restoring its biological activity in a temporally and spatially controlled manner. This approach has been used to control protein phosphorylation with a genetically encoded photocaged amino acid. The compound shows minimal toxicity in cells in the dark at concentrations up to 5 mM, enabling long-term culture and expression studies. |
| ln Vivo |
In vivo activity data for DMNB-caged-Serine is limited, as it is primarily an in vitro and ex vivo research tool. The compound is designed to be incorporated into proteins in living cells or organisms via genetic code expansion techniques. For in vivo applications, the caged amino acid is typically administered to genetically modified organisms that have been engineered to incorporate it into specific protein sites. Upon photolysis, the released serine allows for the optical control of protein function in vivo, for example, in zebrafish embryos or C. elegans. However, detailed mammalian in vivo studies are not widely reported. Challenges for in vivo use include efficient delivery of the caged amino acid to target tissues and the penetration depth of the activating light.
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| Enzyme Assay |
Non-cell-based assays for DMNB-caged-Serine primarily involve photochemical characterization to determine the efficiency and kinetics of the uncaging reaction. A typical protocol uses UV-visible absorption spectroscopy and HPLC analysis. DMNB-caged-Serine is dissolved in a physiological buffer (e.g., 10 mM phosphate buffer, pH 7.4) at a concentration of 50-100 uM. The solution is placed in a quartz cuvette and irradiated with a UV lamp or a laser source at a wavelength of 365 nm (or a blue LED at 405 nm) at varying light intensities and exposure times (e.g., 0, 5, 10, 30, 60 seconds). The absorption spectrum is recorded before and after irradiation to monitor the decrease in the characteristic absorption peak of the DMNB group (around 350 nm). Concurrently, HPLC analysis (C18 reverse-phase column, isocratic elution with a water/acetonitrile mobile phase) can be used to separate the caged compound from the released serine and the photolysis by-products. The rate constant of photolysis (k_photo) and the quantum yield (Φ) are calculated by monitoring the disappearance of the starting material or the appearance of the uncaged serine over time. Mass spectrometry (LC-MS) can be used to confirm the identity of the released product (L-serine, m/z 106.1) and the nitroso byproduct. The half-life of the caging group under specific light conditions can be determined to optimize experimental parameters.
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| Cell Assay |
For cell-based experiments, DMNB-caged-Serine is used in genetic code expansion systems. For example, in Saccharomyces cerevisiae or mammalian cells engineered to express an orthogonal aminoacyl-tRNA synthetase/tRNA pair that recognizes the amber stop codon (TAG), cells are cultured in defined synthetic medium lacking serine. DMNB-caged-Serine is added to the culture medium at a concentration of 1-5 mM, and protein expression is induced. After expression, the caged protein is purified or studied in situ. For live-cell photolysis, cells expressing the caged protein are washed with PBS and then irradiated with a 405 nm LED or confocal laser for 0-10 minutes. Photolysis efficiency is assessed by SDS-PAGE and Western blotting (using antibodies against the caged residue or a reporter tag), or by functional assays such as measuring the restoration of kinase activity or protein interaction. The spatiotemporal control can be demonstrated by confocal microscopy, where a defined region of interest is irradiated, and the diffusion of the activated protein is monitored. Cytotoxicity of the caging group and UV exposure should be assessed using standard viability assays (e.g., MTT, Live/Dead staining).
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| Animal Protocol |
In vivo protocols for DMNB-caged-Serine are not standardized, as it is primarily a tool for targeted protein control. For researchers using model organisms like C. elegans or zebrafish, the caged amino acid is typically delivered via microinjection into the embryo or by addition to the water. For instance, C. elegans expressing a caged protein can be placed on an agar pad with a drop of M9 buffer containing 1-10 mM DMNB-caged-Serine. For photolysis, a UV laser (365 nm) or a 405 nm diode laser focused through a microscope objective is used to illuminate specific cells or tissues for milliseconds to minutes. The biological effect (e.g., rescue of a mutant phenotype, activation of a signaling pathway) is then observed over time. Control animals should be kept in the dark to confirm the caged compound is inactive without light exposure. In mammals, systemic delivery (e.g., intraperitoneal injection) of DMNB-caged-Serine could be explored, but its stability in circulation and ability to cross cell membranes to be incorporated into proteins are major hurdles. Therefore, it is not a standard drug candidate for systemic in vivo studies.
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| ADME/Pharmacokinetics |
Pharmacokinetic data for DMNB-caged-Serine is not available in the context of a therapeutic drug, as it is a research tool for chemical biology and optogenetics. As a protected amino acid, it is not designed for systemic administration. If administered in vivo, the caged amino acid would likely be rapidly cleared by the kidneys due to its small size (MW 300.26 Da) and high polarity (multiple oxygen and nitrogen atoms). It could also be metabolized by esterases or other enzymes, or be photolyzed by ambient light, leading to premature release of serine. The pharmacokinetics are therefore highly dependent on the route of administration and the experimental model. For in vitro uncaging, the half-life is determined by light intensity and wavelength, not by metabolic enzymes. Generally, the compound is stable in solution if protected from light, and solutions can be stored at -20degC for extended periods.
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| Toxicity/Toxicokinetics |
DMNB-caged-Serine is generally considered non-toxic in the dark at concentrations used for protein expression (1-5 mM in cell culture). However, the byproducts of photolysis, such as the 4,5-dimethoxy-2-nitrosobenzyl alcohol, may be cytotoxic at high concentrations or upon prolonged exposure. The compound is also photoreactive, and exposure to UV light should be minimized to prevent accidental uncaging. Standard safety precautions for handling include wearing gloves and eye protection, and working in a fume hood when handling powder. The compound is for research use only and is not intended for human therapeutic use. No genotoxicity, carcinogenicity, or reproductive toxicity studies have been reported for this specific caged compound. Cell viability assays in mammalian cell lines (e.g., HEK293, HeLa) indicate that DMNB-caged-Serine does not significantly affect cell proliferation or viability at concentrations up to 5 mM in the dark for 72 hours.
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| References |
[1]. Edward A Lemke, et al. Control of protein phosphorylation with a genetically encoded photocaged amino acid. Nat Chem Biol. 2007 Dec;3(12):769-72.
[2]. Qing Shao, et al. Photoactive molecules for applications in molecular imaging and cell biology. Chem Soc Rev. 2010 Aug;39(8):2835-46. [3]. Brieke C, et al. Light-controlled tools. Angew Chem Int Ed Engl. 2012 Aug 20;51(34):8446-76. |
| Additional Infomation |
DMNB-caged-Serine is also known as O-(4,5-Dimethoxy-2-nitrobenzyl)-L-serine. It is a photocaged amino acid with a DMNB as a blue light-sensitive caging group. It is soluble in DMSO (e.g., 150 mg/mL) and has low aqueous solubility. The product should be stored as a powder at -20degC, protected from light and moisture, where it is stable for at least 2 years. In solution (e.g., in DMSO), it should be stored in aliquots at -80degC and protected from light. This caged amino acid is a valuable tool for the spatiotemporal control of protein structure and function, enabling studies of dynamic processes in cells and organisms with light. It is commonly used in optogenetics, protein engineering, and studies requiring precise regulation of amino acid availability, such as controlling protein phosphorylation with a genetically encoded photocaged amino acid.
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| Molecular Formula |
C12H16N2O7-
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| Molecular Weight |
300.265
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| Exact Mass |
300.095
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| CAS # |
780009-55-4
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| PubChem CID |
16741276
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| Appearance |
Light yellow to light brown solid powder
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| LogP |
-2.2
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| Hydrogen Bond Donor Count |
2
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| Hydrogen Bond Acceptor Count |
8
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| Rotatable Bond Count |
7
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| Heavy Atom Count |
21
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| Complexity |
360
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| Defined Atom Stereocenter Count |
1
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| SMILES |
COC1=C(C=C(C(=C1)COC[C@@H](C(=O)O)N)[N+](=O)[O-])OC
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| InChi Key |
HYSPNOMZFGNKBR-QMMMGPOBSA-N
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| InChi Code |
InChI=1S/C12H16N2O7/c1-19-10-3-7(5-21-6-8(13)12(15)16)9(14(17)18)4-11(10)20-2/h3-4,8H,5-6,13H2,1-2H3,(H,15,16)/t8-/m0/s1
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| Chemical Name |
(2S)-2-amino-3-[(4,5-dimethoxy-2-nitrophenyl)methoxy]propanoic acid
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| HS Tariff Code |
2934.99.9001
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| Storage |
Powder -20°C 3 years 4°C 2 years In solvent -80°C 6 months -20°C 1 month |
| Shipping Condition |
Room temperature (This product is stable at ambient temperature for a few days during ordinary shipping and time spent in Customs)
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| Solubility (In Vitro) |
DMSO: 250 mg/mL (832.61 mM)
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| Solubility (In Vivo) |
Note: Listed below are some common formulations that may be used to formulate products with low water solubility (e.g. < 1 mg/mL), you may test these formulations using a minute amount of products to avoid loss of samples.
Injection Formulations
Injection Formulation 1: DMSO : Tween 80： Saline = 10 : 5 : 85 (i.e. 100 μL DMSO stock solution → 50 μL Tween 80 → 850 μL Saline)(e.g. IP/IV/IM/SC) *Preparation of saline: Dissolve 0.9 g of sodium chloride in 100 mL ddH ₂ O to obtain a clear solution. Injection Formulation 2: DMSO : PEG300 ：Tween 80 : Saline = 10 : 40 : 5 : 45 (i.e. 100 μL DMSO → 400 μLPEG300 → 50 μL Tween 80 → 450 μL Saline) Injection Formulation 3: DMSO : Corn oil = 10 : 90 (i.e. 100 μL DMSO → 900 μL Corn oil) Example: Take the Injection Formulation 3 (DMSO : Corn oil = 10 : 90) as an example, if 1 mL of 2.5 mg/mL working solution is to be prepared, you can take 100 μL 25 mg/mL DMSO stock solution and add to 900 μL corn oil, mix well to obtain a clear or suspension solution (2.5 mg/mL, ready for use in animals). View More
Injection Formulation 4: DMSO : 20% SBE-β-CD in saline = 10 : 90 [i.e. 100 μL DMSO → 900 μL (20% SBE-β-CD in saline)] Oral Formulations
Oral Formulation 1: Suspend in 0.5% CMC Na (carboxymethylcellulose sodium) Oral Formulation 2: Suspend in 0.5% Carboxymethyl cellulose Example: Take the Oral Formulation 1 (Suspend in 0.5% CMC Na) as an example, if 100 mL of 2.5 mg/mL working solution is to be prepared, you can first prepare 0.5% CMC Na solution by measuring 0.5 g CMC Na and dissolve it in 100 mL ddH2O to obtain a clear solution; then add 250 mg of the product to 100 mL 0.5% CMC Na solution, to make the suspension solution (2.5 mg/mL, ready for use in animals). View More
Oral Formulation 3: Dissolved in PEG400 (Please use freshly prepared in vivo formulations for optimal results.) |
| Preparing Stock Solutions | 1 mg | 5 mg | 10 mg | |
| 1 mM | 3.3303 mL | 16.6517 mL | 33.3034 mL | |
| 5 mM | 0.6661 mL | 3.3303 mL | 6.6607 mL | |
| 10 mM | 0.3330 mL | 1.6652 mL | 3.3303 mL |
*Note: Please select an appropriate solvent for the preparation of stock solution based on your experiment needs. For most products, DMSO can be used for preparing stock solutions (e.g. 5 mM, 10 mM, or 20 mM concentration); some products with high aqueous solubility may be dissolved in water directly. Solubility information is available at the above Solubility Data section. Once the stock solution is prepared, aliquot it to routine usage volumes and store at -20°C or -80°C. Avoid repeated freeze and thaw cycles.
Calculation results
Working concentration： mg/mL；
Method for preparing DMSO stock solution： mg drug pre-dissolved in μL DMSO (stock solution concentration mg/mL). Please contact us first if the concentration exceeds the DMSO solubility of the batch of drug.
Method for preparing in vivo formulation:：Take μL DMSO stock solution, next add μL PEG300, mix and clarify, next addμL Tween 80, mix and clarify, next add μL ddH2O，mix and clarify.
(1) Please be sure that the solution is clear before the addition of next solvent. Dissolution methods like vortex, ultrasound or warming and heat may be used to aid dissolving.
(2) Be sure to add the solvent(s) in order.
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