Methods and materials for detecting genetic or epigenetic elements

Abstract

This document provides methods and materials for detecting genetic and/or epigenetic elements. For example, methods and materials for detecting the presence or absence of target nucleic acid containing a genetic or epigenetic element, methods and materials for detecting the amount of target nucleic acid containing a genetic or epigenetic element within a sample, kits for detecting the presence or absence of target nucleic acid containing a genetic or epigenetic element, kits for detecting the amount of target nucleic acid containing a genetic or epigenetic element present within a sample, and methods for making such kits are provided.

1 . (canceled) 
     
     
         2 . A device for point of care or home use assessment of an organism for a genetic or epigenetic element, wherein said device comprises:
 (a) a sample chamber configured to receive a sample from a user, wherein said sample was obtained from said organism and (i) comprises fragments of single stranded nucleic acid or (ii) is prepared to contain fragments of single stranded nucleic acid within said sample chamber;   (b) a recognition chamber configured to receive said fragments from said sample chamber, wherein said recognition chamber comprises (i) probe nucleic acid comprising an amplifying restriction endonuclease and a nucleotide sequence complementary to a sequence of a target nucleic acid containing said genetic or epigenetic element and (ii) a recognition restriction endonuclease, wherein, if said target nucleic acid is present in said fragments, at least a portion of said target nucleic acid 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 of said recognition restriction endonuclease and 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 said amplifying restriction endonuclease from at least another portion of said probe nucleic acid,   (c) an amplification chamber configured to receive said portion of said probe nucleic acid comprising said amplifying restriction endonuclease from said recognition chamber, wherein said amplification chamber comprises a reporter nucleic acid comprising a label, an amplifying restriction endonuclease, and a double-stranded portion of nucleic acid comprising a restriction endonuclease cut site of said amplifying restriction endonuclease of said probe nucleic acid, wherein, if said portion of said probe nucleic acid comprising said amplifying restriction endonuclease is received from said recognition chamber, said amplifying restriction endonuclease of said probe nucleic acid cleaves said double-stranded portion of nucleic acid of said reporter nucleic acid at said restriction endonuclease cut site, thereby separating a portion of said reporter nucleic acid comprising said label from at least another portion of said reporter nucleic acid, and   (d) a detection chamber configured to receive said portion of said reporter nucleic acid comprising said label from said amplification chamber, wherein said detection chamber provides said user with an indication of the presence or absence of said label, thereby indicating the presence or absence of said genetic or epigenetic element within said organism.   
     
     
         3 . The device of  claim 2 , wherein said organism is a mammal. 
     
     
         4 . The device of  claim 2 , wherein said organism is a human. 
     
     
         5 . The device of  claim 2 , wherein said device is for assessment of said epigenetic element. 
     
     
         6 . The device of  claim 5 , wherein said epigenetic element is a methylated DNA sequence. 
     
     
         7 . The device of  claim 2 , wherein said sample is selected from the group consisting of blood samples, hair samples, skin samples, throat swab samples, cheek swab samples, tissue samples, cellular samples, and tumor samples. 
     
     
         8 . The device of  claim 2 , wherein said recognition restriction endonuclease comprises the ability to recognize a methylated nucleotide. 
     
     
         9 . The device of  claim 2 , wherein said recognition restriction endonuclease is a DpnI, GlaI, HpaII, MspI, AciI, HhaI, or SssI restriction endonuclease. 
     
     
         10 . The device of  claim 2 , wherein said label is a fluorescent label. 
     
     
         11 . The device of  claim 2 , wherein said label is a radioactive label. 
     
     
         12 . The device of  claim 2 , wherein said label is an enzyme label. 
     
     
         13 . The device of  claim 12 , wherein said enzyme label is horse radish peroxidase, alkaline phosphatase, laccase, galactosidase, or luciferase. 
     
     
         14 . The device of  claim 2 , wherein said label is a redox label. 
     
     
         15 . The device of  claim 2 , wherein said device is for point of care, and wherein said user is a medical, laboratory, or veterinarian personnel. 
     
     
         16 . The device of  claim 4 , wherein said device is for home use, and wherein said user is said human.