Biomedical subjects

W Pieken

Publications and source records attributed to W Pieken.

6 recordsLinked to original sources

PubMed2001

Diels--Alder bioconjugation of diene-modified oligonucleotides.

In an effort to offer complementary technology for covalent biomolecule modification (bioconjugation), we have developed a method that exploits the aqueous acceleration of Diels--Alder reactions for this purpose. Three different diene phosphoramidite reagents have been synthesized that enable diene modification of synthetic oligonucleotides prepared by the phosphoramidite method. Clean and efficient Diels--Alder cycloaddition of these diene oligonucleotides with maleimide dieneophiles was carried out, and the labeled oligonucleotide bioconjugates were characterized by HPLC and electrospray mass spectrometry. Dieneophile stoichiometry, temperature, and pH are all parameters that were shown to influence the efficiency of the process.

Biotinylation↗

PubMed1999

Purification of a highly modified RNA-aptamer. Effect of complete denaturation during chromatography on product recovery and specific activity.

To evaluate RNA-aptamers as potential drug candidates, efficient and scaleable purification protocols are needed. Because aptamers are highly structured and rigid molecules, denaturation during the purification process is a critical aspect to obtain a pure and active product. A two-step chromatographic procedure was developed to purify a synthetic anti-VEGF aptamer at the preparative scale. A reversed-phase chromatographic step was optimized with a highly hydrophobic ion pairing reagent, followed by ion-exchange chromatography in which heat and a chaotropic salt were used. Because of the presence of 2'-modified ribose, denaturation conditions had to be optimized in both chromatographic steps to achieve a fully active molecule.

Chromatography, High Pressure Liquid↗

PubMed1998

Efficient activation of nucleoside phosphoramidites with 4,5-dicyanoimidazole during oligonucleotide synthesis.

A new activator for the coupling of phosphoramidites to the 5'-hydroxyl group during oligonucleotide synthesis is introduced. The observed time to complete coupling is twice as fast with 4, 5-dicyanoimidazole (DCI) as the activator, compared with 1 H -tetrazole. The effectiveness of DCI is thought to be based on its nucleophilicity. DCI is soluble in acetonitrile up to 1.1 M at room temperature and can be used as the sole coupling activator during routine automated solid phase synthesis of oligonucleotides. The addition of 0.1 M N -methylimidazole to 0.45 M 1 H -tetrazole also results in higher product yields during oligonucleotide synthesis than observed with 1 H -tetrazole alone.

Base Sequence↗

PubMed1997

Efficient process technologies for the preparation of oligonucleotides.

Efficient process technologies for the preparation of 2'-substituted nucleoside monomers, as well as for oligonucleotide preparation, are introduced. A novel method for efficient preparation of 2'-substituted uridines is presented. This method employs the 3'-hydroxyl group of 2,2'-anhydrouridine as a tether for the facile intramolecular introduction of nucleophiles to the 2'-position. It allows access to 2'-alkoxy substituents from their alcohol precursors and to substituted 2'-amino substituents, such as the novel O-substituted 2'-hydroxylaminouridines. A novel process for large-scale oligonucleotide synthesis is discussed, which allows solution phase coupling of the monomer to the growing oligonucleotide chain. This is followed by selective isolation of productive coupling product by anchoring to a resin. Release from this resin completes a coupling cycle.

Oligonucleotides↗

PubMed1993

Importance of exocyclic base functional groups of central core guanosines for hammerhead ribozyme activity.

The three guanosines of the central core of a hammerhead ribozyme were replaced by 2-aminopurine ribonucleoside, xanthosine, isoguanosine, inosine, and deoxyguanosine. These analogues were incorporated by automated solid-phase synthesis, with the exception of isoguanosine. This was introduced by ligating a donor, which carried the isoguanosine at its 5'-end, and an acceptor oligoribonucleotide by a T4 DNA ligase-catalyzed reaction. Most of these modifications lowered the rate constant of cleavage by the hammerhead ribozyme drastically. Inspection of the possible hydrogen-bonding interactions disturbed by these modifications suggests that there is no G12A9 or A13G8 mismatched base pair in the central region. Increasing the Mg2+ concentration from 10 to 50 mM did not enhance these rates appreciably. This makes it improbable that the guanosines, including their 2'-hydroxyl groups, are involved in the binding of the catalytically active Mg2+. Transition-state destabilizing energies of 0.6-4.7 kcal mol-1 suggest that essentially all guanosines are involved in a hydrogen-bonding network.

Bacteriophage T4↗

PubMed1993

Chemically modified RNA: approaches and applications.

The modification of phosphate into phosphorothioate internucleotidic linkages in various RNAs and their usefulness in identifying phosphate positions essential for function are described. Several modifications of the 2'-hydroxyl group of the ribose, particularly the replacement by fluorine atoms and amino groups, is discussed. These studies have been concentrated on hammerhead ribozymes in order to determine hydroxyl groups important for the catalytic activity. In addition these derivatives have been instrumental in rendering ribozymes more stable toward nucleases.

Base Sequence↗