Parallel G-Quadruplexes Formed by Guanine-Rich Microsatellite Repeats Inhibit Human Topoisomerase I

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A. M. Ogloblina¹, V. A. Bannikova², A. N. Khristich², T. S. Oretskaya², M. G. Yakubovskaya¹, and N. G. Dolinnaya^2*

¹Blokhin Russian Cancer Research Center, 115478 Moscow, Russia; fax: (495) 324-1205; E-mail: globbi@mail.ru

²Faculty of Chemistry, Lomonosov Moscow State University, 119991 Moscow; Russia; fax: (495) 939-3181; E-mail: dolinnaya@hotmail.com

^* To whom correspondence should be addressed.

Received December 15, 2014; Revision received February 16, 2015

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Using UV and CD spectroscopy, we studied the thermodynamic stability and folding topology of G-quadruplexes (G₄), formed by G-rich fragments in human microsatellites that differ in the number of guanosines within the repeating unit. The oligonucleotides d(GGGT)₄ and d(GGT)₄ were shown to form propeller-type parallel-stranded intramolecular G-quadruplexes. The G₄ melting temperature is dramatically decreased (by more than 45°C) in the transition from the tri-G-tetrad to the bi-G-tetrad structure. d(GT)_n-repeats do not form perfect G-quadruplexes (one-G-tetrad); folded G₄-like conformation is not stable at room temperature and is not stabilized by monovalent metal ions. The minimum concentration of K⁺ that promotes quadruplex folding of d(GGT)₄ was found to depend on the supporting Na⁺ concentration. It was demonstrated for the first time that the complementary regions flanking G₄-motifs (as in d(CACTGG-CC-(GGGT)₄-TA-CCAGTG)) cannot form a double helix in the case of a parallel G₄ due to the steric remoteness, but instead destabilize the structure. Additionally, we investigated the effect of the described oligonucleotides on the activity of topoisomerase I, one of the key cell enzymes, with a focus on the relationship between the stability of the formed quadruplexes and the inhibition degree of the enzyme. The most active inhibitor with IC₅₀ = 0.08 µM was the oligonucleotide d(CACTGG-CC-(GGGT)₄-TA-CCAGTG), whose flanking G₄-motif sequences reduced the extreme stability of G-quadruplex formed by d(GGGT)₄.

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KEY WORDS: G-quadruplexes, microsatellite repeats, stability and structure of G-quadruplexes, topoisomerase I inhibitors

DOI: 10.1134/S0006297915080088

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