Assaying the binding strength of G-quadruplex ligands using single-molecule TPM experiments
| Autor: | Hung-Chih Fang, Shih-Wei Liu, Hung-Wen Li, Jen-Fei Chu, Ta-Chau Chang, Cheng-Ting Tsai |
|---|---|
| Rok vydání: | 2012 |
| Předmět: |
Porphyrins
Hoogsteen base pair Kinetics Biophysics Carbazoles Drug Evaluation Preclinical DNA Single-Stranded Pyridinium Compounds G-quadruplex Ligands Biochemistry chemistry.chemical_compound Reaction rate constant Molecule Humans Molecular Biology Chemistry Cell Biology Carbocyanines Telomere Folding (chemistry) G-Quadruplexes Crystallography Tethered particle motion Nucleic Acid Conformation DNA Copper |
| Zdroj: | Analytical biochemistry. 436(2) |
| ISSN: | 1096-0309 |
| Popis: | G-quadruplexes are stable secondary structures formed by Hoogsteen base pairing of guanine-rich single-stranded DNA sequences in the presence of monovalent cations (Na(+) or K(+)). Folded G-quadruplex (G4) structures in human telomeres have been proposed as a potential target for cancer therapy. In this study, we used single-molecule tethered particle motion (TPM) experiments to assay the binding strength of possible G4 ligands. We found that individual single-stranded DNA molecules containing the human telomeric sequence d[AGGG(TTAGGG)3] fluctuated between the folded and the unfolded states in a 10 mM Na(+) solution at 37 °C. The durations of folded and unfolded states were single-exponentially distributed, and in return the folding and unfolding rate constants were 1.68 ± 0.01 and 1.63 ± 0.03 (s(-1)), respectively. In the presence of G4 ligands, such as TMPyP4, DODCI, BMVC, and BMVPA, the unfolding rate constant decreased appreciably. In addition, combining the Cu(2+)-induced G4 unfolding and TPM assay, we showed that BMVC and TMPyP4 are better G4 stabilizers than DODCI. The capability of monitoring the fluctuation between the folded and the unfolded state of G4 DNA in real time allows the determination of both kinetic and thermodynamic parameters in a single measurement and offers a simple way to assay binding strength under various conditions. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|
Full Text from ScienceDirect