Method for Determining the Methylation Pattern of a Polynucleic Acid

Abstract

Particular aspects relate to a method for determining the methylation pattern of a polynucleic acid, comprising: a) preparing a solution comprising a mixture of fragments of the polynucleic acid; b) coupling the fragments with a substance being detectable with a detection method; c) contacting a solution comprising the fragments of b) with a DNA microarray having a plurality of different immobilized oligonucleotides, each comprising at least one methylation site, at respectively assigned different locations thereon, the contacting under conditions affording hybridization of fragments with correlated immobilized oligonucleotides under defined stringency, and wherein the immobilized oligonucleotides have a length of less than 200 bases; d) optionally performing a washing step; and e) detecting, using the physical detection method, such immobilized nucleic acids to which solution fragments are hybridized and/or to which solution fragments are not hybridized.

1 . An oligonucleotide array made according to a method for making an oligonucleotide array, comprising:
 a) testing the genome of an organism for first partial sequences that are bordered by restriction sites of one or more first restriction enzymes used for DNA fragmentation, and which have a length of about 100 to about 1200 base pairs, wherein said first partial sequences are selected;   b) excluding from the selected first partial sequences those sequences that comprise more than about 50% repeats, or more than about 20% repeats to provide for a group of second partial sequences for making the oligonucleotide array, and wherein a) and b) can be in any order.   
     
     
         2 . The oligonucleotide array of  claim 1  wherein the selected oligonucleotides have a length of about 15 to about 80 bases, or about 20 to about 30 bases. 
     
     
         3 . The oligonucleotide array of  claim 1  wherein the immobilized oligonucleotides have been synthesized on the substrate of the array. 
     
     
         4 . The oligonucleotide array of  claim 1  wherein the array exclusively comprises oligonucleotide sequences which hybridize in constant to each other defined distances on a corresponding analyzed complementary DNA, providing a tiling array.