Synthesis of Endcap Dimethoxytrityl Phosphoramidites for Endcapped Oligonucleotides

Abstract

Endcaps may be either aromatic or aliphatic molecules that specifically cross-link the 5' end of one strand with the 3' end of the complementary strand in a DNA duplex. Endcaps may be viewed as a replacement of the loop region nucleotides of a DNA hairpin, with the added advantage of increased thermal stability. An endcap is incorporated into the sequence during oligonucleotide synthesis. Three endcaps are described in this unit. The naphthalene diimide endcap prefers to base stack with GC base pairs. The terthiophene endcap has higher lipophilicity than the naphthalene diimide endcap and provides higher stability when stacked over an AT base pair. The 2,2'-oxydiacetamide endcap provides lower enhancement in stability but a more rigid and well-defined structure than the oligo(ethylene glycol) endcaps. Synthesis of endcapped oligonucleotides can be carried out using standard automated synthesis protocols with only minor modifications.

Synthesis and Evaluation of New Spacers for Use as dsDNA End-Caps

“…Diols 8 and 14 were obtained by reaction of the O-t -butyldimethylsilyl ethers of ethanolamine and propanolamine with diglcolyl chloride, followed by removal of the silyl protecting group with ethanolic HCl. Details for the synthesis of diol 14 have been reported (10). Diols 18 and 22 were obtained more directly by the reaction of either γ-butyrolactone or δ-valerolactone with 1,3-propanediamine.…”

“…Deprotection by catalytic hydrogenation with Pd/C catalyst gives diol 29 in good yield. The synthesis of diols 32 – 34 followed the procedure described by Pingle et al (10) Each diol is symmetrical and could be synthesized as a mono-DMTr derivative by reaction with one equivalent of DMTr chloride. Yields are generally in the 35–50% range, which although low, was not limiting because of the ease with which one can produce large amounts of the diols.…”

Protein-DNA footprinting by endcapped duplex oligodeoxyribonucleotides

“…However, in conjunction with studies to develop amide-containing endcaps for use in the DNA-protein complex crystallization studies we have adopted a simple hydrophilic amide containing endcap for the present study. The chemical synthesis of this endcap has been reported (16).…”

Evaluation of End-Capped DNA Modules for pRNA Capture and Functionalization

“…Bergstrom and coworkers have utilized a method for stabilizing short segments of double-stranded oligonucleotides by covalently linking the 3′ and 5′ ends of the nucleic acid with a simple spacer. 13–15 The simplest spacer is the C12 hydrocarbon ( S2 ) shown in Figure 1D. Nucleic acid duplexes containing just four base pairs and linked by a spacer at one end have melting temperatures ( T m values) in the range 41 to 62 °C (the same duplexes without the spacers are unstable at room temperature, i.e.…”

“…This observation is supported by previous work conducted in the Bergstrom lab on the evaluation of spacers for use as dsDNA endcaps. 13–15 The endcapped duplex stem in the capture modules confers high affinity and specificity for hybridization to overhanging sequences at the termini of pRNA over hybridization to the same sequence within the RNA. This specificity is due to the ‘pre-organization’ of the duplex stem region by the endcap.…”