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Carbonyl diimidazole cdi

Manufactured by Merck Group
Sourced in Switzerland

Carbonyl diimidazole (CDI) is a chemical compound commonly used as a coupling reagent in organic synthesis. It is a versatile tool for the activation of carboxylic acids, enabling their reaction with various nucleophiles. CDI facilitates the formation of amide, ester, and other functional group linkages.

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6 protocols using carbonyl diimidazole cdi

1

Synthesis of Alexa Fluor 488-D-Lysine-NH2

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Alexa Fluor 488-D-Lysine-NH2 was synthesized as in Lebar et al., 2014
4 (link).Briefly,
Boc-D-Lys(Cbz)-OH (Bachem, Switzerland) was reacted with carbonyldiimidazole
(CDI) (MilliporeSigma, MA) in dimethylformamide (DMF) for 1.5 hr, then aqueous
ammonia was added and stirred for 6 hr to form the carboxamide
Boc-D-Lys(Cbz)-NH2. The Cbz protecting group was removed by catalytic
hydrogenation (20% Pd(OH)2/C) in methanol. The product, Boc-D-Lys-NH2, was
reacted with CDI in DMF for 1.5 hr, then Alexa Fluor 488 carboxylic acid in DMF
was added and reacted for 6 hr to yield Boc-D-Lys(Alexa Fluor 488)-NH2. The Boc
protecting group was removed by stirring in neat trifluoroacetic acid (TFA) for
30 min. The reaction was stopped by dropwise addition of TFA solution to
ice-cold ether. The precipitate was then HPLC-purified to obtain Alexa Fluor
488-D-Lysine-NH2.
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2

Synthesis of Alexa Fluor 488-D-Lysine-NH2

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Alexa Fluor 488-D-Lysine-NH2 was synthesized as in Lebar et al., 2014
4 (link).Briefly,
Boc-D-Lys(Cbz)-OH (Bachem, Switzerland) was reacted with carbonyldiimidazole
(CDI) (MilliporeSigma, MA) in dimethylformamide (DMF) for 1.5 hr, then aqueous
ammonia was added and stirred for 6 hr to form the carboxamide
Boc-D-Lys(Cbz)-NH2. The Cbz protecting group was removed by catalytic
hydrogenation (20% Pd(OH)2/C) in methanol. The product, Boc-D-Lys-NH2, was
reacted with CDI in DMF for 1.5 hr, then Alexa Fluor 488 carboxylic acid in DMF
was added and reacted for 6 hr to yield Boc-D-Lys(Alexa Fluor 488)-NH2. The Boc
protecting group was removed by stirring in neat trifluoroacetic acid (TFA) for
30 min. The reaction was stopped by dropwise addition of TFA solution to
ice-cold ether. The precipitate was then HPLC-purified to obtain Alexa Fluor
488-D-Lysine-NH2.
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3

Silanized Surface Antibody Coupling

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After the monolayer formation, the functional amine group needs to be activated to allow the coupling of the antibody to the silanized surface.
There exist several activators commercially available that react with the amine group, such as disuccinimidyl carbonate (DSC), N-hydroxy succinimide (NHS), glutaraldehyde (GA) [29 (link),31 (link),32 (link),33 (link)]. For this purpose, we used carbonyl diimidazole CDI (115533 Sigma Aldrich) since this chemical is easy to use in water solution, and successful results have been reported in the literature [34 (link)].
Modified surfaces were immersed in a solution of 150 mM of CDI in water and stirred for 1h at room temperature. (Figure 2B).
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4

Enzymatic Synthesis of Nucleotide Analogues

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The nucleotides (dGTP and dATP disodium salts) were purchased from Solarbio Science & Technology Co., Ltd. (Beijing, China). AMP was purchased from Sinopharm Chemical Reagents Co., Ltd. (Shanghai, China). Dimethylformamide (DMF) and Dowex-50W ion exchange resin were purchased from Acros Organics. Carbonyldiimidazole (CDI) was purchased from Sigma Aldrich. Klenow fragment DNA polymerase exo was purchased from New England Biolabs (Beijing, China). ATP determination kit (Kinase Glo) was purchased from Promega (Beijing, China). Streptavidin-labeled magnetic beads was purchased from PuriMag Biotech (Xiamen, China). The oligonucleotides were synthesized by Sangon Biotech Co., Ltd. (Shanghai, China) and purified by HPLC. The DNA sequences are listed in Table S2. The luminescence signal was measured by the multimode reader (BioTek, USA). NMR spectra including 1H NMR, and 31P NMR were recorded on a Bruker Ascend-600 spectrometer.
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5

Synthesis and Characterization of Pluronic Copolymers

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Triblock copolymers Pluronic® F127 (EO 200, PO 65), L35 (EO 22, PO 16), and L81 (EO 6, PO 43) were purchased form Sigma-Aldrich (USA) in powder form and dried by azeotropic distillation from benzene before use. Other reagents such as N,N-dimethylethylenediamine (DMEDA), 2-Hydroxypropyl-β-cyclodextrin (with average degree of hydroxypropyl substitution = 6.8), triethylamine (TEA), tris(2-aminoethyl)amine (TAEA), cholesteryl chloroformate, and carbonyldiimidazole (CDI), were also purchased from Sigma-Aldrich (USA) and used without further processing. Except DCM and DMF, all the solvents were used without further purification; DMF and DCM were dried over CaH2, filtered, distilled at low pressure and stored under Ar environment prior to use. Cellulose dialysis membranes (Spectrum Labs, USA) were rinsed thrice followed by immersion in deionized water for at least 30 min at room temperature prior to use. Ultra-pure H2O (resistivity ≈ 18.0 MΩ/cm−1) was used for all the experiments and was obtained from a NANOpure water purification system.
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6

Synthesis of Functionalized Cyclodextrins

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The Pluronic triblock copolymers F127 (EO 200, PO 65, MW = 12600), F68 (EO 153, PO 29, MW = 8350), L35 (EO 22, PO 16, MW = 1900), L64 (EO 26, PO 30, MW = 2900), and L81 (EO 6, PO 43, MW = 2800) were purchased from Sigma-Aldrich and dried by azeotropic distillation from benzene under vacuum before use. 2-Hydroxypropyl-β-cyclodextrin, with an average degree of hydroxypropyl substitution of 6.8, carbonyldiimidazole (CDI), triethylamine (TEA), tris(2-aminoethyl)amine (TAEA), and cholesteryl chloroformate were also purchased from Sigma-Aldrich and used received. 4-Sulfobutylether-β-cyclodextrin (SBEβCD, a.k.a. Captisol) with an average degree of SBE substitution of 7 was generously supplied by Cydex Pharmaceuticals (Lawrence, KS) and was used without further purification. S-2-(4-Isothiocyanatobenzyl)-1,4,7,10-tetraazacyclododecane tetraacetic acid (p-SCN-Bn-DOTA) was obtained from Macrocyclics (Dallas, TX). All solvents were reagent grade, purchased from commercial sources, and were dried over CaH2, filtered, and distilled at reduced pressure before storing under Ar prior to use. Cellulose dialysis membranes were obtained from Spectrum Labs and immersed in deionized water for at least 30 min prior to use. A Barnstead MicroPure water purification system was used to produce ultrapure water (resistivity ≈ 18.2 MΩ/cm−1).
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