title: 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 diimide 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.
authors: Department of Medicinal Chemistry and Molecular Pharmacology, Department of Biological Sciences, and Bindley Bioscience Center, Purdue University, 1205 W State St., West Lafayette, IN 47907, USA.
authors: Pei-Sze
authors: PS
authors: Ng
authors: Brian M
authors: BM
authors: Laing
authors: Ganesan
authors: G
authors: Balasundarum
authors: Maneesh
authors: M
authors: Pingle
authors: Alan
authors: A
authors: Friedman
authors: Donald E
authors: DE
authors: Bergstrom
mesh_terms: D000577:Amides / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D005026:Ethylene Glycols / Q000737:chemistry*; D009841:Oligonucleotides / Q000138:chemical synthesis* / Q000737:chemistry; D009943:Organophosphorus Compounds / Q000737:chemistry*; D013876:Thiophenes / Q000737:chemistry*; D044366:Transition Temperature
chemical_list: D000577:Amides; D005026:Ethylene Glycols; D009841:Oligonucleotides; D009943:Organophosphorus Compounds; D013876:Thiophenes; C434331:phosphoramidite; C019101:alpha-terthienyl; C077067:hexaethylene glycol; D004247:DNA