2-Aminopurine/cytosine base pair containing oligonucleotides: Fluorescence spectroscopy studies on DNA-polyamide binding

Abstract

Studies on the binding of a triamide f-IPI (1) to its cognate sequence labeled with a 2-aminopurine (2AP or G*) group are described. ITC studies showed that f-IPI (1) bound to the cognate site (ACG*CGT) with only 3.5-fold lower affinity than binding to the unlabeled DNA (ACGCGT) (Keq = 2 × 107 and 7 × 107 M-1, respectively). Titration of f-IPI (1) to both sequences gave strong induced bands at 330 nm via circular dichroism studies. The compound also gave comparable ΔTm values of 5.0 and 7.8 °C, respectively. These techniques also proved that the sequence selectivity of f-IPI (1) was uncompromised, as only limited binding to the non-cognate sequence ACCG*GT was observed. Fluorescence studies demonstrated a 2:1 ligand:DNA binding motif as anticipated, and indicated that the limit of detection for this technique was 20 μM DNA concentration. The results demonstrate that 2-aminopurine is a sufficient substitute for guanine in a G·C base pair useful in DNA binding studies. © 2008 Elsevier Inc. All rights reserved.