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The modification of DNA with indole-linked nucleotides alters its sensitivity to enzymatic cleavage
Lingala, Suresh ; Fisiuk, Anastasiia ; Stephen, Michelle , et al. bioRxiv,2025. DOI: 10.1101/2025.01.26.634936
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Abstract: We describe the synthesis of C-5 indole-tagged pyrimidine and C-8 indole-tagged purine nucleoside phosphoramidites and their incorporation into double-stranded DNA 15 base pairs in length. Of the 23 sequence modifications tested, two induced the DNA duplex to adopt a Z-like left-handed conformation under physiological salt conditions, bypassing the specific sequences typically required for a left-handed Z-DNA structure. The impact of these modifications varied with the linker type: flexible propyl linkers exhibited distinct effects compared to rigid propargyl linkers. Notably, modifications positioned directly on or near a restriction site emphasized the pivotal role of linker rigidity in controlling DNA conformation. Specifically, the conformational change induced by the flexible linker impacted nuclease and restriction endonuclease cleavage, reducing sequence specificity. In contrast, the rigid linker suppressed this effect. Furthermore, our findings indicate that nucleic acid duplexes modified with indole-linked nucleotides using a flexible propyl linker have a pronounced tendency to form BZ or Z-like regions in longer DNA sequences. A higher density of modifications may even induce a full Z-like conformation throughout the duplex. These modified nucleotides hold potential for the development of novel antisense therapeutics and introducing valuable tools for in vitro screening of small molecules targeting distorted B-DNA, BZ-DNA, and Z-DNA structures.
Purchased from AmBeed: 14221-01-3 ; 1122-58-3
CAS No. : | 1122-58-3 | MDL No. : | MFCD00006418 |
Formula : | C7H10N2 | Boiling Point : | - |
Linear Structure Formula : | C5NH4N(CH3)2 | InChI Key : | VHYFNPMBLIVWCW-UHFFFAOYSA-N |
M.W : | 122.17 | Pubchem ID : | 14284 |
Synonyms : |
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Signal Word: | Danger | Class: | 6.1 |
Precautionary Statements: | P260-P262-P264-P270-P271-P273-P280-P301+P310+P330-P302+P352+P310-P304+P340+P311-P305+P351+P338+P310-P308+P311-P332+P313-P361+P364-P391-P403+P233-P405-P501 | UN#: | 2811 |
Hazard Statements: | H301+H331-H310-H315-H318-H370-H411 | Packing Group: | Ⅱ |
GHS Pictogram: |
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* 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 |
---|---|---|
32% | In dichloromethane; at 0 - 20℃; | EXAMPLE 13 2-Phenoxy-benzoic acid 3,5-bis-trifluoromethyl-benzyl ester To a solution of 118 mg (0.55 mmol) 2-phenoxybenzoic acid and 122 mg (0.50 mmol) 3,5 bis(trifluoromethyl)benzyl alcohol in 1.5 ml dichloromethane at 0 C. was added a solution of 124 mg (0.60 mmol) 1,3-dicyclohexylcarbodiimide and 7 mg (0.06 mmol) 4-dimethylaminopyridine in 1 ml dichloromethane.. The ice bath was removed and stirring was continued at room temperature overnight.. The solvent was removed in vacuo and the residue re-dissolved in diethyl ether, filtered and evaporated.. The residue was purified by flash chromatography to give 70 mg (32%) of the title compound as white crystals. MS m/e (%): 440 (M+, 51), 347 (39), 227 (36), 197 (100). |
Yield | Reaction Conditions | Operation in experiment |
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With hydrogenchloride; In pyridine; water; | Route b: 1-O-(2-propenyl)-6-O-triphenylmethyl-alpha-D-galactose (III) The Compound (II)(11.1 g, 50.2 mmol) was dissolved in 50 mL of anhydrous pyridine. To the solution, 16.8 g (60.2 mmol) of tritylchloride and 614 mg (5.02 mmol) of p-dimethylaminopyridine (DMAP) were added. The mixture was allowed to react for 24 hours at 40 C. while stirring. Then, the reaction was quenched by addition of 100 mL of cold water, and then extracted with ethyl acetate (3*200 mL). The organic layers were combined, neutralized to pH 4 with 1.0N hydrochloric acid, washed with brine (2*200 mL), dried over anhydrous sodium sulfate, filtered, concentrated in vacuo, and purified by silica gel flash chromatography (chloroform: methanol=20:1?15:1) to give a pale yellowish oily substance (yield:21.3 g, 46.1 mmol, recovery 91.8%). [alpha]D=+64.2 (c 1.48, CHCl3) |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With 1,2-dichloro-ethane; N-ethyl-N,N-diisopropylamine; In 1,4-dioxane; | Step B 1-(tert-Butoxycarbonyl)-4-(3-(4-fluorophenyl)-3-oxopropyl)piperidine Molecular sieve pellets (4 A), N,O-dimethylhydroxylamine hydrochloride (227 mg, 3.32 mmol), and DIEA (0.41 mL, 0.30 g, 2.4 mmol) were added to a solution of 3-(1-(tert-butoxycarbonyl)piperidin-4-yl)propionic acid (500 mg, 1.94 mmol, from Step A) in 1,4-dioxane (10 mL). 4-(Dimethylamino)pyridine (57 mg, 0.47 mmol) and EDC (483 mg, 2.52 mmol) were added and the mixture was stirred for 16 h at rt. The mixture was partitioned between EtOAc (50 mL) and 1 N aq. HCl (50 mL). The aqueous layer was extracted with EtOAc (50 mL). The organic layers were washed with sat'd NaCl (30 mL), dried (Na2SO4), decanted, and evaporated to give 583 mg of N-methoxy-N-methyl-3-(1-(tert-butoxycarbonyl)piperidin-4-yl)propionamide. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With pyridine; acetic anhydride; In dichloromethane; toluene; | (a) 5-Acetoxymethylfuran-2-carboxylic acid A mixture of 5-hydroxymethylfuran-2-carboxylic acid (5.90 g), dry dichloromethane (100 ml), pyridine (6.71 ml), 4-dimethyl-aminopyridine (507 mg), and acetic anhydride (4.21 ml) was stirred for 2 hours at room temperature. The mixture was diluted with ethyl acetate and washed with 5M hydrochloric acid and brine (3 times), dried (MgSO4), and evaporated. The residue was re-evaporated twice from dry toluene to give the title acid as a solid (5.00 g); deltaH [(CD3)2 CO) 2.05 (3 H, s), 5.11 (2 H, s), 6.62 (1 H, d, J 4 Hz), 7.17 (1 H, d, J 4 Hz) and 8.31 (1 H, br s). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
In water; acetonitrile; | EXAMPLE 5 To a stirred mixture of <strong>[1193-24-4]4,6-dihydroxypyrimidine</strong> (5.18 g, 1 equivalent) and 4-(N,N,-dimethylamino)pyridine (0.55 g, 0.1 equivalent) in acetonitrile (100 ml) was added phosgene (28 g, 19.7 ml, 6.2 equivalents) in two aliquots. The resulting mixture was stirred for 10 minutes at room temperature and was then stirred for 4 hours at 55 C. The reaction mixture was purged with air after which water (200 ml) was added. The resulting mixture was extracted with dichloromethane (3*100 ml). The organic extracts were combined, washed with water (100 ml), dried over magnesium sulphate and evaporated to dryness to leave 4,6-dichloropyrimidine (4.63 g). |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
74% | In dichloromethane; | 3',3'-dimethyl-6-nitro-1'-(2-(pent-4-enoyloxy)ethyl)spiro[chromene-2,2'-indolin]-8-yl pent-4-enoateor spiropyran was synthesized according to [15] with the following modifications made tothe amounts of reagents and purification methods. To an oven dried round bottom flask,1'-(2-hydroxyethyl)-3',3'-dimethyl-6-nitrospiro[chromene-2,2'-indolin]-8-ol (3.0 g, 8.14 mmol, 1 equiv)and 4-dimethylaminopyridine (0.099 g, 0.814 mmol, 0.1 equiv.) were dissolved in dry dichloromethane(40 mL). The dark green suspension was stirred and <strong>[63521-92-6]4-pentenoic anhydride</strong> (3.20 mL, 17.51 mmol,2.15 equiv) was added in 3 separate aliquots, with 15 min between each addition. The reaction wasstirred overnight, resulting in a magenta-purple solution. The mixture was extracted with concentratedsodium bicarbonate solution (1 x 75 mL), 1 N hydrochloric acid (1 x 75 mL), water (2 x 75 mL)and brine (1x 75 mL) before drying over sodium sulfate. The crude product was collected fromrotary evaporation as crude purple oil. Boiling petroleum ether (300 mL) was poured into the oil,then the solution was hot filtered and let stand to develop yellow-green crystalline SP (3.21 g, 74%).Characterization matched the compound reported in literature [15]. |
Yield | Reaction Conditions | Operation in experiment |
---|---|---|
With triethylamine; | A. tert-butyl (4-bromo-5-chloropyridin-2-yl)carbamate, cpd 148a A solution of <strong>[1187449-01-9]4-bromo-5-chloropyridin-2-amine</strong> (2 g, 9.64 mmol), di-tert-butyldicarbonate (4.21 g, 19.28 mmol), TEA (2.93 g, 28.92 mmol), N,N-dimethylpyridin-4-amine (117.8 mg, 0.96 mmol) in CH2Cl2 (20 mL) was stirred at rt for 2 h. The mixture was diluted with water (40 mL) and extracted with CH2Cl2 (40 mL*3). The combined organic layers were dried (MgSO4), filtered, and the filtrate concentrated to give the crude product as a white solid. The crude product was purified by FCC (petroleum ether/ethyl acetate=100:0 to 70:30). The solvents were evaporated to afford the title compound as a white solid (1.2 g). |
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