DNA Interaction of Methylene Green and Fast Green with dsDNA and ssDNA and G-quadruplex DNA

Didem Duman; Efkan Bağda; Esra Bağda

doi:10.17776/csj.1830319

DNA Interaction of Methylene Green and Fast Green with dsDNA and ssDNA and G-quadruplex DNA

Abstract

DNA plays an active role in cellular processes not only through the transport of genetic information through its base sequence but also through the secondary structures revealed by folding. In recent years, investigating the interaction of DNA-targeting ligands has emerged as an important area of research, especially considering the importance of these structures in processes such as cancer. The current study investigated the interaction of MG and FG ligands with DNA. The main motivation for the study was to investigate whether these structures, known to interact with DNA, have a specific affinity for ctDNA, ssDNA, and G-quadruplex DNA. The interaction of FG with DNA species did not cause any significant spectral changes, thus concluding that the affinity was very low. Competitive dialysis experiments confirmed the affinity results. Significant spectral changes were observed in the MG-DNA interaction. The interaction of MG with DNA species caused a hypochromic effect of up to 52%, while a bathochromic shift of up to 17 nm was observed. K_b values calculated from the data were also found to be higher than 10⁶ M^-1. The interaction stoichiometry with G-quadruplex DNAs was determined to be 1:2, indicating an end-stacking mechanism. Competitive dialysis experiments also confirmed that MG exhibited high affinity for DNA species.

Keywords

References

[1] Shapiro, J. A. (2006). Genome informatics: The role of DNA in cellular computations. Biological Theory, 1(3), 288–301. https://doi.org/10.1162/biot.2006.1.3.288
[2] Travers, A., & Muskhelishvili, G. (2025). DNA structure and function. The FEBS Journal, 282(12), 2279–2295. https://doi.org/10.1111/febs.13307
[3] Wang, G., & Vasquez, K. (2017). Effects of replication and transcription on DNA structure-related genetic instability. Genes, 8(1), 17. https://doi.org/10.3390/genes8010017
[4] Doluca, O., Withers, J. M., & Filichev, V. V. (2013). Molecular engineering of guanine-rich sequences: Z-DNA, DNA triplexes, and G-quadruplexes. Chemical Reviews, 113(5), 3044–3083. https://doi.org/10.1021/cr300225q
[5] Chen, L., Dickerhoff, J., Sakai, S., & Yang, D. (2022). DNA G-quadruplex in human telomeres and oncogene promoters: Structures, functions, and small molecule targeting. Accounts of Chemical Research, 55(18), 2628–2646. https://doi.org/10.1021/acs.accounts.2c00337
[6] Haider, S. M., Neidle, S., & Parkinson, G. N. (2011). A structural analysis of G-quadruplex/ligand interactions. Biochimie, 93(8), 1239–1251. https://doi.org/10.1016/j.biochi.2011.05.012
[7] Bhattacharyya, D., Mirihana Arachchilage, G., & Basu, S. (2016). Metal cations in G-quadruplex folding and stability. Frontiers in Chemistry, 4, 38. https://doi.org/10.3389/fchem.2016.00038
[8] Hänsel-Hertsch, R., Di Antonio, M., & Balasubramanian, S. (2017). DNA G-quadruplexes in the human genome: Detection, functions and therapeutic potential. Nature Reviews Molecular Cell Biology, 18(5), 279–284. https://doi.org/10.1038/nrm.2017.3

[9] Sheng, J., Gan, J., & Huang, Z. (2013). Structure-based DNA-targeting strategies with small molecule ligands for drug discovery: Targeting DNAs via structural investigations. Medicinal Research Reviews, 33(5), 1119–1173. https://doi.org/10.1002/med.21278
[10] McGown, L. B., Joseph, M. J., Pitner, J. B., Vonk, G. P., & Linn, C. P. (1995). The nucleic acid ligand: A new tool for molecular recognition. Analytical Chemistry, 67(21), 663A–668A. https://doi.org/10.1021/acs.accounts.2c00337
[11] Breaker, R. R. (2004). Natural and engineered nucleic acids as tools to explore biology. Nature, 432(7019), 838–845. https://doi.org/10.1038/nature03195
[12] Asamitsu, S., Bando, T., & Sugiyama, H. (2019). Ligand design to acquire specificity to intended G-quadruplex structures. Chemistry – A European Journal, 25(2), 417–430. https://doi.org/10.1002/chem.201802691
[13] Kostjukov, V. V. (2021). Photoexcitation of methylene green dye in aqueous solution: TD-DFT study. Chemical Physics Letters, 785, 139152. https://doi.org/10.1016/j.cplett.2021.139152
[14] Glusko, C. A., Previtali, C. M., Vera, D. M. A., Chesta, C. A., & Montejano, H. A. (2011). An experimental and theoretical study on the photophysical properties of methylene green. Dyes and Pigments, 90(1), 28–35. https://doi.org/10.1016/j.dyepig.2010.11.003
[15] Al-Harbi, F. F., Darwish, A. A. A., Al-Ghamdi, S. A., Khasim, S., El-Shazly, E. A. A., El-Rahman, K. F. A., & Hamdalla, T. A. (2022). Impedance spectroscopy, electronic transport, and dielectric relaxation studies in methylene green organic semiconductor for photovoltaic application. Physica Scripta, 97(8), 085810. https://doi.org/10.1088/1402-4896/ac7d15
[16] Tchaikovskaya, O., Chaidonova, V., Bocharnikova, E., Telminov, E., Dmitrieva, N., & Ezhov, D. (2023). Solvent effect on the spectra of methylene green and methylene blue. Journal of Fluorescence, 33(2), 685–695. https://doi.org/10.1007/s10895-022-03074-2
[17] Mittal, A., Kaur, D., & Mittal, J. (2009). Batch and bulk removal of a triarylmethane dye, Fast Green FCF, from wastewater by adsorption over waste materials. Journal of Hazardous Materials, 163(2–3), 568–577. https://doi.org/10.1016/j.jhazmat.2008.07.005
[18] Sürme, Y., & Kahve Yıldırım, G. (2025). Ultrasound-assisted d-SPE of Fast Green FCF on chitin bio-adsorbent prior to spectrophotometric determination. Eurasian Journal of Science, Engineering and Technology, 6(2), 89–94. https://doi.org/10.55696/ejset.1732523
[19] Xu, F., Yang, J., Lu, F., Liu, R., Zheng, J., Zhang, J., ... & Chen, J. (2018). Fast Green FCF alleviates pain hypersensitivity and down-regulates the levels of spinal P2X4 expression and pro-inflammatory cytokines in a rodent inflammatory pain model. Frontiers in Pharmacology, 9, 534. https://doi.org/10.3389/fphar.2018.00534
[20] Bağda, E. (2024). Insights into the G-quadruplex DNA interaction landscape: Comparative analysis of anionic Zn(II) and Co(II) phthalocyanine-tetrasulfonate complexes. Journal of Molecular Recognition, 37(3), e3082. https://doi.org/10.1002/jmr.3082
[21] Yaku, H., Murashima, T., Miyoshi, D., & Sugimoto, N. (2012). Specific binding of anionic porphyrin and phthalocyanine to the G-quadruplex with a variety of in vitro and in vivo applications. Molecules, 17(9), 10586–10613. https://doi.org/10.3390/molecules170910586
[22] Murat, P., Singh, Y., & Defrancq, E. (2011). Methods for investigating G-quadruplex DNA/ligand interactions. Chemical Society Reviews, 40(11), 5293–5307. https://doi.org/10.1039/c1cs15102a
[23] Bossi, A., Rausch, A. F., Leitl, M. J., Czerwieniec, R., Whited, M. T., Djurovich, P. I., Yersin, H., & Thompson, M. E. (2013). Photophysical properties of cyclometalated Pt(II) complexes: Counterintuitive blue shift in emission with an expanded ligand π system. Inorganic Chemistry, 52(21), 12403–12415. https://doi.org/10.1021/ic401134w
[24] Caricato, M., Coluccini, C., Vander Griend, D. A., Forni, A., & Pasini, D. (2013). From red to blue shift: Switching the binding affinity from the acceptor to the donor end by increasing the π-bridge in push–pull chromophores with coordinative ends. New Journal of Chemistry, 37(9), 2792–2801. https://doi.org/10.1039/c3nj00346b
[25] Wei, C., Jia, G., Zhou, J., Han, G., & Li, C. (2009). Evidence for the binding mode of porphyrins to G-quadruplex DNA. Physical Chemistry Chemical Physics, 11(20), 4025–4032. https://doi.org/10.1039/b818041c
[26] Pradeep, T. P., & Barthwal, R. (2016). A 4:1 stoichiometric binding and stabilization of mitoxantrone-parallel stranded G-quadruplex complex established by spectroscopy techniques. Journal of Photochemistry and Photobiology B: Biology, 162, 106–114. https://doi.org/10.1016/j.jphotobiol.2016.06.027
[27] Santos, T., Salgado, G. F., Cabrita, E. J., & Cruz, C. (2021). G-quadruplexes and their ligands: Biophysical methods to unravel G-quadruplex/ligand interactions. Pharmaceuticals, 14(8), 769. https://doi.org/10.3390/ph14080769
[28] Wei, C., Jia, G., Yuan, J., Feng, Z., & Li, C. (2006). A spectroscopic study on the interactions of porphyrin with G-quadruplex DNAs. Biochemistry, 45(21), 6681–6691. https://doi.org/10.1021/bi060155v
[29] Zhang, S., Wu, Y., & Zhang, W. (2014). G-quadruplex structures and their interaction diversity with ligands. ChemMedChem, 9(5), 899–911. https://doi.org/10.1002/cmdc.201300566

Details

Primary Language

English

Subjects

Pharmaceutical Analytical Chemistry

Journal Section

Research Article

Authors

Didem Duman
0000-0002-0900-0336
Türkiye

Efkan Bağda
0000-0002-3925-3430
Türkiye

Esra Bağda ^*
0000-0003-1900-4944
Türkiye

Publication Date

February 27, 2026

Submission Date

November 25, 2025

Acceptance Date

January 5, 2026

Published in Issue

Year 2026 Volume: 47 Number: 1

DOI

https://doi.org/10.17776/csj.1830319

IZ

https://izlik.org/JA83FL22HG

Cite

RIS / Bibtex

APA

Duman, D., Bağda, E., & Bağda, E. (2026). DNA Interaction of Methylene Green and Fast Green with dsDNA and ssDNA and G-quadruplex DNA. Cumhuriyet Science Journal, 47(1), 96-102. https://doi.org/10.17776/csj.1830319