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

Abstract

A series of aliphatic and aromatic spacer molecules designed to cap the ends of DNA duplexes have been synthesized. The spacers were converted into dimethoxytrityl protected phosphoramidites as synthons for oligonucleotides synthesis. The effect of the spacers on the stability of short DNA duplexes was assessed by melting temperature studies. Endcaps containing amide groups were found to be less stabilizing than the hexaethylene glycol spacer. Endcaps containing either a terthiophene or a naphthalene tetracarboxylic acid dimide were found to be significantly more stabilizing. The former showed a preference for stacking above an A•T base pair. Spacers containing only methylene (-CH 2 -) and amide (-CONH-) groups interact weakly with DNA and consequently may be optimal for applications that require minimal influence on DNA structure but require a way to hold the ends of double-stranded DNA together.

Hydrophobic Organic Linkers in the Self-Assembly of Small Molecule-DNA Hybrid Dimers: A Computational–Experimental Study of the Role of Linkage Direction in Product Distributions and Stabilities

“… 42 , 43 In a related study, Bergstrom and co-workers end-capped small DNA hairpins with rigid, hydrophobic organic molecules to afford enhanced stability. 44 Moreover, perylenedimide (PDI)-DNA hybrids have been found to form stable hairpin dimers 45 and larger supramolecular oligomers due to the hydrophobicity of the PDI cores, which leads to PDI–PDI stacking via π–π interactions. 2 , 4 …”

Cationic modified nucleic acids for use in DNA hairpins and parallel triplexes

“…The optimal linkages should comprise amines prone to protonation at relative high pH and with a terminal oxygen distance close to the optimal 16-17 A ˚between the 3¢-and 5¢-phosphate-oxygen of the B-type DNA duplex. 13 We designed two simple modified nucleic acids, X and Y (Fig. 1), with a maximal terminal oxygen distance of ~14.5 A ˚to ~19.5 A ˚, respectively.…”

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

“…13 Spacer S2 , when used as the endcap in DNA capture module 7 resulted in a T m value of 67.2 °C for the melting of the 5 bp duplex stem (Table 1), a value slightly higher than spacer S1 . The first dissociation event when hybridized to RNA7 was determined to be 47.4 °C ((Table 2, exp 5 and supplementary Figure S5)).…”

“…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.…”