Methods and materials for assessing rna expression

Abstract

This document provides methods and materials for assessing RNA expression. For example, methods and materials for detecting the presence, absence, or amount of target nucleic acid (e.g., target RNA or target cDNA produced from target RNA), kits for detecting the presence, absence, or amount of target nucleic acid (e.g., target RNA or target cDNA produced from target RNA), and methods for making such kits are provided.

1 - 20 . (canceled) 
     
     
         21 . A device for assessing RNA expression comprising:
 (a) a recognition chamber comprising:
 (i) a probe nucleic acid comprising an amplifying restriction endonuclease and a nucleotide sequence complementary to a sequence of a target RNA or a cDNA of said target RNA, 
   wherein, if said target RNA or said cDNA is present in a sample inserted into said recognition chamber, at least a portion of said target RNA or said cDNA hybridizes to at least a portion of said probe nucleic acid to form a double-stranded portion of nucleic acid comprising a restriction endonuclease cut site, and
 (ii) a recognition restriction endonuclease having the ability to cut said double-stranded portion of nucleic acid at said restriction endonuclease cut site, 
   wherein, if said double-stranded portion of nucleic acid comprising said restriction endonuclease cut site is formed, said recognition restriction endonuclease cleaves said double-stranded portion of nucleic acid at said restriction endonuclease cut site, thereby separating a portion of said probe nucleic acid comprising an amplifying restriction endonuclease from at least another portion of said probe nucleic acid,   (b) a signal expansion chamber in fluid communication with said recognition chamber, wherein said signal expansion chamber comprises:
 (i) a first nucleic acid comprising an amplifying restriction endonuclease and a double-stranded portion of nucleic acid comprising a restriction endonuclease cut site of the amplifying restriction endonuclease of said portion of said probe nucleic acid comprising an amplifying restriction endonuclease, 
   wherein, if said portion of said probe nucleic acid comprising an amplifying restriction endonuclease is separated from at least another portion of said probe nucleic acid, the amplifying restriction endonuclease of said portion of said probe nucleic acid comprising an amplifying restriction endonuclease cleaves said first nucleic acid at said restriction endonuclease cut site of the amplifying restriction endonuclease of said portion of said probe nucleic acid comprising an amplifying restriction endonuclease, thereby separating a portion of said first nucleic acid comprising an amplifying restriction endonuclease from at least another portion of said first nucleic acid, and
 (ii) a second nucleic acid comprising an amplifying restriction endonuclease and a double-stranded portion of nucleic acid comprising a restriction endonuclease cut site of the amplifying restriction endonuclease of said portion of said first nucleic acid comprising an amplifying restriction endonuclease, 
   wherein, if said portion of said first nucleic acid comprising an amplifying restriction endonuclease is separated from at least another portion of said first nucleic acid, the amplifying restriction endonuclease of said portion of said first nucleic acid comprising an amplifying restriction endonuclease cleaves said second nucleic acid at said restriction endonuclease cut site of the amplifying restriction endonuclease of said portion of said first nucleic acid comprising an amplifying restriction endonuclease, thereby separating a portion of said second nucleic acid comprising an amplifying restriction endonuclease from at least another portion of said second nucleic acid, and   (c) an amplification chamber in fluid communication with said signal expansion chamber, wherein said amplification chamber comprises:
 (i) a reporter nucleic acid comprising a double-stranded portion of nucleic acid comprising a restriction endonuclease cut site of the amplifying restriction endonuclease of said portion of said probe nucleic acid comprising an amplifying restriction endonuclease, the amplifying restriction endonuclease of said portion of said first nucleic acid comprising an amplifying restriction endonuclease, or the amplifying restriction endonuclease of said portion of said second nucleic acid comprising an amplifying restriction endonuclease, 
   wherein, if said portion of said probe nucleic acid comprising an amplifying restriction endonuclease is separated from at least another portion of said probe nucleic acid, said portion of said first nucleic acid comprising an amplifying restriction endonuclease is separated from at least another portion of said first nucleic acid, or said portion of said second nucleic acid comprising an amplifying restriction endonuclease is separated from at least another portion of said second nucleic acid, then the amplifying restriction endonuclease of said portion of said probe nucleic acid comprising an amplifying restriction endonuclease, the amplifying restriction endonuclease of said portion of said first nucleic acid comprising an amplifying restriction endonuclease, or the amplifying restriction endonuclease of said portion of said second nucleic acid comprising an amplifying restriction endonuclease cleaves said reporter nucleic acid at said restriction endonuclease cut site of the amplifying restriction endonuclease of said portion of said probe nucleic acid comprising an amplifying restriction endonuclease, the amplifying restriction endonuclease of said portion of said first nucleic acid comprising an amplifying restriction endonuclease, or the amplifying restriction endonuclease of said portion of said second nucleic acid comprising an amplifying restriction endonuclease, thereby separating a portion of said reporter nucleic acid from at least another portion of said reporter nucleic acid,   wherein the presence of said portion of said reporter nucleic acid indicates that said sample contains said target RNA or said cDNA, thereby indicating expression of said target RNA, and   wherein the absence of said portion of said reporter nucleic acid indicates that said sample does not contain said target RNA or said cDNA, thereby indicating a lack of expression of said target RNA.   
     
     
         22 . The device of  claim 21 , wherein said probe nucleic acid is attached to a surface of said recognition chamber. 
     
     
         23 . The device of  claim 21 , wherein said first nucleic acid is attached to a surface of said signal expansion chamber. 
     
     
         24 . The device of  claim 21 , wherein said second nucleic acid is attached to a surface of said signal expansion chamber. 
     
     
         25 . The device of  claim 21 , wherein said reporter nucleic acid is attached to a surface of said amplification chamber. 
     
     
         26 . The device of  claim 21 , wherein said probe nucleic acid is attached to a surface of said recognition chamber, wherein said first nucleic acid is attached to a surface of said signal expansion chamber, wherein said second nucleic acid is attached to a surface of said signal expansion chamber, and wherein said reporter nucleic acid is attached to a surface of said amplification chamber.