title: Position dependent mismatch discrimination on DNA microarrays - experiments and model.
abstract: BACKGROUND
  The propensity of oligonucleotide strands to form stable duplexes with complementary sequences is fundamental to a variety of biological and biotechnological processes as various as microRNA signalling, microarray hybridization and PCR. Yet our understanding of oligonucleotide hybridization, in particular in presence of surfaces, is rather limited. Here we use oligonucleotide microarrays made in-house by optically controlled DNA synthesis to produce probe sets comprising all possible single base mismatches and base bulges for each of 20 sequence motifs under study.
  
  
  RESULTS
  We observe that mismatch discrimination is mostly determined by the defect position (relative to the duplex ends) as well as by the sequence context. We investigate the thermodynamics of the oligonucleotide duplexes on the basis of double-ended molecular zipper. Theoretical predictions of defect positional influence as well as long range sequence influence agree well with the experimental results.
  
  
  CONCLUSIONS
  Molecular zipping at thermodynamic equilibrium explains the binding affinity of mismatched DNA duplexes on microarrays well. The position dependent nearest neighbor model (PDNN) can be inferred from it. Quantitative understanding of microarray experiments from first principles is in reach.
authors.affiliation: Experimentalphysik I, Universität Bayreuth, D-95440 Bayreuth, Germany. thomas.naiser@googlemail.com
authors.forename: Thomas
authors.initials: T
authors.lastname: Naiser
authors.forename: Jona
authors.initials: J
authors.lastname: Kayser
authors.forename: Timo
authors.initials: T
authors.lastname: Mai
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Michel
authors.forename: Albrecht
authors.initials: A
authors.lastname: Ott
mesh_terms: D020137:Base Pair Mismatch; D004247:DNA / Q000737:chemistry / Q000235:genetics; D007700:Kinetics; D008957:Models, Genetic; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D013816:Thermodynamics
chemical_list: D004247:DNA