Substituent effects on indole universal bases in DNA

Abstract

A series of eleven 5-substituted-indole nucleoside residues were synthesized and incorporated into 15-mer oligodeoxynucleotide duplexes with each of the four natural bases (A, G, C, T) paired with the non-natural residues. The universal base properties of these residues were evaluated by comparing the stabilities of these complexes determined by UV thermal denaturation experiments. All of the substituted indoles were more stable than an unsubstituted indole residue, and measures of electronic influences of substituents on the indole pi system correlate with stability. Several residues were more promiscuous than the previously studied 5-nitroindole residue, but the relationship between substituents and selectivity is not clear.

Keywords:

• Indole 2′-deoxynucleosides
• universal bases
• duplex stabilities
• substituent effects

Disclosure statement

The authors report there are no competing interests to declare.

Additional information

Funding

The authors acknowledge the University of Alabama for support of this research. We also acknowledge funding from the NSF Major Instrumentation Program (NSF CHE-1726812) for the purchase of the RapifleX MALDI/TOF-TOF mass spectrometer.