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Snowprint: a predictive tool for genetic biosensor discovery
Simon d’Oelsnitz ; Sarah K. Stofel ; Joshua D. Love , et al. Commun. Biol.,2024,7(1):163. DOI: 10.1038/s42003-024-05849-8
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Abstract: Bioengineers increasingly rely on ligand-inducible transcription regulators for chemical-responsive control of gene expression, yet the number of regulators available is limited. Novel regulators can be mined from genomes, but an inadequate understanding of their DNA specificity complicates genetic design. Here we present Snowprint, a simple yet powerful bioinformatic tool for predicting regulator:operator interactions. Benchmarking results demonstrate that Snowprint predictions are significantly similar for >45% of experimentally validated regulator:operator pairs from organisms across nine phyla and for regulators that span five distinct structural families. We then use Snowprint to design promoters for 33 previously uncharacterized regulators sourced from diverse phylogenies, of which 28 are shown to influence gene expression and 24 produce a >20-fold dynamic range. A panel of the newly repurposed regulators are then screened for response to biomanufacturing-relevant compounds, yielding new sensors for a polyketide (olivetolic acid), terpene (geraniol), steroid (ursodiol), and alkaloid (tetrahydropapaverine) with induction ratios up to 10.7-fold. Snowprint represents a unique, protein-agnostic tool that greatly facilitates the discovery of ligand-inducible transcriptional regulators for bioengineering applications.
Purchased from AmBeed: 486460-32-6
CAS No. : | 486460-32-6 | MDL No. : | MFCD19684081 |
Formula : | C16H15F6N5O | Boiling Point : | - |
Linear Structure Formula : | - | InChI Key : | MFFMDFFZMYYVKS-SECBINFHSA-N |
M.W : | 407.31 | Pubchem ID : | 4369359 |
Synonyms : |
MK-0431
|
Chemical Name : | (R)-3-Amino-1-(3-(trifluoromethyl)-5,6-dihydro-[1,2,4]triazolo[4,3-a]pyrazin-7(8H)-yl)-4-(2,4,5-trifluorophenyl)butan-1-one |
Signal Word: | Warning | Class: | N/A |
Precautionary Statements: | P261-P305+P351+P338 | UN#: | N/A |
Hazard Statements: | H302-H315-H319-H335 | Packing Group: | N/A |
GHS Pictogram: |
* All experimental methods are cited from the reference, please refer to the original source for details. We do not guarantee the accuracy of the content in the reference.
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
86% | With 4-methyl-morpholine; benzotriazol-1-ol; In ethanol; dichloromethane; at 10 - 25℃; for 3h; | Example 8Synthesis of compound Sitagliptin 1:To a 100 mL three-neck round bottom flask equipped with mechanical stirrer was added the amine A 13-Trifluoromethyl-5,6,7,8-tetrahydro-[ 1 ,2,4jtriazolo[4,3-ajpyrazinej (1.97 g, 10.29mmol), ethanol (10 mL), NMM (2.28 g, 22.63 mmol), carboxylic acid 10, (2.4 g, 10.29 mmol), and HOBt (0.208 g, 1.54 mmol). The contents were then cooled to 10 C, and EDC (1.91 g,12.34 mmol) was added. The reaction was stirred at 25 C for 3 h followed by the addition of water (20 mL). Product was isolated via extractive workup with methanol (3 x 15 mL) then dried over anhydrous sodium sulphate and concentrated in vacuo. Purification via flash columnchromatography (eluent CH2C12/MeOH, 10:1) gave 1 as colourless oil (3.60 g, 8.84 mmol, 86%). The Spectral Analysis of all compounds: Rf = 0.13 (Ethyl acetate); [aID25 (c 0.92, CHC13) = -22.4. ?H NMR (300 MHz, CDC13) 67.11-7.09 (m, 1H, Aromatic), 6.99-6.92 (m, 1H, Aromatic), 5.10-4.99 (m, 2H, CH2), 4.31-4.28 (m,4H, NCH2CH2N), 3.60 (brs, 1H, CH), 2.83-2.80 (m, 1H, CHH?), 2.70-2.65 (m, 1H, CHH?), 2.60-2.50 (m, 2H, CH2), 2.03 (brs, 2H, NH2) ppm. ?3C NMR (75 MHz, CDC13) 6171.2, 170.8, 151.2,149.6, 156.8, 148.3, 146.8, 142.7, 122.1, 118.8, 118.3, 105.7, 48.9, 43.5, 42.4, 39.9, 37.9, 36.2 ppm. JR (CHC13) v 3372, 1645 cm?; ESIMS: mlz (%) 430 [M + Naj Analysis calculated for C,6H,5F6N50C47.18,H3.71,N 17.19. FoundC47.01,H3.62,N 17.10. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
97% | With triethylamine; In tetrahydrofuran; for 1h;Reflux; | In 100 mL of tetrahydrofuran,4.11 g (41 mmol) of triethylamine was added,6.60g (20mmol) of compound IV and4.81 g (25 mmol) of 3-trifluoromethyl-1,2,4-triazolo[4,3-a]pyrazine was refluxed for 1 hour.TLC monitors the progress of the reaction,After the reaction is completed,Concentrated under reduced pressure,Purified by column chromatography,That is, the product sitagliptin 7.90g (19.4mmol),The yield was 97%, HPLC purity = 99.88%. |