Synthesis and g-quadruplex-binding properties of defined acridine oligomers

Abstract

The synthesis of oligomers containing two or three acridine units linked through 2-aminoethylglycine using solid-phase methodology is described. Subsequent studies on cell viability showed that these compounds are not cytotoxic. Binding to several DNA structures was studied by competitive dialysis, which showed a clear affinity for DNA sequences that form G-quadruplexes and parallel triplexes. The fluorescence spectra of acridine oligomers were affected strongly upon binding to DNA. These spectral changes were used to calculate the binding constants (K). Log K were found to be in the order of 4-6.

Figure 1

Structure of the acridine derivatives prepared.

Figure 2

Solid-phase synthesis of dimer and trimer acridine derivatives. (a) (i) Fmoc-Sar-OH, PyBOP, DIEA; (ii) 20% piperidine, DMF; (iii) Boc–NH–(CH₂)₆–OCH₂CH₂COOH, PyBOP, DIEA; (b) (i) 40% TFA, DCM; (ii) Fmoc-Aeg(Boc)-OH, PyBOP, DIEA; (iii) Repeat steps (i) and (ii) n times; (c) (i) 40% TFA, DCM; (ii) Ac₂O, DIEA, DMF; (d) (i) 20% piperidine, DMF; (ii) Fmoc-Gly-OH, PyBOP, DIEA; (e) (i) 20% piperidine, DMF; (ii) acridine-9-carboxylic acid, PyBOP, DIEA; (f) anhydrous HF (0°); (g) 32% aqueous NH₃.

Figure 3

Results obtained by the competitive dialysis assay. The amount of ligand bound to each DNA structure is shown as a bar graph. The fluorescence of each sample was measured using an excitation wavelength of 252 nm and an emission wavelength of 435 nm, respectively.

Figure 4

Fluorescence titration spectra. Fluorescence spectra of a 0.2 μM solution of the acridine derivative after the addition of increasing amounts of oligonucleotide (from 0 to 10 μM) in potassium phosphate buffer. Excitation wavelength is 252 nm.