Collect. Czech. Chem. Commun. 2006, 71, 899-911

Effect of a Hydrogen Bonding Carboxamide Group on Universal Bases

Kathleen Too, Daniel M. Brown, Philipp Holliger and David Loakes*

Medical Research Council, Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK


A number of aromatic universal base analogues have been described in the literature, but most are non-hydrogen bonding. We have examined the effect of introducing hydrogen bonding carboxamide groups onto the pyrrole ring of 5-nitroindole. The modified analogues retain universal base features, but there are no overall effects on duplex stability. This leads to the suggestion that the nitro group is within the hydrogen bonding face of the duplex, and the hydrogen bonding carboxamide group is in the duplex major groove.

Keywords: Nucleosides; Universal nucleobases; 5-Nitroindole; Indoles; Hydrogen bonding; Stacking energies; Duplex stability; Oligonucleotides; DNA duplexes.

References: 14 live references.