Isobutyryl protecting groups

The bases adenine, guanine, and cytosine all contain exocyclic amino substituents that require protection, since these are potential nucleophiles. They are converted into amides that are stable to the other reagents used in the process, yet can be removed readily by basic hydrolysis. The most effective protecting groups have been found to be isobutyryl for the amino group of guanine, and benzoyl for adenine and cytosine. Thymine has no exocyclic nitrogen and does not need protection. 

New amino acid-tetrahydropterin conjugates were synthesized from A2-isobutyryl-6,7-dimethyl-5,6,7,8-tetrahydropterin (169) by either direct acylation (170) or via a succinate linker (171) followed by removal of protecting groups and ammonia treatment to deblock selectively the isobutyryl group (Scheme 26) <89MI 718-08). 

B = adenine (Ade), cytosine (Cyt), guanine (Gua), thymine (Thy), uracil (Ura), or other natural or unnatural nucleobase p = nucleobase protecting group, e.g. benzoyl for Ade and Cyt or isobutyryl for Gua, Thy and Ura are normally left unprotected R = 5 -protecting group, e.g. 4,4 -dimethoxytrityl (DMTr)... 

Nucleoside phosphoramidites or methylphosphonamidites with protecting groups on the bases that are removed faster or milder than the conventional benzoyl and isobutyryl groups have been developed, and several are commercially available. Papers in this area include one on the preparation and use of dialkylformamidine protected dA and dG phosphoramidites, which together with dC yielded oligonucleotides that were completely deprotected by cone, aqueous ammonia in 1 h at 65... 

One other synthesis change was to use 7V-isobutyryl-protected deox-ycytidine, instead of the more commonly used 7V-benzoyl-protecting group. This change is necessary because the improved deprotection conditions described below generate transamination side products with benzoylated cytosine, but not with isobutyryl-protected cytosine (14). The isobutyryl-protected dC monomer and the corresponding isobutyryl-protected dC DNA synthesis support can be obtained from JBL Scientific (San Luis Obispo, CA). 

Synthesis of the oligo(nucleoside O-isopropyl phosphates) required preparation of 5 -DMT-nucleoside (N-protected with standard conventional groups) 3 -0- (0- isopropyl )M iV-diisopropylphosphoramidites. They appeared to be easily incorporable into the growing oligonucleotide chain at preselected position(s), and conditions required for the removal of / -protective groups (N -benzoyl of adenosine, N -ben-zoyl of cytidine, and N -isobutyryl of guanosine), and (9-methyl or 0-2-... 

Circular dichroism (CD) is another interesting example of an optical property of the small Au SR clusters. Since the first observation of Schaaff et al. [23,24], several reports have appeared regarding the CD activities of gold clusters protected by chiral thiols such as penicillamine [25] and A-isobutyryl-cysteine [26]. Figure 11 shows the CD spectra of 1-9, which is a good reproduction of the original report by Whetten s group [23,24]. 

Protection of the 3 -hydroxyl group in stepwise synthesis of oligo(deoxyribonucleotides) has usually involved the acetyl or, sometimes, the isobutyryl group, with removal after each condensation by brief treatment with base (so as not to remove alkali-labile, N-acyl pro-... 

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