Measurement of distances between DNA segments for increasing the effectiveness of sequencing using hybridization on an oligonucleotide matrix

DNA sequencing by hybridization on oligonucleotide matrix (SHOM) makes use of a matrix of immobilized oligonucleotides. Yet the method is not directly applicable for sequencing of fragments with long monotonous repeats. Measurement of the distances between certain segments within the DNA fragment analyzed provide additional information for sequencing. This information can be obtained by digesting DNA with a set of restriction endonucleases, or by PCR with primers complementary to certain DNA regions, with subsequent measurement of the length of the resulting fragments in gel electrophoresis. Use of this additional information increases the reconstruction efficiency and in many cases solves the problem of repeating and monotonous segments within analyzed DNA fragment. The current work presents the use of this information and the estimated efficiency of its usage.