Side oligonucleotide synthesis

Reese CB, Ubasawa A. Namre of side-reactions in oligonucleotide synthesis involving arenesulphonyl derivatives of 3-nitro-1,2,4-triazole and related condensing agents. Nucleic Acids Symp. Ser. 1980 (7) 5-21. 

The basic success of an automated biopolmyer synthesis depends on the chemistry used for chain assembly. A well-understood and well-characterized chemical process has the best chance for success on an automated instrument. Fortunately, many of the reactions used in peptide and oligonucleotide synthesis are well characterized and approach 100% stepwise yields with minimal side reactions. Advances in this field are continually resulting in higher quality products. 

C. B. Reese and A. Ubasawa (1980), Reaction between l-arenesulfonyl-3-nitro-l, 2,4-triazoles and nucleoside base residues. Elucidation of the nature of side-reactions during oligonucleotide synthesis. Tetrahedron Lett. pp. 2265-2268. 

To facilitate the design of deoxyribonucleoside phosphoramidite analogs, information regarding the activation of deoxyribonucleoside phosphoramidites will be provided to emphasize the importance imparted by the steric bulk of the substituents attached to the phosphorus center and to specific nucleobases on the coupling rates. The capping and oxidation steps of the synthetic cycle will also be discussed in relation to the potential formation of side products during oligonucleotide synthesis. 

Gdaniec, Z., Mielewczyk, S., and Adamiak, R. W (1987) Side reactions in oligonucleotide synthesis. NMR study of 4-chlorophenyl-phosphoro-di/1,2,4-triazolide/preparations and their reactivity toward nucleoside lactam systems, in Biophosphates and Their Analogs—Synthesis, Structure, Metabolism and Activity (Bruzik, K. S and Stec, W, J, eds.), Elsevier Science, Amsterdam, pp. 127-132... 

ICAM-1, VCAM-1 and E-selectin synthesis was successfully blocked in vitro using these types of molecules [113]. In vivo, the systemic administration of ICAM-1 antisense oligonucleotide prevented and reversed murine colitis without serious side-effects [114]. In a place-bo-controUed trial of the human analogue, the antisense oligonucleotide was effective and well tolerated [115]. 

The polymerase chain reaction (PCR) is an important procedure in genetic engineering that allows any DNA segment to be replicated (amplified) without the need for restriction enzymes, vectors, or host cells (see p. 258). However, the nucleotide sequence of the segment has to be known. Two oligonucleotides (primers) are needed, which each hybridize with one of the strands at each end of the DNA segment to be amplified also needed are sufficient quantities of the four deoxyribonucleo-side triphosphates and a special heat-tolerant DNA polymerase. The primers are produced by chemical synthesis, and the polymerase is obtained from thermostable bacteria. 

Synthesis of oligonucleotide analogs with modified side chains 93SL621. 

---