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

Pei-Sze Ng, Purdue University - Main Campus
Brian Laing, Purdue University - Main Campus
Ganesan Balasundarum, Purdue University - Main Campus
Mancesh Pingle, Purdue University - Main Campus
Alan Friedman, Purdue University - Main Campus
Donald E. Bergstrom, Birck Nanotechnology Center and Bindley Bioscience Center, Purdue University

Date of this Version


This document has been peer-reviewed.



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.


Engineering | Nanoscience and Nanotechnology