Triplex-forming DNA Probe Approach for Silver Detection and the Effect of C-G·C Triplet Distribution on Triplex Stability

Year 2019, , 303 - 308, 31.12.2019

Osman Doluca

https://doi.org/10.17350/HJSE19030000161

Abstract

I n this study novel triplex forming DNA probes have been designed in order to detect Ag+ ion in low concentrations. The use of triplex forming oligonucleotides is a convenient in applications of sensing biomolecules due to their sequence specificity and programmability. However, the use of triplexes has its own obstacles. While antiparallel triplex forming sequences tend to prefer G-quadruplex formation over triplexes, parallel triplexes are also challenging because their formation is triggered by lowering the pH, or using of high concentrations of cations for the stabilization of C-G·C triplets, ie. Ag+. While due to electrostatic forces C-G·C triplets stabilize in the presence of cations, this limits possible choices for a triplex forming sequence. A better understanding of the impact of the sequence and designing accordingly may improve the stability of a triplex and lower the need for high cation concentration. Here we have present Triplex-forming DNA-based probes with different distributions of C-G·C triplets for detection of Ag+ and show the impact of the C-G·C triplet distribution on the stability of parallel triplexes. Our results indicate Ag+ detection as low as 20 nM and show dramatic increase in stability when C-G·C triplets are positioned at the flanks of the triplex

Keywords

Parallel triplex DNA, Triple helical DNA, Triplex DNA, DNA topology, Ag, Silver.

References

• 1. Pugeta N, Miller KM, Legube G. Non-canonical DNA/RNA structures during Transcription-Coupled Double-Strand Break Repair: Roadblocks or Bona fide repair intermediates? DNA Repair (2019) 102661.
• 2. Travers A, Muskhelishvili G. DNA structure and function. FEBS Journal 282 (2015) 2279–2295.
• 3. Frank-Kamenetskii MD, Mirkin SM. Triplex DNA structures. Annual Reviews of Biochemistry 64 (1995) 65–95.
• 4. Christensen LA, Finch RA, Booker AJ, Vasquez KM. Targeting oncogenes to improve breast cancer chemotherapy. Cancer Research 66 (2006) 4089–4094.
• 5. Rusling DA. The stability of triplex DNA is affected by the stability of the underlying duplex. Biophysical Chemistry 145 (2009) 105– 110.
• 6. Maldonado R, Filarsky M, Grummt I, Längst G. Purine- and pyrimidine-triple-helix-forming oligonucleotides recognize qualitatively different target sites at the ribosomal DNA locus. RNA 24 (2018) 371–380.
• 7. Jain A, Wang G, Vasquez KM. DNA triple helices: biological consequences and therapeutic potential. Biochimie 90 (2008) 1117– 1130.
• 8. Bacolla A, Wang G, Vasquez KM. New Perspectives on DNA and RNA Triplexes As Effectors of Biological Activity. PLoS Genetics 11 (2015) e1005696.
• 9. Hu Y, Cecconello A, Idili A, Ricci F, Willner I. Triplex DNA Nanostructures: From Basic Properties to Applications. Angewandte Chemie International Edition 56 (2017) 15210–15233.
• 10. Yang Y, Huang Y, Li C. A reusable electrochemical sensor for one-step biosensing in complex media using triplex-forming oligonucleotide coupled DNA nanostructure. Analytica Chimica Acta 1055 (2019) 90–97.
• 11. Ma DL, Ma VPY, Chan DSH, Leung KH, He HZ, Leung CH. Recent advances in luminescent heavy metal complexes for sensing. Coordination Chemistry Reviews 256 (2012) 3087–3113. doi:10.1016/j.ccr.2012.07.005.
• 12. Torigoe H, Nakagawa O, Imanishi T, Obika S, Sasaki K. Chemical modification of triplex-forming oligonucleotide to promote pyrimidine motif triplex formation at physiological pH. Biochimie 94 (2012) 1032–1040.
• 13. Ihara T, Ishii T, Araki N, Wilson AW, Jyo A. Silver ion unusually stabilizes the structure of a parallel-motif DNA triplex. Journal of the American Chemical Society 131 (2009) 3826–3827.
• 14. Aktepe N, Kocyigit A, Yukselten Y, Taskin A, Keskin C, Celik H. Increased DNA damage and oxidative stress among silver jewelry workers. Biological Trace Element Research 164 (2015) 185–191.
• 15. Villena AN. Exploring confocal microscopy to analyze ancient photography. Journal of Cultural Heritage 36 (2019) 191–199.
• 16. Zhang H, Suganuma K. Sintered Silver for LED Applications, in: Siow KS (Ed) Die-Attach Materials for High Temperature Applications in Microelectronics Packaging. Springer, pp 35–65, 2019. doi:10.1007/978-3-319-99256-3_2.
• 17. Abbasi S. The thermal conductivity modeling of nanofluids involving modified Cu nanorods by Ag nanoparticles. Heat and Mass Transfer 55 (2019) 891–897. doi:10.1007/s00231-018-2476-2.
• 18. Sun G, Wang Z, Huang J. Electromagnetic shielding effectiveness and electrical conductivity of a thin silver layer deposited onto cellulose film via electroless plating. Journal of Materials Science: Materials in Electronics 30 (2019) 12044–12053. doi:10.1007/ s10854-019-01562-z.
• 19. Chung S, Jeong J, Kim D, Park Y, Lee C, Hong Y. Contact Resistance of Inkjet-Printed Silver Source–Drain Electrodes in BottomContact OTFTs. Journal of Display Technology 8 (2012) 48–53.
• 20. Sarkar R. Aqueous synthesis and antibacterial activity of Silver nanoparticles against pseudomonas putida. Materials Today: Proceedings 11 (2019) 686–694.
• 21. Bocate KP. Antifungal activity of silver nanoparticles and simvastatin against toxigenic species of Aspergillus. International Journal of Food Microbiology 291 (2019) 79–86.
• 22. Streitbuerger A, Henrichs MP, Hauschild G, Nottrott M, Guder W, Hardes J. Silver-coated megaprostheses in the proximal femur in patients with sarcoma. European Journal of Orthopaedic Surgery & Traumatology 29 (2019) 79–85.
• 23. Mohammadi Z, Mesgar AS, Rahmdar S, Farhangi E. Effect of setting time and artificial saliva on the strength evaluated by different methods of dental silver amalgam: A comparative study. Materialwissenschaft Und Werkstofftechnik 50 (2019) 747–760. doi:10.1002/mawe.201800022.
• 24. Akcam FZ, Kaya O, Temel EN, Buyuktuna SA, Unal O, Yurekli VA. An investigation of the effectiveness against bacteriuria of silver-coated catheters in short-term urinary catheter applications: A randomized controlled study. Journal of Infection and Chemotherapy 25 (2019) 797-800. doi:10.1016/j.jiac.2019.04.004.
• 25. Gulbranson SH, Hud JA, Hansen RC. Argyria following the use of dietary supplements containing colloidal silver protein. Cutis 66 (2000) 373–374.
• 26. Drake PL, Hazelwood KJ. Exposure-Related Health Effects of Silver and Silver Compounds: A Review. Annals of Occupational Hygiene 49 (2005) 575–585.
• 27. Molina-Hernandez AI, Diaz-Gonzalez JM, Saeb-Lima M, Dominguez-Cherit J. Argyria after Silver Nitrate Intake: Case Report and Brief Review of Literature. Indian Journal of Dermatology 60 (2015) 520.
• 28. Pala G, Fronterré A, Scafa F, Scelsi M, Ceccuzzi R, Gentile E, Candura SM. Ocular argyrosis in a silver craftsman. Journal of Occupational Health 50 (2008) 521–524.
• 29. Lansdown ABG. A pharmacological and toxicological profile of silver as an antimicrobial agent in medical devices. Advances in Pharmacological Science 2010 (2010) 910686.