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In this work, the use of DNA-stabilized fluorescent silver nanoclusters for the detection of target pyrimidine-rich DNA sequences by formation of parallel and antiparallel triplex structures is studied by molecular fluorescence spectroscopy. In the case of parallel triplexes, the probe DNA fragments are Watson-Crick stabilized hairpins, and whereas in the case of antiparallel triplexes, the probe fragments are reverse-Hoogsteen clamps. In all cases, the formation of the triplex structures has been assessed by means of polyacrylamide gel electrophoresis, circular dichroism, and molecular fluorescence spectroscopies, as well as multivariate data analysis methods. The results have shown that it is possible the detection of pyrimidine-rich sequences with an acceptable selectivity by using the approach based on the formation of antiparallel triplex structures.
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http://dx.doi.org/10.1016/j.saa.2023.122752 | DOI Listing |
Biochem Biophys Rep
September 2025
Nucleic Acids Research Lab, Department of Chemistry, University of Delhi (North Campus), Delhi, 110007, India.
DNA is polymorphic, as with four nucleobases, it can be configured in a number of secondary structures. The four-stranded DNA structures consisting of G-tetrads have especially been intriguing because of their proven existence in human cells. Due to the high prevalence of putative G-quadruplex-forming sequence motifs in the human genome, scientists in recent years have highlighted the potential of exploiting these exotic structures for targeted therapies for various cancers.
View Article and Find Full Text PDFTalanta
June 2025
Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Marti i Franquès 1-11, E-08028, Barcelona, Spain. Electronic address:
Triplex DNA structures, which are formed by the addition of an extra strand to a target B-DNA duplex, have attracted increasing interest due to their analytical and therapeutic applications. These structures are classified into parallel and antiparallel, depending on the orientation of the Triplex-Forming Oligonucleotide (TFO) relative to the B-DNA duplex. Whereas the formation of parallel triplexes is easily detected by monitoring spectral changes in the UV region, the formation of antiparallel triplexes produces small or even no spectral variations, which makes their detection difficult and uncertain.
View Article and Find Full Text PDFSpectrochim Acta A Mol Biomol Spectrosc
March 2025
Dept. of Chemical Engineering and Analytical Chemistry, University of Barcelona, Marti i Franquès 1-11, E-08028 Barcelona, Spain. Electronic address:
In this work, strategies for the detection of pyrimidine-rich DNA target sequences based on the formation of duplex and antiparallel triplex structures are studied. The presence of the target is detected from the changes in fluorescence of silver nanoclusters stabilized by the corresponding complementary DNA probes. In all cases, the formation of intermolecular structures has been assessed by means of melting experiments and multivariate analysis.
View Article and Find Full Text PDFInt J Mass Spectrom
May 2024
C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA.
Chembiochem
May 2024
Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße7, 60438, Frankfurt am Main, Germany.
Long non-coding RNAs (lncRNAs) are important regulators of gene expression and can associate with DNA as RNA : DNA heteroduplexes or RNA ⋅ DNA : DNA triple helix structures. Here, we review in vitro biochemical and biophysical experiments including electromobility shift assays (EMSA), circular dichroism (CD) spectroscopy, thermal melting analysis, microscale thermophoresis (MST), single-molecule Förster resonance energy transfer (smFRET) and nuclear magnetic resonance (NMR) spectroscopy to investigate RNA ⋅ DNA : DNA triple helix and RNA : DNA heteroduplex formation. We present the investigations of the antiparallel triplex-forming lncRNA MEG3 targeting the gene TGFB2 and the parallel triplex-forming lncRNA Fendrr with its target gene Emp2.
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