Protection, blocking, masking groups

Fig. 1. Light-directed synthesis of polynucleotide probe arrays. Exposure to light through a photolithographic mask is used to remove protecting groups from surface sites in pre-defined regions of a functionalized glass substrate. A solution of an activated polynucleotide building block is then applied, which reacts specifically in the exposed regions of the substrate. Repeated cycles of illumination-deprotection and monomer coupling are used to construct a two-dimensional array of probe sequences...

The masked disilene procednre was nsed by Saknrai and co-workers to synthesize two samples of diblock copolymers of 1,1-dimethyl-2,2-dihexylsilane (MHS) and 2-(trimethylsilyloxy)ethyl methacrylate, which differed only in the relative lengths of their blocks. Hydrolysis of the trimethylsilyl protecting groups gave the corresponding amphiphilic diblock copolymers, poly(l,l-dimethyl-2,2-dihexyldisilene)-fe-poly(2-hydroxyethyl methacrylate) (PMH S-fc-PHEMA), depicted in Pig. 22 [48]. 

Amino protecting groups fall into four broad categories nitrobenzyl (e.g., nitrobenzyloxy-carbonyl and 4,5-dimethoxy-2-nitrobenzyloxycarbonyl), phenacyl (e.g., 4-methoxyphen-acyloxycarbonyl), benzyloxycarbonyl (e.g., a,a-dimethyl-3,5-dimethoxybenzyloxycarbonyl), and arylsulfonamides (e.g., tosyl). All but the sulfonamides mask the amino group as a carbamate. Removal of the blocking moiety releases an unstable carbamic acid, which spontaneously decarboxylates to give the unprotected amine. 

In nucleotide chemistry amide-type protecting functions have proven to be very useful and are widely used. The amino group in guanine is usually blocked as the isobutyramide (20), adenine is masked as the... 

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