Dilip V. Jarikote

Forced intercalation probes (FIT Probes): thiazole orange as a fluorescent base in peptide nucleic acids for homogeneous single-nucleotide-polymorphism detection.

Fluorescent base analogues in DNA are versatile probes of nucleic acid–nucleic acid and nucleic acid–protein interactions. New peptide nucleic acid (PNA) based probes are described in which the intercalator dye thiazole orange (TO) serves as a base surrogate. The investigation of six TO derivatives revealed that the linker length and the conjugation site decided whether a base surrogate conveys sequence‐selective DNA binding and whether fluorescence is increased or decreased upon single‐mismatched hybridization. One TO derivative conferred universal PNA–DNA base pairing while maintaining duplex stability and hybridization selectivity. TO fluorescence increased up to 26‐fold upon hybridization. In contrast to most other probes, in which fluorescence is invariant once hybridization had occurred, the emission of TO‐containing PNA probes is attenuated when forced to intercalate next to a mismatched base pair. The specificity of DNA detection is therefore not limited by the selectivity of probe–target binding and a DNA target can be distinguished from its single‐base mutant under nonstringent hybridization conditions. This property should be of advantage for real‐time quantitative PCR and nucleic acid detection within living cells.

FIT probes: peptide nucleic acid probes with a fluorescent base surrogate enable real-time DNA quantification and single nucleotide polymorphism discovery.

The ability to accurately quantify specific nucleic acid molecules in complex biomolecule solutions in real time is important in diagnostic and basic research. Here we describe a DNA-PNA (peptide nucleic acid) hybridization assay that allows sensitive quantification of specific nucleic acids in solution and concomitant detection of select single base mutations in resulting DNA-PNA duplexes. The technique employs so-called FIT (forced intercalation) probes in which one base is replaced by a thiazole orange (TO) dye molecule. If a DNA molecule that is complementary to the FIT-PNA molecule (except at the site of the dye) hybridizes to the probe, the TO dye exhibits intense fluorescence because stacking in the duplexes enforces a coplanar arrangement even in the excited state. However, a base mismatch at either position immediately adjacent to the TO dye dramatically decreases fluorescence, presumably because the TO dye has room to undergo torsional motions that lead to rapid depletion of the excited state. Of note, we found that the use of d-ornithine rather than aminoethylglycine as the PNA backbone increases the intensity of fluorescence emitted by matched probe-target duplexes while specificity of fluorescence signaling under nonstringent conditions is also increased. The usefulness of the ornithine-containing FIT probes was demonstrated in the real-time PCR analysis providing a linear measurement range over at least seven orders of magnitude. The analysis of two important single nucleotide polymorphisms (SNPs) in the CFTR gene confirmed the ability of FIT probes to facilitate unambiguous SNP calls for genomic DNA by quantitative PCR.

Ultrasound promoted Suzuki cross-coupling reactions in ionic liquid at ambient conditions

Palladium catalyzed Suzuki cross-coupling reactions of halobenzenes including chlorobenzenes with phenylboronic acid have been achieved at ambient temperature (30 degrees C) in the absence of a phosphine ligand using the ionic liquid 1,3-di-n-butylimidazolium tetrafluoroborate [bbim][BF4] with methanol as co-solvent under ultrasonic irradiation.

Ensemble hybridisation – a new method for exploring sequence dependent fluorescence of dye–nucleic acid conjugates

The fluorescence of thiazole orange as artificial base in PNA was investigated in a nearest neighbour analysis; library-to-library hybridisation allowed the identification of probe sequences suitable for homogeneous DNA detection.

Forced intercalation as a tool in gene diagnostics and in studying DNA–protein interactions

Aromatic and heteroaromatic groups that are forced to intercalate at specific positions in DNA are versatile probes of DNA–DNA and DNA–protein recognition. Fluorescent nucleobases are of value since they are able to report on localized alterations of DNA duplex structure. However, the fluorescence of the vast majority of base surrogates becomes quenched upon intercalation in DNA. Peptide nucleic acid (PNA)-based probes are presented in which the intercalator dye thiazole orange (TO) serves as a fluorescent base surrogate. In these probes, fluorescence increases (5–60-fold) upon hybridization. PNA-bearing TO as fluorescent base surrogate could hence prove useful in real-time polymerase chain reaction (PCR) applications and in live cell analysis. Forced intercalation of aromatic polycycles can help to explore the binding mechanism of DNA-modifying enzymes. We discuss studies of DNA-methyltransferases (MTases) which commence methylation of nucleobases in DNA by flipping the target nucleotide completely out of the helix. A method for probing the base-flipping mechanism is suggested. It draws upon the observation that large hydrophobic base surrogates in the face of the swung-out base can enhance the DNA-enzyme binding affinity possibly by disrupting target base-stacking and stabilizing the apparent abasic site.