dorsal/arxiv
View SchemaHybridization to surface-bound oligonucleotide probes: Influence of point defects
| Authors | Thomas Naiser, Oliver Ehler, Timo Mai, Wolfgang Michel, Albrecht Ott |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0612043 |
| URL | https://arxiv.org/abs/q-bio/0612043 |
Abstract
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.
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"abstract": "Microarray-based genotyping is based on the high discrimination capability of\noligonucleotide probes. For detection of Single Nucleotide Polymorphisms (SNPs)\nsingle-base discrimination is required. We investigate how various\npoint-mutations, comprising single base mismatches (MMs), insertions and\ndeletions, affect hybridization of DNA-DNA oligonucleotide duplexes. Employing\nlight-directed in situ synthesis we fabricate DNA microarrays with\ncomprehensive sets of cognate point-mutated probes, allowing us to\nsystematically investigate the influence of defect type, position and nearest\nneighbor effects. Defect position has been identified as the dominating\ninfluential factor. This positional effect which is almost identical for the\ndifferent point-mutation types, is biased from the local sequence environment.\nThe impact of the MM type is largely determined by the type of base pair\n(either AT or CG) affected by the mismatch. We observe that single base\ninsertions next to like-bases result in considerably larger hybridization\nsignals than insertions next to nonidentical bases. The latter as well as the\ndistinct position dependence could be explained by a kinetic zipper model in\nwhich point defects represent a barrier for the rapid closure of the DNA\nduplex.",
"arxiv_id": "q-bio/0612043",
"authors": [
"Thomas Naiser",
"Oliver Ehler",
"Timo Mai",
"Wolfgang Michel",
"Albrecht Ott"
],
"categories": [
"q-bio.BM",
"q-bio.GN"
],
"title": "Hybridization to surface-bound oligonucleotide probes: Influence of point defects",
"url": "https://arxiv.org/abs/q-bio/0612043"
},
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