Direct Quantification of Loop Interaction and π–π Stacking for G‑Quadruplex Stability at the Submolecular Level

• Published in: Journal of the American Chemical Society Vol. 136; no. 44; pp. 15537 - 15544
• Main Authors: Ghimire, Chiran, Park, Soyoung, Iida, Keisuke, Yangyuoru, Philip, Otomo, Haruka, Yu, Zhongbo, Nagasawa, Kazuo, Sugiyama, Hiroshi, Mao, Hanbin
• Format: Journal Article
• Language: English
• Published: WASHINGTON American Chemical Society 05.11.2014; Amer Chemical Soc
• Subjects: Chemistry; Chemistry, Multidisciplinary; Circular Dichroism; G-Quadruplexes; Physical Sciences; Science & Technology; Surface Plasmon Resonance; TELOMERIC G-QUADRUPLEX; CLICK CHEMISTRY; DNA; TELOMESTATIN; INHIBITOR; MOLECULES; LONG
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/ja503585h

The well-demonstrated biological functions of DNA G-quadruplex inside cells call for small molecules that can modulate these activities by interacting with G-quadruplexes. However, the paucity of the understanding of the G-quadruplex stability contributed from submolecular elements, such as loops and tetraguanine (G) planes (or G-quartets), has hindered the development of small-molecule binders. Assisted by click chemistry, herein, we attached pulling handles via two modified guanines in each of the three G-quartets in human telomeric G-quadruplex. Mechanical unfolding using these handles revealed that the loop interaction contributed more to the G-quadruplex stability than the stacking of G-quartets. This result was further confirmed by the binding of stacking ligands, such as telomestatin derivatives, which led to similar mechanical stability for all three G-quartets by significant reduction of loop interactions for the top and bottom G-quartets. The direct comparison of loop interaction and G-quartet stacking in G-quadruplex provides unprecedented insights for the design of more efficient G-quadruplex-interacting molecules. Compared to traditional experiments, in which mutations are employed to elucidate the roles of specific residues in a biological molecule, our submolecular dissection offers a complementary approach to evaluate individual domains inside a molecule with fewer disturbances to the native structure.