DNA linker reagents

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Background: This invention describes structures, and a method for the production, of a universal nucleic acid linker, comprised of a functional group linked to a polynucleotide through an activating leaving group and a tether. Such functional groups can be fluorescence quenchers, fluorochromes, prodrugs, drugs, among others, and can provide for detection of chemical changes following their release from the modified polynucleotide. These linkers can be used to modify polynucleotide probes in ligation reactions, as well as transfer reactions. The probes are useful in a variety of reactions triggered by specific hybridization to a target nucleic acid, and can be used with in vitro and in vivo applications to detect and quantify nucleic acid target sequences. The linkers also promote fast reaction and amplification of signals. Applications: DIAGNOSTIC APPLICATIONS: Detection and quantification of RNA and DNA sequences in solution, blots, microarrays, and beads for diagnostics/clinical diagnostics Identification of RNAs and SNPs directly in bacteria and human cells Genetic markers for sorting intact bacteria and human cells (such as stem cells) Genotyping at single nucleotide level for clinical diagnosis, i.e. prenatal screening or cancer diagnosis/prognosis, identification of drug resistance Veterinary diagnostics Environmental testing Food Testing (e.g., Salmonella, E. coli) Industrial process monitoring Agricultural-genetics testing   Advantages: The described linker reagents for the synthesis of the modified polynucleotides are simple and inexpensive to prepare. A standard DNA synthesizer is sufficient to attach them to any polynucleotide in an automated fashion using conventional solid state oligonucleotide synthesis.