Ure of acetonitrile/dichloromethane (1:3). Otherwise the coupling reaction at the 5′ terminus is standard with a 3 minute coupling time recommended. 5′-Stearyl oligonucleotides can be purified using standard procedures on RP cartridges, such as Glen-PakTM cartridges, as well as standard chromatographic techniques.
tEChNiCaL BRiEF COMpatiBiLity OF ULtRaMiLd MONOMERs OR aC-dC with hydRaziNE REaGENt
UltraMild Phosphoramidites (PacdA, iPr-Pac-dG, Ac-dC) are versatile phosphoramidites commonly used for the incorporation of modifications that are sensitive to standard deprotection conditions. These phosphoramidites are compatible with a range of deprotection conditions. For UltraMild deprotection we recommend room temperature deprotection with ammonium hydroxide or potassium carbonate in methanol. Acetyl-dC is also a popular monomer in its own right since it is compatible with UltraMild deprotection, as well as regular deprotection using ammonium hydroxide, and is necessary for AMA deprotection. See our overview of deprotection schemes for further information: http:// w w w. g l e n r e s e a r c h . c o m / Te c h n i c a l / Deprotection.pdf Glen Research offers one of the largest selections of phosphoramidites for DNA and RNA synthesis. A popular product is our 5-Me-dC Brancher Phosphoramidite (101018; (1)), which is used for synthesizing branched DNA or comb-like DNA structures. 1,2 This sequence modifier incorporates a levulinyl-protected alcohol that can serve as a branch point for a second sequence. The process for generating these structures starts by synthesizing the first sequence that incorporates the dC-brancher. After the full-length oligo is synthesized, the DMT is removed and the 5′-hydroxyl is capped with standard Cap A/B reagents. The levulinyl protecting group is then selectively removed with hydrazine hydrate in pyridine/ acetic acid solution. The second sequence is then synthesized from the dC brancher. Recently, we received feedback from our customers that seemed to indicate an incompatibility between the UltraMild phosphoramidites or Ac-dC alone and the protocol for removing the levulinyl protecting group. We suspected the protecting groups of these monomers were prematurely removed during the hydrazine treatment of the dC Brancher, resulting in unwanted branching. The branched sequences were observed as smears on the subsequent PAGE analysis of the final products. To investigate if the problems were caused by deprotection of the base protecting groups by the hydrazine reagent, we analyzed the stability of Ac-dC to the recommended procedure for removing the levulinyl protecting group. We duly found that the hydrazine reagent can partially deprotect the Ac-dC, leading to chain branching in subsequent coupling cycles.2930690-12-1 IUPAC Name We conclude that the standard phosphoramidites (Bz-dA, ibu-dG, Bz-dC, and T) should be used when making a branched oligo with our 5-Me-dC Brancher.1129435-60-4 MedChemExpress
1.PMID:30000673 2. 3. 4. 5. 6. 7. 8. Synthesize a control T12 oligo DMT-Off (with no dC incorporations). Synthesize two 12-mer T oligos DMT-Off, one with a single internal incorporation of Ac-dC and the other containing Bz-dC. Cap the 5′-OH with standard Cap A/B mix. Treat oligos with 0.5M hydrazine hydrate in pyridine/acetic acid (1:1) for 15 minutes at room temperature. Rinse with pyridine/ acetic acid followed by acetonitrile. Continue syntheses, adding T6, DMT-ON. Deprotect oligos with ammonium hydroxide. Analyze on RP-HPLC.
T12 did not show any signs of branching as seen by.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