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

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.,

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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.