  Microarray-based genotyping is based on the high discrimination capability of
oligonucleotide probes. For detection of Single Nucleotide Polymorphisms (SNPs)
single-base discrimination is required. We investigate how various
point-mutations, comprising single base mismatches (MMs), insertions and
deletions, affect hybridization of DNA-DNA oligonucleotide duplexes. Employing
light-directed in situ synthesis we fabricate DNA microarrays with
comprehensive sets of cognate point-mutated probes, allowing us to
systematically investigate the influence of defect type, position and nearest
neighbor effects. Defect position has been identified as the dominating
influential factor. This positional effect which is almost identical for the
different point-mutation types, is biased from the local sequence environment.
The impact of the MM type is largely determined by the type of base pair
(either AT or CG) affected by the mismatch. We observe that single base
insertions next to like-bases result in considerably larger hybridization
signals than insertions next to nonidentical bases. The latter as well as the
distinct position dependence could be explained by a kinetic zipper model in
which point defects represent a barrier for the rapid closure of the DNA
duplex.
