Homothymidine DNA oligonucleotides bearing a 3'-terminal 6-phenyl-9H-carbazole C-nucleoside, mercurated at position 1, 8 or both, were synthesized and tested for their potential to form triple helices with homoadenine ⋅ homothymine duplexes. The monomercurated triplex-forming oligonucleotides favored hybridization with fully matched double helices and in some cases considerable increase of the melting temperature could be attributed to Hoogsteen-type Hg(II)-mediated interaction with the homoadenine strand. The dimercurated one, on the other hand, favored hybridization with double helices placing a homo mispair opposite to the carbazole residue, suggesting that simultaneous coordination of each of the two Hg(II) ions to a different strand is only possible in the absence of competition from Watson-Crick base pairing.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1002/cbic.202401006 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Recent Progress of Triplex DNA Formation and Its Applications.
J Med Chem
February 2025
School of Pharmacy, Jiangsu Province Key Laboratory for Inflammation and Molecular Drug Target, Nantong University, Nantong 226001, China.
Recently, much attention has been focused on oligonucleotide drugs that precisely control the gene expression. Among these, triplex-forming oligonucleotides (TFOs) represent common antigene strategies because they bind specifically to the major groove position of genomic DNA to form a triplex DNA structure. Thus far, this promising triplex formation technique represents a successful strategy with strong application prospects for gene manipulation applications (e.
View Article and Find Full Text PDFResolution of complex mixtures of duplex and antiparallel triplex DNA structures by capillary electrophoresis and multivariate analysis.
Talanta
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 PDFCovalently Mercurated 6-Phenylcarbazole Residues Promote Hybridization of Triplex-Forming Oligonucleotides.
Chembiochem
February 2025
Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland.
Homothymidine DNA oligonucleotides bearing a 3'-terminal 6-phenyl-9H-carbazole C-nucleoside, mercurated at position 1, 8 or both, were synthesized and tested for their potential to form triple helices with homoadenine ⋅ homothymine duplexes. The monomercurated triplex-forming oligonucleotides favored hybridization with fully matched double helices and in some cases considerable increase of the melting temperature could be attributed to Hoogsteen-type Hg(II)-mediated interaction with the homoadenine strand. The dimercurated one, on the other hand, favored hybridization with double helices placing a homo mispair opposite to the carbazole residue, suggesting that simultaneous coordination of each of the two Hg(II) ions to a different strand is only possible in the absence of competition from Watson-Crick base pairing.
View Article and Find Full Text PDFDevelopment and functional evaluation of a psoralen-conjugated nucleoside mimic for triplex-forming oligonucleotides.
Commun Chem
January 2025
Chemistry of Functional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
Article Synopsis
- Psoralen-conjugated triplex-forming oligonucleotides (Ps-TFOs) are used for regulating gene expression through photo-cross-linking with DNA, but their effectiveness is reduced by disruptions in the purine base sequences.
- A new design called 1'-psoralen-conjugated triplex-forming oligonucleotide (OPTO) is proposed to stabilize triplex formation, even with pyrimidine interruptions, by incorporating a nucleoside mimic that enhances thermodynamic stability.
- The OPTO’s effectiveness was shown in conjunction with locked nucleic acid (LNA) and 5-methylcytosine, suggesting it can broaden the scope of target sequences for photodynamic gene regulation.
Anti-gene oligonucleotide clamps invade dsDNA and downregulate expression.
Mol Ther Nucleic Acids
December 2024
Department of Laboratory Medicine, Karolinska Institutet, ANA Futura, Alfred Nobels Allé 8, 14152 Huddinge, Stockholm, Sweden.
Anti-gene oligonucleotides belong to a group of therapeutic compounds, which, in contrast to antisense oligonucleotides, bind to DNA. Clamp anti-gene oligonucleotides bind through a double-stranded invasion mechanism. With two arms connected by a linker, they hybridize to one of the DNA strands forming Watson-Crick and Hoogsteen hydrogen bonds.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!