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 triplexe...
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| Format: | Article |
| Language: | English |
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Hitit University
2019-12-01
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| Series: | Hittite Journal of Science and Engineering |
| Subjects: | |
| Online Access: | https://dergipark.org.tr/tr/download/article-file/1506545 |
| _version_ | 1797662651862482944 |
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| author | Osman Doluca |
| author_facet | Osman Doluca |
| author_sort | Osman Doluca |
| collection | DOAJ |
| description | 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 |
| first_indexed | 2024-03-11T19:03:26Z |
| format | Article |
| id | doaj.art-7b816a8c929642a9893fd8962f4b52a4 |
| institution | Directory Open Access Journal |
| issn | 2148-4171 |
| language | English |
| last_indexed | 2024-03-11T19:03:26Z |
| publishDate | 2019-12-01 |
| publisher | Hitit University |
| record_format | Article |
| series | Hittite Journal of Science and Engineering |
| spelling | doaj.art-7b816a8c929642a9893fd8962f4b52a42023-10-10T11:17:27ZengHitit UniversityHittite Journal of Science and Engineering2148-41712019-12-016430330810.17350/HJSE19030000161150Triplex-forming DNA Probe Approach for Silver Detection and the Effect of C-G·C Triplet Distribution on Triplex StabilityOsman Doluca0Izmir University of Economics, Biomedical Engineering, Izmir, TurkeyI 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 triplexhttps://dergipark.org.tr/tr/download/article-file/1506545parallel triplex dnatriple helical dnatriplex dnadna topology agsilver. |
| spellingShingle | Osman Doluca Triplex-forming DNA Probe Approach for Silver Detection and the Effect of C-G·C Triplet Distribution on Triplex Stability Hittite Journal of Science and Engineering parallel triplex dna triple helical dna triplex dna dna topology ag silver. |
| title | Triplex-forming DNA Probe Approach for Silver Detection and the Effect of C-G·C Triplet Distribution on Triplex Stability |
| title_full | Triplex-forming DNA Probe Approach for Silver Detection and the Effect of C-G·C Triplet Distribution on Triplex Stability |
| title_fullStr | Triplex-forming DNA Probe Approach for Silver Detection and the Effect of C-G·C Triplet Distribution on Triplex Stability |
| title_full_unstemmed | Triplex-forming DNA Probe Approach for Silver Detection and the Effect of C-G·C Triplet Distribution on Triplex Stability |
| title_short | Triplex-forming DNA Probe Approach for Silver Detection and the Effect of C-G·C Triplet Distribution on Triplex Stability |
| title_sort | triplex forming dna probe approach for silver detection and the effect of c g·c triplet distribution on triplex stability |
| topic | parallel triplex dna triple helical dna triplex dna dna topology ag silver. |
| url | https://dergipark.org.tr/tr/download/article-file/1506545 |
| work_keys_str_mv | AT osmandoluca triplexformingdnaprobeapproachforsilverdetectionandtheeffectofcgctripletdistributionontriplexstability |