Stable nanoreporters

Abstract

The present invention relates to compositions and methods for detection and quantification of individual target molecules in biomolecular samples. In particular, the invention relates to improved, stable nanoreporter probes that are capable of binding to and identifying target molecules based on the probes' uniquely detectable signal. Methods for identifying target-specific sequences for inclusion in the probes are also provided, as are methods of making and using such probes. Polynucleotide sequences of certain nanoreporter components are also provided. The probes can be used in diagnostic, prognostic, quality control and screening applications.

What is claimed is: 
     
         1 . A probe pair comprising:
 (a) a first probe comprising
 (i) a first region that selectively binds to a first sequence of a target nucleic acid; and 
 (ii) a second region comprising a plurality of designed label attachment regions covalently attached together in a synthetic linear combination, wherein each label attachment region is hybridized to a complementary polynucleotide sequence having attached thereto one or more detectable molecules,
 wherein the second region comprises less than 85% homology to any sequence described in the REF SEQ public database; 
 
   (b) a second probe comprising a region that selectively binds to a second sequence of the target nucleic acid;
 wherein the first sequence and the second sequence of the target nucleic acid are different. 
   
     
     
         2 . The probe pair of  claim 1 , wherein the target nucleic acid is DNA or RNA. 
     
     
         3 . The probe pair of  claim 1 , wherein the first probe further comprises a constant region wherein the constant region comprises a plurality of repeat nucleotide sequences. 
     
     
         4 . The probe pair of  claim 1 , wherein at least one of the plurality of designed label attachment regions comprises a regularly repeated pattern of adenine bases. 
     
     
         5 . The probe pair of  claim 4 , wherein the adenine bases are spaced about an average of every 8 to 16 nucleotide bases. 
     
     
         6 . The probe pair of  claim 1 , wherein the complementary polynucleotide sequence comprises an RNA polynucleotide sequence. 
     
     
         7 . The probe pair of  claim 6 , wherein the RNA polynucleotide sequence comprises at least one amino-allyl modified uracil base. 
     
     
         8 . The probe pair of  claim 7 , wherein a detectable molecule is attached to the amino-allyl modified uracil base. 
     
     
         9 . The probe pair of  claim 1 , wherein the one or more detectable molecules are fluorescent dyes. 
     
     
         10 . The probe pair of  claim 1 , wherein each label attachment region comprises about 800 to 1300 nucleotide bases. 
     
     
         11 . The probe pair of  claim 1 , wherein each label attachment region has a G/C content of about 50%. 
     
     
         12 . The probe pair of  claim 1 , wherein each label attachment region has a thymine content of about 35-45%. 
     
     
         13 . The probe pair of  claim 1 , wherein each label attachment region is different from the other label attachment regions in the plurality of designed label attachment regions. 
     
     
         14 . The probe pair of  claim 1 , wherein the second region of the first probe comprises less than about 1% of inverted repeats or direct repeats. 
     
     
         15 . The probe pair of  claim 14 , wherein the inverted repeats or direct repeats are 9 nucleotides or greater. 
     
     
         16 . The probe pair of  claim 1 , wherein each label attachment region lacks a direct or inverted repeat that is greater than 12 nucleotides in length. 
     
     
         17 . The probe pair of  claim 16 , wherein each label attachment region lacks a direct or inverted repeat that is greater than about 7 nucleotides in length. 
     
     
         18 . The probe pair of  claim 1 , wherein the complementary polynucleotide sequence has a G/C ratio of at least 1/1. 
     
     
         19 . The probe pair of  claim 18 , wherein the complementary polynucleotide sequence has a G/C ratio of about 3/2. 
     
     
         20 . The probe pair of  claim 1 , wherein the second probe further comprises an affinity tag. 
     
     
         21 . The probe pair of  claim 20 , wherein the affinity tag is selected from the group consisting of biotin, avidin/streptavidin, digoxigenin, HA epitope, myc epitope, and FLAG epitope. 
     
     
         22 . The probe pair of  claim 21 , wherein the affinity tag is a digoxigenin tag. 
     
     
         23 . The probe pair of  claim 21 , wherein the affinity tag is a biotin tag. 
     
     
         24 . The probe pair of  claim 1 , wherein the first probe further comprises an affinity tag. 
     
     
         25 . The probe pair of  claim 24 , wherein the affinity tag is selected from the group consisting of biotin, avidin/streptavidin, digoxigenin, HA epitope, myc epitope, and FLAG epitope. 
     
     
         26 . The probe pair of  claim 25 , wherein the affinity tag of the first probe is a biotin tag. 
     
     
         27 . The probe pair of  claim 25 , wherein the affinity tag of the first probe is a digoxigenin tag. 
     
     
         28 . A population of probe pairs, wherein each probe pair in the population comprises:
 (a) a first probe comprising
 (i) a first region that selectively binds to a first sequence of a target nucleic acid; and 
 (ii) a second region comprising a plurality of designed label attachment regions covalently attached together in a synthetic linear combination, wherein each label attachment region is hybridized to a complementary polynucleotide sequence having attached thereto one or more detectable molecules,
 wherein the second region comprises less than 85% homology to any sequence described in the REF SEQ public database; 
 
   (b) a second probe comprising a region that selectively binds to a second sequence of the target nucleic acid;
 wherein the first sequence and the second sequence of the target nucleic acid are different. 
   
     
     
         29 . The population of probe pairs of  claim 28 , wherein the first probe or the second probe of each probe pair in the population further comprises an affinity tag.