During iodine oxidation, therefore the N2 position should be protected by an acyl group. In order to achieve deprotection of the N2 position under mild conditions, a labile acyl group like Pac or Methoxyacetyl (Mac) should be chosen. These criteria led us to choose the PacProtected 2-Amino-dA and we prepared the phosphoramidite (2) for evaluation. SYNTHESIS AND DEPROTECTION It was quickly confirmed that Pac2-Amino-dA coupled as well as regular DNA monomers under identical coupling conditions with no change in coupling time. It was also gratifying to find that iodine oxidation had no effect on the coupling
efficiency as confirmed by HPLC analysis of the resulting oligo. So no chain scission was observed using regular iodine oxidation. Deprotection of oligos containing Pac-2-Amino-dA was analyzed using AMA and ammonium hydroxide. The results are shown below. We found that complete deprotection required about the same time as oligos containing dmf-dG.219766-25-3 Formula
Deprotection Solution AMA NH4OH NH4OH NH4OH Temperature 65 65 55 room temp Time 20 min 4 hr 8-17 hr 24-36 hr
From previous development work, it is well known that protecting groups at the N2 position are much less labile than identical protecting groups at the N6 position of 2,6-diaminopurine. Therefore, two different protecting groups for these positions were called for. We also rejected the use of two acyl protecting groups since the N6-acyl group would destabilize the glycosidic bond, 6
So far so good, but how would the new product perform in the test we carried out a few years ago with our existing monomer In that test, we added 2-Amino-dA six times in a mixed base 16mer. The results are shown in Figure 3, where the full length oligo in the crude mixture was only 13% using iodine oxidation but was raised to 60% using non aqueous oxidation with CSO. As noted above, with an electron-donating
formamidine protecting group on the N2, the N3 becomes nucleophilic and can attack the C3′ causing strand scission and a lower yield of full-length oligo. Also shown in Figure 3 is the chromatogram of the same oligo sequence with six additions of Pac2-Amino-dA using standard coupling and deprotected with ammonium hydroxide.2930690-12-1 manufacturer In this case, the yield of full length oligo was raised to over 95%.PMID:28722955 DUPLEX STABILITY STUDY With the optimal system in place for the preparation of oligos containing multiple additions of 2-Amino-dA, we carried out an experiment to determine if the increase in melting temperature inherent in the 2-Amino-A-T base pair is cumulative as the substitution of A by 2-Amino-A increases. The following oligos were prepared and their melting behavior examined.
The runs were performed in degassed 0.1 M Tris-HCl, pH 7.4 with the oligos at 1.25 concentration, using a Jasco V-530 fitted with a Peltier temperature control unit. by replacing the A-T base pair with the 2-Amino-A-T base pair is cumulative over five additions in an 18mer. SBC OLIGOS Selective Binding Complementary (SBC) oligonucleotides1 are able to form stable, sequence specific hybrids with complementary unmodified DNA or RNA but are unable to form stable hybrids with each other. Oligos in which A has been replaced with 2-amino-A and T with 2-thio-T represent an excellent example of SBC oligos. While 2-amino-A forms a very stable base pair with T containing three hydrogen bonds, the stability of the base pair with 2-thio-T is greatly diminished. The steric interactions between the 2-thio group of thymidine and the 2-amino group of ad.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