Targeting chromosomal sites with locked nucleic acid-modified triplex-forming oligonucleotides: study of efficiency dependence on DNA nuclear environment
Open Access
- 1 September 2006
- journal article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 34 (16) , 4546-4553
- https://doi.org/10.1093/nar/gkl630
Abstract
Triplex-forming oligonucleotides (TFOs) are synthetic DNA code-reading molecules that have been demonstrated to function to some extent in chromatin within cell nuclei. Here we have investigated the impact of DNA nuclear environment on the efficiency of TFO binding. For this study we have used locked nucleic acid-containing TFOs (TFO/LNAs) and we report the development of a rapid PCR-based method to quantify triplex formation. We have first compared triplex formation on genes located at different genomic sites and containing the same oligopyrimidine*oligopurine sequence. We have shown that efficient TFO binding is possible on both types of genes, expressed and silent. Then we have further investigated when gene transcription may influence triplex formation in chromatin. We have identified situations where for a given gene, increase of transcriptional activity leads to enhanced TFO binding: this was observed for silent or weakly expressed genes that are not or are only slightly accessible to TFO. Such a transcriptional dependence was observed for integrated and endogenous loci, and chemical and biological activations of transcription. Finally, we provide evidence that TFO binding is sequence-specific as measured on mutated target sequences and that up to 50% of chromosomal targets can be covered by the TFO/LNA in living cells.Keywords
This publication has 25 references indexed in Scilit:
- Targeted Cross-linking of the Human β-Globin Gene in Living Cells Mediated by a Triple Helix Forming OligonucleotideBiochemistry, 2006
- Triplex-Forming Oligonucleotides as Potential Tools for Modulation of Gene ExpressionCurrent Medicinal Chemistry - Anti-Cancer Agents, 2005
- Triplex-Forming Oligonucleotides - Sequence-Specific DNA Ligands as Tools for Gene Inhibition and for Modulation of DNA-Associated FunctionsCurrent Drug Targets, 2004
- Characterization and Quantification of Triple Helix Formation in Chromosomal DNAJournal of Molecular Biology, 2004
- Cell Cycle Modulation of Gene Targeting by a Triple Helix-forming OligonucleotidePublished by Elsevier ,2003
- Transcription Dependence of Chromosomal Gene Targeting by Triplex-forming OligonucleotidesPublished by Elsevier ,2003
- Sequence-Specific Gene Cleavage in Intact Mammalian Cells by 125I-Labeled Triplex-Forming Oligonucleotides Conjugated with Nuclear Localization Signal PeptideAntisense and Nucleic Acid Drug Development, 2002
- Triple helix-forming oligonucleotides target psoralen adducts to specific chromosomal sequences in human cellsNucleic Acids Research, 1999
- Triplex targeting of a native gene in permeabilized intact cells: covalent modification of the gene for the chemokine receptor CCR5Nucleic Acids Research, 1998
- Accessibility of nuclear DNA to triplex-forming oligonucleotides: The integrated HIV-1 provirus as a targetProceedings of the National Academy of Sciences, 1997