Pyrimidines linked to a quencher
First Claim
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1. A derivatized pyrimidine compound having the structure ##STR10## wherein Pyr represents a pyrimidine substituted at the 5 position with a linker L and said linker comprising at least three carbon atoms and is linking the pyrimidine with the quencher;
- wherein Q is a quencher andwhenever x is an activated phosphorus group capable of intermolecular bond formation with a 3'"'"' hydroxyl of another nucleotide, then y is a protected hydroxyl group and z is --H, --F, --OCH3, --O-allyl or a protected hydroxyl or amine group andwhenever y is an activated phosphorus group capable of intermolecular bond formation with a 5'"'"' hydroxyl of another nucleotide then x is a protected hydroxyl group and z is --H, --F, --OCH3, --O-allyl or a protected hydroxyl or amine group.
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Abstract
Compounds are described comprising pyrimidines substituted at the C-5 position with a linker and quencher. These compounds when incorporated into hairpin oligonucleotides quench the fluorescence of fluorophores linked to the 5'"'"'-terminus of the oligonucleotide. These nucleotide-quencher compounds are also easy to incorporate into oligonucleotides using conventional, automated, oligonucleotide synthetic techniques.
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Citations
23 Claims
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1. A derivatized pyrimidine compound having the structure ##STR10## wherein Pyr represents a pyrimidine substituted at the 5 position with a linker L and said linker comprising at least three carbon atoms and is linking the pyrimidine with the quencher;
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wherein Q is a quencher and whenever x is an activated phosphorus group capable of intermolecular bond formation with a 3'"'"' hydroxyl of another nucleotide, then y is a protected hydroxyl group and z is --H, --F, --OCH3, --O-allyl or a protected hydroxyl or amine group and whenever y is an activated phosphorus group capable of intermolecular bond formation with a 5'"'"' hydroxyl of another nucleotide then x is a protected hydroxyl group and z is --H, --F, --OCH3, --O-allyl or a protected hydroxyl or amine group. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23)
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Specification