Deletion sequences

Because coupling is not always quantitative, the non-reacted terminal deoxynucteoside must be excluded from the following synthesis cycles. Otherwise deletion sequences will render the isolation of the pure final product difficult. Therefore a capping step (step 3) follows, e.g., acetylation with acetic anhydride and N,N-dimethyl-4-pyridinamine (DMAP) in dioxane. Capping times should be as short as possible, especially with 2-cyanoethyl phosphite triesters, which are sensitive to bases such as DMAP. 

Connection of the glycosyl acceptor to the solid support (case 1) allows for the use of excess donor D (usually more fragile than A), a feature that can be used to advantage to drive reactions to completion. Nevertheless, this strategy requires a capping step to prevent the formation of deletion sequences, which would complicate... 

S Hancock, DJ Prescott, PR Vagelos, GR Marshall. Solvation of the polymer matrix. Source of truncated and deletion sequences in solid phase synthesis. J Org Chem 38, 774, 1973. 

The formation of deletion sequences in solid-phase peptide synthesis either occurs as a result of incomplete coupling or incomplete N-terminal deprotection.P l The former is less common nowadays due to the extremely efficient coupling agents used and this problem is now... 

Sequence alterations in viruses are common. Areas of high sequence variation may be interspersed between conserved domains. Higher frequencies of variation can be correlated with lower polymerase fidelity and may allow escape from antibody recognition and from antiviral drugs. Common mutations in viruses include point mutations, insertions, and deletions. Sequence diversity within a viral species may be so great that consensus sequences for molecular typing are difficult to find. 

The IgKlight chain gene is located on chromosome 2pl 1-13, and contains approximately 76 Vk genes, 5 JK segments, and 1 Ck gene. There is a K-deleting sequence (element)... 

Another germanium-based hnker has been developed for solid-phase synthesis of a pyrazole hbrary [79]. A new iterative synthesis of regioregular oligothiophenes has been developed in which double-couphng after each iteration minimizes deletion sequences. The method exploits the susceptibility of a-silyl- but not a-ger-myl-substituted thiophene derivatives towards nucleophilic ipso protodemetalation and features an unusual base-free Suzuki-type coupling product. The strategy... 

Figure 6 Immunoglobulin heavy chain class switch recombination. (A) The murine heavy chain locus is shown before and after recombination from g. to yl, which results in expression of IgGl antibodies. Deleted sequences can be recovered in circular DNA molecules from B cells which have recently completed switch recombination. V, variable region C, constant region and S, switch region. (B) Examples of consensus G-rich repeats from some murine S regions...

To obtain a relatively pure product in a process with many synthetic steps, all reactions must be very efficient. This is especially true for longer sequences that can become lost in a mixture of by-products (mainly deletion sequences) if the stepwise efficiencies are not very close to 100%. Figure 3 shows the yield of desired biopolymer versus the length of the sequence at various stepwise yields. Even at 99% stepwise efficiency, the final yield of a biopolymer 100 monomers in length (broken line) is less than 40%. As more undesired synthetic by-products are generated, it also becomes increasingly difficult to purify the desired product. 

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