Method for the detection of cytosine methylations in immobilized DNA samples

Abstract

A method is described for the analysis of cytosine methylation patterns in genomic DNA samples. In the first method step, the genomic DNA is isolated from cells or other accompanying materials and bound essentially irreversibly to a surface. Then the DNA bound to the surface is treated, preferably with a bisulfite, in such a way that cytosine is converted into a base that is different in its base pairing behavior in the DNA duplex, while 5-methylcytosine remains unchanged. Then the reagents that were used are removed in a washing step. Finally, selected segments of the immobilized DNA are amplified in a polymerase reaction and the amplified products are investigated with respect to their sequence.

1 . A method for the analysis of cytosine methylation patterns in genomic DNA samples, said method comprising the steps of:
 a) isolating the genomic DNA from cells or other accompanying materials and immobilizing the isolated genomic DNA to a surface by covalent bonding;   b) treating the immobilized DNA in such a way that cytosine is converted into a base that is different in its base pairing behavior in the DNA duplex, while 5-methylcytosine remains unchanged;   c) removing the reagents used in step b) in a washing step;   d) amplifying selected segments of the immobilized DNA in a polymerase reaction;   e) investigating the amplified products with respect to their sequence.   
     
     
         2 . The method according to  claim 1 , further comprising the steps of:
 f) removing the reagents and products of the polymerase reaction in a washing step;   g) amplifying other selected segments of the immobilized DNA, which are different from those in step d), in a polymerase reaction;   h) investigating the amplified products with respect to their sequence.   
     
     
         3 . The method according to  claim 2 , further comprising repeating steps f)-g) several times, whereby in each amplification according to step g), segments other than those in one of the preceding amplifications are amplified. 
     
     
         4 . The method according to  claim 1 , wherein the treating step comprises treating the immobilized DNA with a bisulfite. 
     
     
         5 . The method according to  claim 1 , wherein the DNA is also isolated directly in the immobilizing step. 
     
     
         6 . The method according to  claim 5 , wherein the DNA is isolated from whole blood or blood serum. 
     
     
         7 . The method according to  claim 5 , wherein the DNA is isolated from lysed tissue. 
     
     
         8 . The method according to  claim 7 , wherein the lysis is conducted by means of proteinase K. 
     
     
         9 . The method according to  claim 1 , wherein the immobilization is conducted in the wells of a microtiter plate with 96 wells or 384 wells, in which different DNA samples are immobilized in the wells. 
     
     
         10 . The method according to  claim 1 , wherein the immobilization is conducted in PCR reaction wells, whereby different DNA samples are immobilized in the wells. 
     
     
         11 . The method according to  claim 1 , wherein the isolating of the DNA occurs on a metal oxide. 
     
     
         12 . The method according to  claim 1 , wherein the immobilization is made on a non-hydrophobic surface. 
     
     
         13 . The method according to  claim 1 , wherein the amplification step is conducted with several pairs of primers as a multiplex PCR. 
     
     
         14 . The method according to  claim 1 , wherein all amplified products of an immobilized DNA sample are pooled, and thus are jointly introduced to further analysis. 
     
     
         15 . The method according to  claim 14  wherein said further analysis involves the hybridization to an oligonucleotide array or PNA (peptide nucleic acid) array. 
     
     
         16 . The method according to  claim 1 , wherein the investigating step is conducted during the amplification by a realtime PCR method. 
     
     
         17 . The method according to  claim 1 , wherein the investigating step is conducted after the amplification in the same reaction well and comprises plotting a melting-point curve. 
     
     
         18 . The method according to  claim 1 , wherein the investigating step comprises allele-specific hybridization of oligonucleotides or PNAs (peptide nucleic acids) at the positions to be investigated in the amplified products. 
     
     
         19 . The method according to  claim 1 , wherein the investigating step comprises hybridization of oligonucleotide primers and a subsequent primer extension reaction or a sequencing reaction. 
     
     
         20 . A method for the conversion of unmethylated cytosine in genomic DNA samples, said method comprising the steps of:
 a) isolating the genomic DNA from cells or other accompanying materials and immobilizing the isolated genomic DNA to a surface by covalent bonding;   b) treating the immobilized DNA with a bisulfite in such a way that cytosine is converted into a base that is different in its base pairing behavior in the DNA duplex, while 5-methylcytosine remains unchanged; and   c) removing the reagents used in step b) in a washing step.   
     
     
         21 . A kit, comprised of a reagent for the treatment of DNA according to  claim 1 , at least two primer oligonucleotides for producing the amplified products, a solid phase for immobilizing the sample DNA, as well as, optionally, other solutions, and instructions for conducting an assay according to  claim 1 .