Protecting groups in oligonucleotide synthesis

Chloro-8-quinolyl protecting group in oligonucleotide synthesis ... 

McBride LJ, Kierzek R, Beaucage SL, Caruthers, MH. Amidine protecting groups in oligonucleotide synthesis. J Am Chem Soc 108 2040-2048, 1986. Vinayak R, Anderson P, McColum C, Hampel A. Chemical synthesis of RNA using fast oligonucleotide deprotection chemistry. Nucleic Acids Res 20 1265-1269, 1992. 

Ravikumar VT, Cheruvallath ZS, Cole DL. 4-Cyano-2-butenyl group A new type of protecting group in oligonucleotide synthesis via phosphoramidite approach. Tetrahedron Lett 37 6643-6646, 1996. 

Wada T, Sekine M. TSE as a phosphate protecting group in oligonucleotide synthesis. Tetrahedron Lett 35 757-760, 1994. 

One of the more remarkable ideas to have emerged during the past year concerns the use of colour-coded triarylmethyl protecting groups in oligonucleotide synthesis. If, after each coupling of a mononucleotide to an T. Dorper and E.-L. Winnacker, Nucleic Acids Res., 1983, 11, 2575. 

Sonveaux, E. Protecting Groups in Oligonucleotide Synthesis, in Methods in Molecular Biology, Vol. 26 Agrawal, S., Ed. Humana Press Totowa, NJ, 1994, pp. 1-71. 

This group was developed as a fluorescent silyl protective group for oligonucleotide synthesis. It has excitation and emission wavelengths of 346 nm and 390 nm, respectively, which are outside the range of the DNA-damaging wavelength of 254-260 nm. It is prepared from the in situ prepared silyl chloride. It is stable to 0.01 M HCl and 30% ammonia. It is cleaved with 0.1 M TBAF in 3 min at rt. ... 

A universal allyl linker for the synthesis of oligonucleotides, 9-0-(4,4 -dimethoxytrityl)-10-undecenoic (116), has been described. Allyl cleavage occurs under conditions that are orthogonal to the conventional protecting groups in DNA synthesis thus allowing post-synthetic manipulations to be carried out on the solid support. A novel thymidine silyl linked support, (117), has also been... 

Some attention has been devoted to the use of photolabile protecting groups in DNA synthesis and a comparative study has been carried out. A particular problem is associated with the use of benzoyl protecting groups which react under the photolysis conditions. The solid support (120) has been demonstrated to produce yields of oligonucleotides which when compared to hydrolytic cleavage vary between 67% and 82%. ... 

The facile preparation of deoxyribonucleoside phosphoramidites from the selective activation of phosphorodiamidites by N.N-diiso-propylammonium tetrazolide (16) or 1/f-tetrazole (77) provides an excellent tool for the incorporation of new phosphate-protecting groups during oligonucleotide synthesis. Several phosphorodiamidites have recently been prepared, and a few of them are shown in Table 2. 

Use of the 8-hydroxyquinolyl group to protect phosphate groups in oligonucleotide synthesis. Removed using CuCl in DMSO/H O. 

Use of phenylthio group to protect phosphates in oligonucleotide synthesis. 

Figure 4 The use of PGA-labile protecting group in the synthesis of oligonucleotides, both in solution and in solid phases.

The Dnseoc group was developed as a base-labile protective group for the 5 -hydroxyl in oligonucleotide synthesis. It is cleaved with DBU in aprotic solvents. The condensation of oligonucleotide synthesis can be monitored by UV detection at 350 nm or by fluorescence at 530 nm of the liberated vinylsulfone. ... 

The steps involved in automated oligonucleotide synthesis illustrate the current use of protective groups in phosphate chemistry (Scheme 1). Oligonucleotide synthesis involves the protection and deprotection of the 5 -OH, the amino groups on adenine, guanine, and cytosine, and -OH groups on phosphorus. 

This group, used for 5 -phosphate protection, has hydrophobicity similar to that of the dimethoxytrityl group and thus was expected to assist in reverse-phase HPLC purification of product from failure sequences in oligonucleotide synthesis. The group is cleaved with Bu4N F in DMSO at 70°. ... 

This lipophilic group, developed for 5 -phosphate protection in oligonucleotide synthesis, is removed with 80% AcOH in 1 h. The related trityloxyethylamino group has been used in a similar capacity for phosphate protection and is also cleaved with 80% AcOH. ... 

A wide range of techniques is available for the separation and purification of oligonucleotides after the removal of protecting groups. Obviously, chemical synthesis is not the only source of such compounds, and those derived by purely enzymic syntheses, or after isolation from biological sources, have been examined in similar ways. The literature is correspondingly extensive, and only those methods routinely used after a chemical synthesis will be discussed in detail here. 

The wide use of acid-labile linkers and protecting groups in peptide SPS has reduced efforts toward the development of base-labile linkers. The commonly used SP Fmoc peptide coupling protocols require Fmoc deprotection under basic conditions during the synthesis, thus ruling out base-labile linkers. However, base-labile linkers are popular in oligonucleotide SPS and will be described in Section 2.2. Other examples of base- or nucleophile-labile linkers are shown in Fig. 1.10. 

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