Endcaps for Stabilizing Short DNA Duplexes

Ng, Pei-Sze; Pingle, Maneesh; Balasundarum, Ganesan; Friedman, Alan M.; Zu, Xiaolin; Bergstrom, Donald E.

doi:10.1002/chin.200409202

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“…In addition, we prepared the terthiophene spacer 2 , which provided an opportunity to study and compare an exceptionally hydrophobic endcap. Several research groups had reported that hydrophobic, aromatic molecules such as naphthalene diimides 32–34 (3,12,17), N , N -dimethylstilbene dicarboxamide (8), trimethoxystilbenes(18) and stilbene ether (9) stabilized DNA duplexes through stacking interactions with the DNA bases. We expected that endcap 2, with a terthiophene core, would also have significant stacking interactions with the base pairs in a DNA duplex.…”

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confidence: 99%

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

Laing

Balasundarum

et al. 2010

Bioconjugate Chem.

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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.

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