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. End-caps containing amide groups were found to be less stabilizing than the hexaethylene glycol spacer. End-caps containing either a terthiophene or a naphthalene tetracarboxylic acid diimidc were found to be significantly more stabilizing. The former showed a preference for stacking above an A.T base pair. Spacers containing only methylene (-CH2-) 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.
Keywords
DNA HAIRPINS; LINKERS; OLIGONUCLEOTIDES; STABILIZATION; STABILITY; SEQUENCE; DUMBBELL; DUPLEXES; DESIGN; LOOP
Date of this Version
8-2010
Recommended Citation
Ng, Pei-Sze; Laing, Brian; Balasundarum, Ganesan; Pingle, Mancesh; Friedman, Alan; and Bergstrom, Donald E., "Synthesis and Evaluation of New Spacers for Use as dsDNA End-Caps" (2010). Birck and NCN Publications. Paper 625.
https://docs.lib.purdue.edu/nanopub/625