Oligonucleotides containing arylacetylene residues: Synthesis and post-synthetic modification via [3+2] cycloaddition

1-Phenylethynylpyrene (PEPy) as a novel blue-emitting dye for qPCR assay

An alkyl azide derivative of 1-phenylethynylpyrene (PEPy) dye was prepared and used in the functionalization of oligonucleotides via click chemistry. Spectral and photo-physical properties of the PEPy-modified oligonucleotides as a single strand, and in perfect or mismatched duplexes, have been studied. A series of PEPy-Dabcyl fluorogenic TaqMan probes were synthesized and tested in qPCR. PEPy proved to be a superior substitute for AMCA as a short wavelength fluorescent dye for qPCR probes. PEPy probes were shown to significantly reduce Cq (a fractional PCR cycle used for quantification) vs. AMCA labeled probes, thus improving on the reliability of detection. Moreover, a larger increase of fluorescence during amplification was observed in the case of PEPy probes that makes this dye very suitable for an end-point PCR technique. This study broadens the panel of fluorescent dyes suitable for the use in probes for quantitative real-time PCR.

Design of molecular beacons: 3' couple quenchers improve fluorogenic properties of a probe in real-time PCR assay

Convenient preparation of fluorogenic hairpin DNA probes (molecular beacons) carrying a pair of FAM fluorophores (located close to 5'-terminus of the probe) or a pair of BHQ1 quenchers on 3'-terminus (with (BHQ1)2 or BHQ1-BHQ1 composition) is reported. These probes were used for the first time in a real-time PCR assay and showed considerable improvements in fluorogenic properties (the total fluorescence increase or signal-to-background ratio) in assay conditions vs. conventional one-FAM-one-BHQ1 molecular beacon probes as well as vs. hydrolyzable one-FAM-one-BHQ1 TaqMan probes. At the same time, such multiple modifications of the probe do not influence its Cq (a fractional PCR cycle used for quantification). The probe MB14 containing a BHQ1-BHQ1 pair showed a PCR fluorescence/background value of 9.6 which is more than two times higher than that of a regular probe MB2 (4.6). This study demonstrates prospects for the design of highly fluorogenic molecular beacon probes suitable for quantitative real-time PCR and for other potential applications (e.g. intracellular RNA detection and SNP/mutation analysis).

Labeling of an antisense oligonucleotide with [(18)F]FPy5yne

Functional imaging of gene expression in vivo with short-lived positron emitter (18)F remains an unrealized goal, in part because the long reaction times and challenging protocols typically required to label nucleic acid-based molecular probes with this radionuclide (t(1/2) = 109.8 minutes). To this end, we synthesized prosthetic group 2-[(18)F]fluoro-3-(hex-5-ynyloxy)pyridine ([(18)F]FPy5yne), used previously to label peptides, and coupled it to an oligodeoxyribonucleotide with (18)F by way of a Cu(I)-mediated azide/alkyne cycloaddition reaction. HPLC-purified [(18)F]FPy5yne was ligated to a 5'-azide-modified DNA sequence antisense to mdr1 mRNA in the presence of Cu(I)-stabilizing ligand tris(benzyltriazolylmethyl)amine and 2,6-lutidine. Non-decay corrected, collected yields of the (18)F-labeled oligonucleotide from end-of-bombardment were 3.9% +/- 0.5% (n = 3; 24.6% +/- 0.5% decay corrected). Shortest preparation time was 276 minutes from start of synthesis.

Azide solid support for 3'-conjugation of oligonucleotides and their circularization by click chemistry

A solid support bearing an azido linker was used to synthesize a 3'-azido-alkyl-oligonucleotide by phosphoramidite chemistry. The resulting oligonucleotide was either conjugated by 1,3-dipolar cycloaddition on solid support or in solution with mannose-propargyl derivative and in solution with dansyl propargyl. Besides, after introduction of an alkyne function at the 5'-end, the resulting oligonucleotide bearing both 3'-azide and 5'-alkyne functions was circularized.

Fast, copper-free click chemistry: a convenient solid-phase approach to oligonucleotide conjugation

Solid-phase oligonucleotide conjugation by nitrile oxide-alkyne click cycloaddition chemistry has been successfully demonstrated; the reaction, compatible with all nucleobases, requires no metal catalyst and proceeds under physiological conditions.

Perylene diimide-oligonucleotide conjugates constructed by click chemistry

Oligonucleotide conjugates were prepared by copper-catalyzed cycloaddition of acetylene-modified oligonucleotides to diazido derivative of perylene 3,4,9,10-tetracarboxylic acid diimide.

Triazole-linked dumbbell oligodeoxynucleotides with NF-kappaB binding ability as potential decoy molecules

Triazole-cross-linked oligodeoxynucleotides were synthesized with use of the Cu(I) catalyzed alkyne-azide cycloaddition (CuAAC) with oligodeoxynucleotides possessing N-3-(azidoethyl)thymidine and N-3-(propargyl)thymidine at the 3'- and 5'-termini. The newly synthesized oligodeoxynucleotides were thermally stable and their global structures retained those of non-cross-linked oligodeoxynucleotides. The newly synthesized dumbbell oligodeoxynucleotides showed excellent stability against snake venom phosphodiesterase (3'-exonuclease) and high thermal stability, which are necessary for decoy molecules to achieve biological responses leading to alteration of gene expression. Moreover, dumbbell oligodeoxynucleotides have the ability to bind to NF-kappaB p50 homodimer within a similar range to that of a control double-stranded decoy oligodeoxynucleotide. This strategy allows us to prepare triazole-linked dumbbell oligodeoxynucleotides with a range of loop lengths, and we found that the greater the number of the thymidine residues constituting the loop region, the higher the binding affinity of the dumbbell oligodeoxynucleotides to the nuclear factor kappaB. This means that a protein binding ability of the dumbbell oligodeoxynucleotides could be modulated by altering the loop size. This study clearly shows that cross-linking by the triazole structure does not prevent the dumbbell oligodeoxynucleotides from binding to the nuclear factor kappaB transcription factor. Therefore, the results obtained conclusively demonstrate that the triazole cross-linked dumbbell oligodeoxynucleotides could be proposed as powerful decoy molecules.