DNA G-Quadruplexes: Special Secondary Structures with Surprising Anticancer Implications

Reading time: 5 minutes

Jessica Desamero

From the start, our mission here at OncoBites has been to share the complicated nature of cancer with our readers and to shed light on breakthroughs in understanding and treating the disease. One of our biggest messages has been that “cancer” is really a family of different but related diseases, and it’s unlikely that there will be one unifying cure. However, one of the ways in which all cancers are similar is that cancer cells grow and spread rapidly, no matter what tissue or organ they come from. This knowledge is what first gave us chemotherapy, as many cancer drugs target the DNA of rapidly growing cells. 

In cells, DNA is packaged into thread-like structures called chromosomes. At the ends of these chromosomes are sections of DNA called telomeres, which cap the chromosomes, protecting them from sticking to each other and from deteriorating. As cells divide, the telomeres gradually become shorter. Once they become too short, they signal the cells to stop dividing, and these cells eventually die. However, 80-85% of cancer cells have a way of making themselves effectively immortal by reactivating a normally inactive enzyme called telomerase that lengthens their telomeres, thereby extending their lives. Stopping cancer cells from keeping themselves alive indefinitely is therefore a huge area of research, and one promising direction is by modifying telomeres so that telomerase won’t be able to bind and repair them. And one way to do that is to stabilize the DNA secondary structures found at the ends of telomeres called G-quadruplexes

DNA is basically two organized strings of nucleotides known as adenine (A), cytosine (C), guanine (G), and thymidine (T) form a ladder-like arrangement that then twists around itself into a helix. In regions of the DNA that have a lot of guanine, however, an alternative secondary structure can be seen. Four G’s interact with each other and join together through hydrogen bonds to form tetrads, and these tetrads then stack on top of each other, forming G-quadruplex structures (see Figure 1). Human telomeres consist of repeating TTAGGG sequences and consequently have a very high potential to form quadruplexes. At the telomeres, quadruplexes would block the telomerase enzyme from being able to bind to the telomeres, thereby inhibiting its activity and ultimately stopping cancer cells from multiplying further. Additionally, cancer-associated genes (oncogenes) are often controlled by sections of DNA called promoters that are also rich in G and therefore likely to form G-quadruplexes. Oncogenes tend to be overexpressed in cancer cells, but quadruplexes in oncogene promoters would help repress the transcription of these oncogenes, thereby blocking their expression. Quadruplexes can play important roles in enzyme and gene regulation, and stabilizing the structure of quadruplexes can further reinforce these two biological activities. 

Figure 1: Structure of a G-tetrad (left) and a G-quadruplex (right).

Because of the anticancer implications of these quadruplexes, numerous studies have been done to design small molecules that can interact with these quadruplexes and help stabilize them. Small molecules that bind strongly to quadruplexes are called G-quadruplex ligands. A wide variety of quadruplex ligands, each with their own unique properties, exist, but in order for these ligands to be efficient, they all need to satisfy certain requirements. First, ligands should be highly selective for quadruplexes. This means that they would highly prefer to bind to quadruplexes rather than to any other nucleic acid structure. They should also greatly influence cells and induce death in cancer cells via a quadruplex-related biological event, such as inhibiting telomerase activity. Moreover, they should remain stable under physiological conditions

Natural alkaloids are one class of chemical compounds that have potential as G-quadruplex ligands. Natural alkaloids are a diverse class of organic compounds found in nature, and most contain nitrogen atoms. These compounds have significant biological activities, and some alkaloids even exhibit anticancer properties. In China, a research team led by Dr. Shuo-Bin Chen has investigated various quadruplex-targeting natural alkaloids. The objective of their studies was to modify the structures of natural alkaloids in the hopes of improving how well alkaloids interact with their targets. Modified structures of these alkaloids are called their derivatives.  

Figure 2: Structure of quindoline

Quindoline derivatives are one of the many sets of alkaloid derivatives studied. Quindoline is a naturally occurring alkaloid with anti-inflammatory activities (see Figure 2). A derivative of this compound was previously found to bind to quadruplexes at the human telomeres and inhibit telomerase activity. Chen et al. then synthesized additional derivatives of quindoline by attaching different side chains to position 11. In one synthesized derivative, named SYUIQ-5, a group containing nitrogen and carbon atoms was added. This ligand was promising in that it improved the inhibition of telomerase activity, stopped cell growth, and halted cell division in human leukemia and colon cancer cell lines. Additionally, SYUIQ-5 was found to interact with quadruplexes at the promoter of the c-Myc proto-oncogene and consequently inhibited the expression of this gene. This is important since c-Myc is often overexpressed in malignant tumors. Studies with other quindoline derivatives and with derivatives of other natural alkaloids allowed them to explore more combinations of side chain modifications and their effects on stable quadruplex stacking and ligand binding interactions both in solution and in cells. 

Many factors and challenges come into play when designing small molecules specifically for quadruplex stabilization. For example, some ligands could be very quadruplex-selective and could effectively stabilize these structures in test tube solution, but this ability for stabilization could possibly be compromised once they are put into cells. Or it could be that ligands have good biological effects but have low quadruplex selectivity, lowering their overall efficiency. Some ligands can also be toxic when administered in higher doses. Moreover, the quadruplex structure alone is already complex, as it can exist in different forms depending on the conditions of the solution it is found in. But as more studies are done and as these factors are explored more extensively, we will be one step closer to successfully developing these ligands as effective anticancer agents. 


Alkaloid. (2015). Retrieved from https://www.sciencedirect.com/topics/chemistry/alkaloid

Che, T., Wang, Y., Huang, Z., Tan, J., Huang, Z., & Chen, S. (2018). Natural Alkaloids and Heterocycles as G-Quadruplex Ligands and Potential Anticancer Agents. Molecules, 23(2), 493. doi:10.3390/molecules23020493

Ilyinsky, N. S., Varizhuk, A. M., Beniaminov, A. D., Puzanov, M. A., Shchyolkina, A. K., & Kaluzhny, D. N. (2014). G-quadruplex ligands: Mechanisms of anticancer action and target binding. Molecular Biology, 48(6), 778-794. doi:10.1134/s0026893314060077

Rhodes, D., & Lipps, H. J. (2015). G-quadruplexes and their regulatory roles in biology. Nucleic Acids Research, 43(18), 8627-8637. doi:10.1093/nar/gkv862

Sun, Z.-Y., Wang, X.-N., Cheng, S.-Q., Su, X.-X., & Ou, T.-M. (2019). Developing Novel G-Quadruplex Ligands: from Interaction with Nucleic Acids to Interfering with Nucleic Acid–Protein Interaction. Molecules, 24(3), 396. doi: 10.3390/molecules24030396

Image citations:

Telomere Quadruple


Quindolina numerada

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