Nucleobase protecting group

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)... 

J. Deprotection step Specific reagents for the deprotection of certain phosphate-protecting groups may be necessary (see Tables 1 and 2 and references therein). Otherwise, concentrated ammonium hydroxide may be used at ambient temperature or at 55 C for 1-16 h, depending on the sensitivity of the nucleobases and nucleobase-protecting groups to alkaline conditions. 

PNA oligomers have been synthesized by either Boc[31"33] or Fmoc134 methods on polymer beads. The Fmoc method has also been used in array synthesis of PNAsJ8,35 The synthesis of PNA/DNA chimera requires base-labile protection groups on the PNA nucleobases and will not be discussed herein.b-3S 3Sl... 

The Fmoc synthesis of PNAs was introduced by Thompson et al.[34] and has further largely been developed by Nielsen and EgholmA The synthesis was performed on a DNA synthesizer. The four monomers are shown in Scheme 11. The nucleobases are protected with the benzhydryl-oxycarbonyl (Bhoc) group. This protecting group is cleaved with TFA in less than a minute. 

The nucleophilicity of the N-7 atom of guanosine, and some of its O - and N -substituted derivatives, has been studied by following the N chemical shifts of the protonated species.The effect of protecting groups of the nucleobases during... 

The synthesis of a range of thiono triester modified oligonucleotides has been reported using reagents (ISSa-e). The syntheses employed very base labile tert-butylphenoxyacetyl protecting groups for the exocyclic amino functions of the nucleobases which requires only a two hour treatment with ammonia at room temperature for deprotection. 

Synthesis of standard ODN building blocks proceeds from the nucleosides and comprises the following steps protection of nucleobases, protection of the 5 -hydroxy group and attachment of the phosphoramidite moiety. A comprehensive review on protective groups for use in oligonucleotide synthesis is given in [34]. 

Figure 3. Protective group strategy in DNA-synthesis by the standard phosphoramidite method on solid support. I Protected 5 -hydroxy group by the DMT (dimethoxytrityl) group, 3 -cyanoethyl-phosphora-midite II, III, IV Protection of nucleobases V Thymine remains unprotected.

On the one hand, alternative basic deprotection cocktails were developed using various combinations of hydrazine, ethanolamine, and alcohol [146] or incorporating the use of more nucleophilic alkylamines [7,16]. The latter method favors 40% aqueous methylamine in place of or in addition to 30% ammonium hydroxide, which cleaves the acyl protecting groups present on the nucleobases in a few minutes at 65°C or in over 1 h at room temperature. 

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