Comparison of complex DNA mixtures with generic oligonucleotide microchips

The reproducibility of melting curves for repeated hybridizations of target DNA with generic oligonucleotide microchips is shown experimentally to dep end on the character of matching between fragments of target DNA and immobi lized oligonucleotides. The reproducibility of melting curves is higher for the perfect match duplexes and decreases as the number of mismatched pairs within duplexes increases. This effect was applied to the comparative anal ysis of complex DNA mixtures. We developed a scheme in which we can identif y and discriminate between the probe oligonucleotides responsible for the d istinctions between target DNA mixtures. A scheme is illustrated by compari ng DNA mixtures corresponding to V-D-J genes connected with populations of mRNAs CDR3 TCR Vb (T-cell receptor beta complementarity determining region 3) from the thymus and pancreas of NOD mice. Our results demonstrate that g eneric microchips can be applied efficiently to the analysis of DNA mixture s.