Dual polarity analysis of nucleic acids

Abstract

This invention provides methods for characterizing the amounts of nucleic acids, including plus/minus determinations, the use of different constructs, the use of a library and a reference library. Expression may also be compared in two or more samples using the methods of this invention. Also provided are heterophasic arrays comprising labeled positive copies of nucleic acids hybridized to the array and labeled negative copies of nucleic acids hybridized to the array, in which the labeled positive copies are separately quantifiable from the labeled negative copies.

1 . A method for determining the amounts of nucleic acids in a library of nucleic acids, said method consisting essentially of the steps of:
 (i) generating
 (a) labeled RNA copies of said nucleic acids in said library, and 
 (b) labeled DNA copies of said nucleic acids in said library, 
 wherein said RNA copies and said DNA copies have opposite polarities to each other; 
   (ii) hybridizing said RNA copies and said DNA copies to a nucleic acid array or arrays; and   (iii) measuring the amount of hybridization of said labeled RNA copies and said labeled DNA copies to said array or arrays, wherein the amount of hybridization of said labeled RNA copies and the amount of hybridization of said labeled DNA copies are independently quantified, thereby determining the amounts of nucleic acids in said library of nucleic acids.   
     
     
         2 . The method of  claim 1 , wherein said RNA copies comprise [−] copies of said nucleic acids and said DNA copies comprise [+] copies of said nucleic acids. 
     
     
         3 . The method of  claim 1 , wherein said RNA copies comprise [+] copies of said nucleic acids and said DNA copies comprise [−] copies of said nucleic acids. 
     
     
         4 . The method of  claim 1 , wherein the nucleic acids in said library comprise RNA and wherein said labeled RNA copies generated in step (i)(a) are derived by labeling RNA in said library. 
     
     
         5 . The method of  claim 1 , wherein said labeled DNA copies generated in step (i)(b) are copied from RNA templates. 
     
     
         6 . The method of  claim 1 , wherein said array or arrays is a biphasic array or a heterophasic array. 
     
     
         7 . The method of  claim 1 , wherein said labeled RNA copies comprise a label selected from the group consisting of fluorescent compound, a phosphorescent compound, a chemiluminescent compound, a chelating compound, an electron dense compound, a magnetic compound, an intercalating compound, an energy transfer compound, and a combination of any of the foregoing. 
     
     
         8 . The method of  claim 7 , wherein said array or arrays is a biphasic array or a heterophasic array. 
     
     
         9 . The method of  claim 7 , wherein said labeled DNA copies comprise a label selected from the group consisting of fluorescent compound, a phosphorescent compound, a chemiluminescent compound, a chelating compound, an electron dense compound, a magnetic compound, an intercalating compound, an energy transfer compound, and a combination of any of the foregoing. 
     
     
         10 . The method of  claim 9 , wherein said RNA copies comprise [−] copies of said nucleic acids and said DNA copies comprise [+] copies of said nucleic acids. 
     
     
         11 . The method of  claim 9 , wherein said RNA copies comprise [+] copies of said nucleic acids and said DNA copies comprise [−] copies of said nucleic acids. 
     
     
         12 . The method of  claim 9 , wherein said array or arrays is a biphasic array or a heterophasic array. 
     
     
         13 . The method of  claim 12 , wherein said RNA copies comprise [−] copies of said nucleic acids and said DNA copies comprise [+] copies of said nucleic acids. 
     
     
         14 . The method of  claim 12 , wherein said RNA copies comprise [+] copies of said nucleic acids and said DNA copies comprise [−] copies of said nucleic acids. 
     
     
         15 . The method of  claim 1 , wherein said labeled DNA copies comprise a label selected from the group consisting of fluorescent compound, a phosphorescent compound, a chemiluminescent compound, a chelating compound, an electron dense compound, a magnetic compound, an intercalating compound, an energy transfer compound, and a combination of any of the foregoing. 
     
     
         16 . The method of  claim 15 , wherein said array or arrays is a biphasic array or a heterophasic array.