Ulysse Asseline

Oligodeoxynucleotides covalently linked to intercalating dyes as base sequence-specific ligands. Influence of dye attachment site.

New molecules with high and specific affinity for nucleic acid base sequences have been synthesized. They involve an oligodeoxynucleotide covalently attached to an intercalating dye. Visible absorption spectroscopy and fluorescence have been used to investigate the binding of poly(rA) to octadeoxythymidylates substituted by a 9‐aminoacridine derivative in different positions along the oligonucleotide chain. The 9‐amino group of the acridine dye was linked through a polymethylene bridge to the 3′‐phosphate, the 5′‐phosphate, the fourth internucleotidic phosphate or to both the 3′‐ and 5′‐phosphates. Different interactions of the acridine dye were exhibited by these different substituted oligodeoxynucleotides when they bind to poly(rA). The interaction was shown to be specific for adenine‐containing polynucleotides. The stability of these complexes was compared with that of oligodeoxynucleotides substituted by an alkyl group on the 3′‐phosphate. The increase in stability due to the presence of the intercalating dye has been determined from the comparison of melting temperatures. These results are discussed with respect to the strategy of synthesis of a new class of molecules with high affinity and high specificity for nucleic acid base sequences.

Oligodeoxynucleotides covalently linked to intercalating agents: a new class of gene regulatory substances.

Oligodeoxynucleotides have been covalently linked to a 9-aminoacridine derivative via their 3-phosphate group. Specific complexes are formed with the complementary sequence of the oligonucleotide. The stability is strongly increased due to intercalation of the acridine derivative. Absorption, fluorescence, nuclear magnetic resonance and circular dichroism have been used to characterize complex formation. The stability of the complexes depends on the length of the linker between the acridine derivative and the 3-phosphate group of the oligonucleotide. Oligonucleotides covalently linked to an intercalating agent can be used to selectively control gene expression. Transcription initiation can be blocked when such an oligonucleotide binds to the transcribed strand in the open complex formed by E. coli RNA polymerase with the bla promoter. With some oligonucleotides, non-specific effects on transcription can be detected, most probably due to binding of the modified oligonucleotide to RNA polymerase. Translation of the messenger RNA from gene 32 of phage T4 can be prevented by using an oligonucleotide complementary to the sequence upstream from the Shine-Dalgarno sequence. Inhibition of translation does not occur in the absence of the intercalating agent covalently linked to the oligonucleotide nor with oligonucleotides which do not have a target sequence on the mRNA.

Solid-phase synthesis of modified oligodeoxyribonucleotides with an acridine derivative or a thiophosphate group at their 3' end

Abstract Use of a derivatized support involving the 2,2′-diethyldithio-group 7 allows the automated synthesis of oligodeoxyribonucleotide bearing acridine derivative (via nucleoside-3′-acridinylphosphoramidite 3 ) or 3′phosphorothioate group (including the sulfurization step for attachment of the first nucleoside to the support).

Oligothymidylates Substitubs en Position 3’ Par un Derive De L'Acridine

Abstract Oligothymidylates covalently linked at the 3′position to an acridine dye derivative via a polymethylene bridge have been synthetized by the phosphotriester method in solution.

Oligonucleotides tethered via nucleic bases. A potential new set of compounds for alternate strand triple-helix formation

Abstract The solid-phase preparation of oligonucleotides tethered via nucleic bases and with opposite polarities has been performed starting from a bridged dimer bound to a support.

Oligothymidylates Substitues Par Un Derive De L'Acridine en Position 5′, A La Fois En Position 5′ et 3′ Ou Sur Un Phosphate Internucleotidique

Abstract Oligothyraidylates covalently linked to an acridine derivative (2-methoxy-6-chloro-9-aminoacridine) have been synthesized by the phosphotriester method in solution. The substitution has been carried out at the 5′ position, both at the 5′ and 3′ positions or on an internucleotidic phosphate. A polymethylene linker was used to tether the acridine derivative via its 9-amino group to the terminal or internucleotidic phosphate.

Chemical synthesis of natural and modified oligodeoxynucleotides

This paper reports chemical synthesis of natural and modified oligodeoxynucleotides. In the first part after a short review of protective groups for the deoxynucleosides and for the phosphate groups, the different phosphorylating and coupling methods are listed and also the application fields for the different techniques (phosphotriester method in solution or solid-phase synthesis). The second part involves oligodeoxynucleotides in which phosphodiester groups are partially or fully replaced by alkylphosphotriester, phosphonate, phosphoramidate, phosphorothioate or phosphorothiolate groups. The last part describes synthesis of oligodeoxynucleotides bearing chemically reactive groups or an intercalating agent.

STUDIES TOWARDS THE DESIGN OF A MODIFIED GC BASE PAIR WITH STABILITY SIMILAR TO THAT OF THE AT BASE PAIR

Abstract Modified G ∗ C, ∗ GC or ∗ G ∗ C base pairs have been incorporated at the 3 rd and 8 th positions of a self-complementary decadeoxyoligonucleotide. The influence of these modifications on duplex stabilities has been studied by absorption spectroscopy. It has been found that a few of them have thermal stabilities similar to that of the AT base pair.

5′-5′ tethered oligonucleotides via nucleic bases: A potential new set of compounds for alternate strand triple-helix formation

Abstract The solid-phase synthesis of 5′-5′-linked oligonucleotides tethered via nucleic bases and with opposite polarities has been performed using a modified dinucleoside bearing a phosphoramidite group at the 3′-position of one nucleoside and a dimethoxytrityl group at the 3′-position of the second nucleoside.

Oligo-α-deoxyribonucleotides with a modified nucleic base and covalently linked to reactive agents

Abstract Solid-phase preparation of oligo-α-deoxyribonucleotides attached to intercalator, chemically or photochemically reactive groups through either their 5′- or 3′-ends, including use of the 5-methyl-α-deoxycytidine.