Synthesis of novel phosphoramidite derivatives bearing pyrenyl and dansyl groups

Fine Tuning of Pyrene Excimer Fluorescence in Molecular Beacons by Alteration of the Monomer Structure

Oligonucleotide probes labeled with pyrene pairs that form excimers have a number of applications in hybridization analysis of nucleic acids. A long excited state lifetime, large Stokes shift, and chemical stability make pyrene excimer an attractive fluorescent label. Here we report synthesis of chiral phosphoramidite building blocks based on (R)-4-amino-2,2-dimethylbutane-1,3-diol, easily available from an inexpensive d-(-)-pantolactone. 1-Pyreneacetamide, 1-pyrenecarboxamide, and DABCYL derivatives have been used in preparation of molecular beacon (MB) probes labeled with one or two pyrenes/quenchers. We observed significant difference in the excimer emission maxima (475-510 nm; Stokes shifts 125-160 nm or 7520-8960 cm^-1) and excimer/monomer ratio (from 0.5 to 5.9) in fluorescence spectra depending on the structure and position of monomers in the pyrene pair. The pyrene excimer formed by two rigid 1-pyrenecarboxamide residues showed the brightest emission. This is consistent with molecular dynamics data on excimer stability. Increase of the excimer fluorescence for MBs after hybridization with DNA was up to 24-fold.

Novel non-nucleosidic building blocks for the preparation of multilabeled oligonucleotides

Synthesis of new non-nucleosidic phosphoramidites 1 and 2 derived from achiral precursors containing two reporter groups or amino functions is described. Among them, only phosphoramidites 1a-c allow multiple derivatization of synthetic oligonucleotides. The usefulness of building blocks 1a-c is demonstrated by introduction of several amino functions or fluorescent dansyl reporters at the 3'- and 5'-termini of synthetic oligonucleotides and their phosphorothioate analogues. It is demonstrated that multilabeled non-nucleosidic tether has no or only minor influence on the hybridization properties of the oligonucleotides.

A convenient method for the preparation of hapten phosphoramidites

Automated incorporation of haptens at the 3' or 5' end of oligonucleotides required the preparation of the corresponding hapten phosphoramidites. The requisite 1,3-diol framework was prepared in two steps from a carboxylic acid precursor first by a two-carbon homologation using Meldrum's acid to form the corresponding 3-oxo ester and then subsequent reduction to the diol. The primary alcohol was protected with a dimethoxytrityl group, while the secondary alcohol was converted to the reactive phosphoramidite.