Comparative Analysis of 1,9-Dimethyl-Methylene Blue and Toluidine Blue Interactions with ct-DNA, G-Quadruplex DNA, and ssDNA
DOI:
https://doi.org/10.24925/turjaf.v12i4.601-607.6704Anahtar Kelimeler:
1,9-Dimethyl-Methylene Blue- Toluidine Blue- c-MYC- ct-DNA- ssDNAÖzet
This study presents a comprehensive investigation into the interactions of two distinct synthetic dyes—1,9-Dimethyl-Methylene Blue and Toluidine Blue —with different DNA structures, namely calf thymus DNA (ct-DNA), G-quadruplex DNA, and single stranded DNA (ssDNA). The objective of this research is to elucidate the molecular affinities of these dyes for specific DNA structures and explore their potential applications in molecular biology and diagnostics. The experimental approach involved detailed UV-visible spectroscopic analyses, to probe the binding affinities of each dye with ct-DNA, G-quadruplex DNA, and ssDNA. The study aimed to assess the selectivity of these dyes towards the unique structural features of each DNA entity. The binding stoichiometry is defined from Job’s method. The selectivity of the dyes towards DNA also investigated with competitive dialysis experiments. The binding stoichiometry were 1:1 for 1,9-Dimethyl-Methylene Blue and Toluidine Blue and G-quadruplex DNA or ssDNA. Besides, results indicate that 1,9-Dimethyl-Methylene Blue and Toluidine Blue exhibit a pronounced affinity for G-quadruplex DNA, and ct-DNA. While single-stranded DNA is a fundamental component of DNA replication and transcription, our dyes exhibit lower affinity for this structure. The selectivity is advantageous, as it allows for the discrimination between single-stranded and structured DNA regions. The potential applications in studying DNA dynamics and unwinding processes are vast.
Referanslar
Awadasseid, A., Ma, X., Wu, Y., & Zhang, W. (2021). G-quadruplex stabilization via small-molecules as a potential anti-cancer strategy. Biomedicine & Pharmacotherapy, 139, 111550.
Biver, T. (2022). Discriminating between parallel, anti-parallel and hybrid G-quadruplexes: mechanistic details on their binding to small molecules. Molecules, 27(13), 4165.
Davalos, V., & Esteller, M. (2023). Cancer epigenetics in clinical practice. CA: a cancer journal for clinicians, 73(4), 376-424.
Du, Y. H., Huang, J., Weng, X. C., & Zhou, X. (2010). Specific recognition of DNA by small molecules. Current medicinal chemistry, 17(2), 173-189.
Feizi-Dehnayebi, M., Dehghanian, E., & Mansouri-Torshizi, H. (2021). A novel palladium (II) antitumor agent: Synthesis, characterization, DFT perspective, CT-DNA and BSA interaction studies via in-vitro and in-silico approaches. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 249, 119215.
Figueiredo, J., Djavaheri-Mergny, M., Ferret, L., Mergny, J. L., & Cruz, C. (2023). Harnessing G-quadruplex ligands for lung cancer treatment: a comprehensive overview. Drug Discovery Today, 103808.
Hirt, B. V., Wattis, J. A., & Preston, S. P. (2014). Modelling the regulation of telomere length: the effects of telomerase and G-quadruplex stabilising drugs. Journal of Mathematical Biology, 68, 1521-1552.
Holden, L., Gkika, K. S., Burke, C. S., Long, C., & Keyes, T. E. (2023). Selective, disruptive luminescent Ru (II) polypyridyl probes of G-quadruplex. Inorganic Chemistry, 62(5), 2213-2227.
Kaushik, M., Kaushik, S., Bansal, A., Saxena, S., & Kukreti, S. (2011). Structural diversity and specific recognition of four stranded G-quadruplex DNA. Current Molecular Medicine, 11(9), 744-769.
Kocak, A., Yilmaz, H., Faiz, O., & Andac, O. (2016). Experimental and theoretical studies on Cu (II) complex of N, N′-disalicylidene-2, 3-diaminopyridine ligand reveal indirect evidence for DNA intercalation. Polyhedron, 104, 106-115.
Lerner, L. K., & Sale, J. E. (2019). Replication of G quadruplex DNA. Genes, 10(2), 95.
Li, D., Song, S., & Fan, C. (2010). Target-responsive structural switching for nucleic acid-based sensors. Accounts of Chemical Research, 43(5), 631-641.
Mendes, E., Aljnadi, I. M., Bahls, B., Victor, B. L., & Paulo, A. (2022). Major achievements in the design of quadruplex-interactive small molecules. Pharmaceuticals, 15(3), 300.
O'Hagan, M. P., Morales, J. C., & Galan, M. C. (2019). Binding and Beyond: What Else Can G‐Quadruplex Ligands Do?. European Journal of Organic Chemistry, 2019(31-32), 4995-5017.
Pirota, V., Stasi, M., Benassi, A., & Doria, F. (2020). An overview of quadruplex ligands: Their common features and chemotype diversity. Annual Reports in Medicinal Chemistry, 54, 163-196.
Reichmann, M. E., Rice, S. A., Thomas, C. A., & Doty, P. (1954). A further examination of the molecular weight and size of desoxypentose nucleic acid. Journal of the American Chemical Society, 76(11), 3047-3053.
Salvati, E., Leonetti, C., Rizzo, A., Scarsella, M., Mottolese, M., Galati, R., ... & Biroccio, A. (2007). Telomere damage induced by the G-quadruplex ligand RHPS4 has an antitumor effect. The Journal of clinical investigation, 117(11), 3236-3247.
Takahashi, S., Kotar, A., Tateishi-Karimata, H., Bhowmik, S., Wang, Z. F., Chang, T. C., ... & Sugimoto, N. (2021). Chemical modulation of DNA replication along G-quadruplex based on topology-dependent ligand binding. Journal of the American Chemical Society, 143(40), 16458-16469.
Yang, D., Campolongo, M. J., Nhi Tran, T. N., Ruiz, R. C., Kahn, J. S., & Luo, D. (2010). Novel DNA materials and their applications. Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology, 2(6), 648-669.
Yılmaz, H. E., Bağda, E., Bağda, E., & Durmuş, M. (2021). Interaction of water soluble cationic gallium (III) phthalocyanines with different G-quadruplex DNAs. Polyhedron, 208, 115404.
Zegers, J., Peters, M., & Albada, B. (2023). DNA G-quadruplex-stabilizing metal complexes as anticancer drugs. JBIC Journal of Biological Inorganic Chemistry, 28(2), 117-138.
Mathad, R. I., Hatzakis, E., Dai, J., & Yang, D. (2011). c-MYC promoter G-quadruplex formed at the 5′-end of NHE III 1 element: insights into biological relevance and parallel-stranded G-quadruplex stability. Nucleic acids research, 39(20), 9023-9033.
Chen, S. B., Shi, Q. X., Peng, D., Huang, S. Y., Ou, T. M., Li, D., ... & Huang, Z. S. (2013). The role of positive charges on G-quadruplex binding small molecules: Learning from bisaryldiketene derivatives. Biochimica et Biophysica Acta (BBA)-General Subjects, 1830(11), 5006-5013.
Ren, J., & Chaires, J. B. (1999). Sequence and structural selectivity of nucleic acid binding ligands. Biochemistry, 38(49), 16067-16075.
Guittat, L., Alberti, P., Rosu, F., Van Miert, S., Thetiot, E., Pieters, L., ... & Mergny, J. L. (2003). Interactions of cryptolepine and neocryptolepine with unusual DNA structures. Biochimie, 85(5), 535-547.
İndir
Yayınlanmış
Nasıl Atıf Yapılır
Sayı
Bölüm
Lisans
Bu çalışma Creative Commons Attribution-NonCommercial 4.0 International License ile lisanslanmıştır.
