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

Abstract

In 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 program-mability. 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 se-quence 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 f lanks of the triplex.

Keywords:

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

DOI: 10.17350/HJSE19030000161

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Published
2019-12-31
How to Cite
Doluca, O. (2019). Triplex-forming DNA Probe Approach for Silver Detection and the Effect of C-G·C Triplet Distribution on Triplex Stability. Hittite Journal of Science & Engineering, 6(4), 303-308. Retrieved from https://www.hjse.hitit.edu.tr/hjse/index.php/HJSE/article/view/427
Section
SCIENCE