Oligonucleotide linkers structure

The chemistry of attachment of the leader 3 -nucleoside to an amino-linked support is of importance in oligonucleotide chemistry because it allows efficient release of the oligonucleotide from the support when the synthesis is complete. This section will focus on linker structures that generate unmodified 3 -hydroxyl-containing oligonucleotides as opposed to the wealth of specialty linkers that have been developed to introduce a variety of functional groups (phosphates, thiols, etc.) at the 3 -terminus of the oligonucleotide. 

Silyl-based linkers were investigated to effect a nonbasic fluoride-mediated cleavage of the oligonucleotide from the solid support. The siloxyl, 42 [112,113], or disiloxyl, 43 [114], backbones were grafted on CPG or polystyrene supports. Release of the oligonucleotide was achieved by use of 0.5 M tetrabutylammonium fluoride in THF or DMF. Such conditions render the use of this linker structure less compatible with conventional 2 -0-TBDMS RNA chemistry. 

Specific groups involved in covalent immobilization of biomolecules to the surface are very often introduced into the structure of this molecule, especially in oligonucleotides and carbohydrates. Carboxylic and amino functionalities are the modifications most frequently used, although aldehyde, thiol, and oxyamino are useful alternatives. In some cases coupling molecules (cross-linkers) are necessary to increase the affinity (or reactivity) of the interacting groups. 

Another interesting modification of glass surfaces was introduced by Beier and Hoheisel.23 They synthesized a flexible, dendritic linker system that enables covalent immobilization of oligonucleotides and PNAs with high loading capacity in a controlled manner. This method facilitates the modulation of surface properties such as hydrophobicity and charge. The synthesis of the linker system involves two consecutive reactions an acylation of surface-bound amine groups with acid chloride (4-nitrophenyl-chloroformate or acryloylchloride) and subsequent reaction with an amine. A bis-amine results in a linker system, while a polyamine produces a dendritic structure (Fig. 14.3). Because polyamines possess primary and secondary amine... 

In the oligonucleotide additives used, a monophosphate group is bound to either the 3 - or the 5 -end via a (CH2)i2 linker (Figure 7.3). When these additives are combined with the substrate DNA, gap-structures are formed at a predetermined site in the... 

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