Where the mRNA target exhibits significant secondary structure. SBC oligos possess this unique ability because, although they exhibit high affinity for natural oligonucleotides, they show little affinity for other SBC oligos even of a complementary sequence. Oligos in which A has been replaced with 2-amino-A and T with 2thio-T represent an excellent example of SBC oligos.4 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. Model building suggests
that steric interactions between the 2thio group of thymidine and the 2-amino group of adenine tilt the bases relative to each other yielding a base pair that contains only a single hydrogen bond.4 However, 2-thio-T base pairs perfectly well with A, as shown in Figure 1. But the real proof is not in models: SBC 20mers annealed against a DNA 20mer
target exhibited Tm values 10higher than the corresponding DNA-DNA hybrid, whereas the SBC-SBC hybrid yielded Tm values 30lower.4 Because of the resistance to hydrolysis of the protecting groups of our earlier 2-amino-dA monomer, the aggressive deprotection was not compatible with the presence of 2-thiodT in the same oligo. Fortunately, our new 2-amino-dA monomer is rapidly deprotected in ammonium hydroxide and is compatible with 2-thio-dT (6). Now SBC oligos containing 2-amino-dA and 2-thio-dT can be easily prepared. Hybridization Independent of Base Composition Any technique that involves hybridization of multiple sequences simultaneously, as in DNA chip and reverse hybridization technologies, is subject to inaccuracies due to differences in GC content. Sequences with high GC content may contain mismatches and still hybridize, whereas a low GC content probe may match perfectly and yet disassociate from the target, leading to false positives and negatives respectively. An elegant way of circumventing this problem would be to use a modified base that normalized the stability of the GC and AT base pairs.5451-09-2 web With this goal in mind, a series of modified dC bases was evaluated to develop a system where hybridization was independent of base composition and only dependent upon oligonucleotide length.1306760-87-1 manufacturer 5 It was found that the N4-ethyl analogue (N4-Et-dC) hybridizes specifically to natural dG but the stability of the base pair is reduced to about the level of an AT base pair. In a series of probes whose GC content ranged from 0 to 100%, the range in Tm values when N4-Et-dC was used was only 7 when dC was used, that range was 39 We are happy to offer N4-EtdC (7) for oligo synthesis.PMID:31424857 References
(1) Y. Lebedev, et al., Genetic Analysis Biomolecular Engineering, 1996, 13, 1521. (2) L.E. Xodo, G. Manzini, F. Quadrifoglio, G.A.v.d. Marel, and J.H.v. Boom, Nucleic Acids Res., 1991, 19, 5625-5631. (3) B.C. Froehler, S. Wadwani, T.J. Terhorst, and S.R. Gerrard, Tetrahedron Lett., 1992, 33, 5307-5310. (4) I.V. Kutyavin, R.L. Rhinehart, E.A. Lukhtanov, V.V. Gorn, R.B. Meyer, and H.B. Gamper, Biochemistry, 1996, 35, 11170-11176. (5) H.K. Nguyen, P. Auffray, U. Asseline, D. Dupret, and N.T. Thuong, Nucleic Acids Res., 1997, 25, 3059-65.
ore than eight years ago, we introduced an oligo affinity support (OAS)1 which allowed normal oligonucleotide synthesis but on treatment with ammonium hydroxide, the fully-deprotected oligonucleotide remained attached to the support. After annealing the complementary strand to the support-bound oligonucleotide, an affinity support for the purificat.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