Ion prevented any loss of the trityl group. Thermal Stability of Trityl-Amino-Modifiers The data noted above prompted us to revisit our recommended deprotection conditions for both the 5′-DMS(O)MT Amino-Modifer C6 and the MMT-protected 5′-Amino-Modifier C6. For these products, we have always recommended deprotection at 40 or lower to avoid reported thermallyinduced trityl loss. We deprotected tritylamino-modified oligos in three ways: room temperature ammonium hydroxide, ammonium hydroxide for 17 hr at 55, and finally deprotection in AMA at 65 for 10 minutes. HPLC analysis revealed that there was no indication of any loss
of the trityl protecting group during any of the deprotection conditions at elevated temperatures. We are now able to remove the recommendation that these aminomodified oligos should be deprotected at 40 or lower. Salt-Free Retention of Trityl During Drying The addition of large amounts of salt can be problematic for downstream applications. A good example of this would be the synthesis of a 5′-amino-modified RNA in which the 5′-trityl is maintained for trityl-on purification. While the addition of the Tris would maintain the trityl, its presence would severely inhibit the removal of the 2′-silyl protecting groups in either TEA.3HF or TBAF. Therefore, we tested the possibility of converting the oligonucleotide to the nonvolatile sodium salt to maintain the trityl upon drying. The following desalting protocol was used on the model oligo 5′-DMS(O)MT Amino-Modifier T12:
Deprotect the oligo in NH 4 OH or AMA. 2) Add 45 mg Tris base/mL of deprotection solution. 3) Desalt on a Glen-Pak DNA cartridge. i) Condition cartridge with 0.5 mL ACN, followed by 1 mL 2 M TEAA. ii) Dilute with 1 mL water and load oligo drop-wise onto Glen-Pak DNA Cartridge. iii) Rinse with 2 mL distilled water. iv) Rinse 2x with 2 mL 0.5 M aqueous sodium hydroxide. v) Rinse with 2 mL distilled water. vi) Elute with 1 mL 75% ACN/water and dry down. HPLC analysis revealed that the crude amino-modified oligo without drying, the Glen-Pak purified oligo converted to the sodium salt prior to drying, and finally the eluted and dried oligo were identical in purity and that the trityl group was maintained throughout the process.879085-55-9 medchemexpress 17
FLUORESCEIN DERIVATIVES A triumvirate of fluorescein derivatives has dominated fluorescent labelling of oligonucleotides over the last decade.21829-25-4 manufacturer Fluorescein, hexachlorofluorescein and tetrachlorofluorescein, better known as FAM, HEX and TET, have been in the forefront of DNA analysis in the fields of sequencing and genetic analysis using instruments with multicolor detection.PMID:29489203 However, HEX has proved to be the weakest performer of the three due to its instability to the basic conditions of oligonucleotide deprotection. HEXlabelled oligonucleotides must be treated with care to avoid some level of degradation. Moreover, the mechanism of degradation involves the loss of chlorine residues from the ring systems leading to products that are fluorescent at lower wavelengths, even covering the wavelength of TET. In t he pre v i ous Gl e n R e p or t , we int ro duce d a ne w f luores cein phosphoramidite, 5′- dichloro-dimethoxy fluorescein, better known as JOETM in the world of multicolor sequencing. This fluorescein derivative exhibits excellent stability to a range of deprotection conditions. In addition, its fluorescence is much less pH sensitive than fluorescein itself. Now, we are happy to introduce further fluorescein-based products: SIMA (HE.MedChemExpress (MCE) offers a wide range of high-quality research chemicals and biochemicals (novel life-science reagents, reference compounds and natural compounds) for scientific use. We have professionally experienced and friendly staff to meet your needs. We are a competent and trustworthy partner for your research and scientific projects.Related websites: https://www.medchemexpress.com
