An important consideration in the design of oligonucleotide probes for homogeneous hybridization assays is the efficiency of energy transfer between the fluorophore and quencher used to label the probes. We have determined the efficiency of energy transfer for a large number of combinations of commonly used fluorophores and quenchers. We have also measured the quenching effect of nucleotides on...

Zip nucleic acids (ZNAs) are oligonucleotides conjugated with cationic spermine units that increase affinity for their target. ZNAs were recently shown to enable specific and sensitive reactions when used as primers for polymerase chain reaction (PCR) and reverse-transcription. Here, we report their use as quantitative PCR hydrolysis probes. Ultraviolet duplex melting data demonstrate that atta...

This unit describes the in situ synthesis of DNA microarrays using a light-controlled process. In a highly parallel fashion, multiple oligonucleotide probes are created from scratch on a glass support using phosphoramidite building blocks carrying a photolabile protecting group. Spatial resolution is achieved by carefully controlling the illumination of defined spots on the glass substrate, on ...

A novel nanoparticles-based fluorescence detection method has been developed by taking advantage of magnetic separation and amplified fluorescence detection. This DNA sensor relies on a "sandwich" hybridization strategy, in which the DNA targets are first hybridized to captured oligonucleotide probes immobilized on magnetic nanoparticles, and then hybridized with thiol-modified oligonucleotide ...

Microarrays printed on glass slides are often constructed by covalently linking oligonucleotide probes to a derivatized surface. These procedures typically require relatively expensive amine- or thiol-modified oligonucleotide probes that add considerable expense to larger arrays. We describe a system by which unmodified oligonucleotide probes are bound to either nonderivatized or epoxy-silane-d...