Inhibition of HIV-1 Replication by Triple-Helix-Forming Phosphorothioate Oligonucleotides Targeted to the Polypurine Tract

Tsukahara, Satoru; Suzuki, Junji; Hiratou, Takashi; Takai, Kazuyuki; Koyanagi, Yoshio; Yamamoto, Naoki; Takaku, Hiroshi

doi:10.1006/bbrc.1997.6536

Cited by 9 publications

(2 citation statements)

References 27 publications

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“…Intracellular potassium concentrations (), nucleosomes ( , ), and nucleases are all challenges for triplex formation inside the cell. Modified backbones and nucleotides ( − ) can minimize the effects of potassium and nucleases, and recent in vitro evidence suggests that a triplex can be formed on the nucleosome, dependent upon target site positioning within the core (). We are now testing the DNA damaging effects of single and multiple TFOs on transcription inhibition, homologous recombination, and mutation induction on mammalian chromosomes in tissue culture.…”

Section: Discussionmentioning

confidence: 99%

Psoralen Photo-Cross-Linking by Triplex-Forming Oligonucleotides at Multiple Sites in the Human Rhodopsin Gene

1999

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Targeting DNA damage by triplex-forming oligonucleotides (TFOs) represents a way of modifying gene expression and structure and a possible approach to gene therapy. We have determined that this approach can deliver damage with great specificity to sites in the human gene for the G-protein-linked receptor rhodopsin, mutations of which can lead to the genetic disorder autosomal dominant retinitis pigmentosa. We have introduced DNA monoadducts and interstrand cross-links at multiple target sites within the gene using TFOs with a photoactivatable psoralen group at the 5'-end. The extent of formation of photoadducts (i.e., monoadducts and cross-links) was measured at target sites with a 5'-ApT sequence at the triplex-duplex junction and at a target site with 5'-ApT and 5'-TpA sequences located four and seven nucleotides away, respectively. To improve psoralen reactivity at more distant sites, psoralen moieties were attached to TFOs with nucleotide "linkers" from two to nine nucleotides in length. High-affinity binding was maintained with linkers of up to 10 nucleotides, but affinities tended to decrease somewhat with increasing linker length due to faster dissociation kinetics. DNase I footprinting indicated little, if any, interaction between linkers and the duplex. Psoralen-TFO conjugates formed DNA cross-links with high efficiency (56-65%) at 5'-ApT sequences located at triplex junctions. At a 5'-ApT site four nucleotides away, the efficiency varied with linker length; a four-nucleotide linker gave the highest efficiency. Duplexes with 5'-TpA and 5'-ApT sites two nucleotides away, in otherwise identical sequences, were cross-linked with efficiencies of 56 and 38%, respectively. These results indicate that TFO-linker-psoralen conjugates allow simultaneous, efficient targeting of multiple sites in the human rhodopsin gene.

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Section: Discussionmentioning

confidence: 99%

Psoralen Photo-Cross-Linking by Triplex-Forming Oligonucleotides at Multiple Sites in the Human Rhodopsin Gene

1999

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“…Cp S G < normalized DE tot . d(GC) 4 The in¯uence of the phosphorothioate con®guration is more complicated. These theoretical results are in line with several experimental data which have shown a clear sequence eect.…”

Section: Molecular Modelling Of Phosphorothioate Oligomersmentioning

confidence: 99%

Determination of a set of parameters for the molecular modelling of phosphorothioate DNA

Bertrand

Pullman

Zakrzewska

et al. 1999

Theoretical Chemistry Accounts: Theory, Computation, and Modeli

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Phosphorothioate DNAs, have emerged as a new class of potent drugs. They are obtained by the replacement of the anionic oxygens of the phophodiester backbone by sulphur. A set of parameters has been developed for the FLEX force ®eld implemented in JUMNA 10.0 to take into account the in¯uence of sulphur on the structure of the DNA double helix. The consistency of our parameters was tested by modelling a phosphorothioate oligomer namely d(GC)8. d(GC)8. Results, obtained on both R-p S and S-p S diastereoisomers, were compared to the phosphodiester counterpart and are in agreement with available experimental data. Thus, our set of parameters seems suitable for further molecular modelling of other phosphorothioate oligomers.

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Effect of phosphorothioate chirality on the grooves of DNA double helices: A molecular dynamics study

Mukherjee

Bhattacharyya

2004

Biopolymers

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Phosphorothioate oligonucleotides (PS-ODNs) have gained considerable attention in drug therapy, primarily as potent antisense or antigene oligomers, which bind to specific DNA or mRNA sequences and lead to transcriptional or translational arrest. These are obtained by substituting one of the anionic oxygen of the phosphate group by a sulfur atom, which introduces chirality to the phosphorus atom of the DNA backbone. In this molecular dynamics simulation study, structural parameters like groove widths, environmental parameters like hydration or cation binding, and electrostatic energy surfaces of both the chiral forms of DNA/PS-DNA duplexes were assessed and compared with that of a normal DNA. Results indicate that, PS-S form with its sulfur atoms facing the minor groove has a widened minor groove, while the scenario is reverse for the PS-R form. Further analysis reveals the existence of several factors like large van der Waals radius of sulfur and the effect it has on its neighboring hydration pattern along with the net electrostatic environment, influencing such structural alterations. This also indicates, for the first time, the effect of absolute phosphorothioate chirality on the global structure of a DNA/PS-DNA hybrid that otherwise resembles a regular B-DNA structure.

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Inhibition of HIV-1 Replication by Triple-Helix-Forming Phosphorothioate Oligonucleotides Targeted to the Polypurine Tract

Cited by 9 publications

References 27 publications

Psoralen Photo-Cross-Linking by Triplex-Forming Oligonucleotides at Multiple Sites in the Human Rhodopsin Gene

Psoralen Photo-Cross-Linking by Triplex-Forming Oligonucleotides at Multiple Sites in the Human Rhodopsin Gene

Determination of a set of parameters for the molecular modelling of phosphorothioate DNA

Effect of phosphorothioate chirality on the grooves of DNA double helices: A molecular dynamics study

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