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

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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 × 107and 7 × 107M-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 ΔTmvalues 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.

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Sielaff, A., Mackay, H., Brown, T., & Lee, M. (2008). 2-Aminopurine/cytosine base pair containing oligonucleotides: Fluorescence spectroscopy studies on DNA-polyamide binding. Biochemical and Biophysical Research Communications, 369(2), 630–634. https://doi.org/10.1016/j.bbrc.2008.02.049

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