title: The effects of mismatches on hybridization in DNA microarrays: determination of nearest neighbor parameters.
abstract: Quantifying interactions in DNA microarrays is of central importance for a better understanding of their functioning. Hybridization thermodynamics for nucleic acid strands in aqueous solution can be described by the so-called nearest neighbor model, which estimates the hybridization free energy of a given sequence as a sum of dinucleotide terms. Compared with its solution counterparts, hybridization in DNA microarrays may be hindered due to the presence of a solid surface and of a high density of DNA strands. We present here a study aimed at the determination of hybridization free energies in DNA microarrays. Experiments are performed on custom Agilent slides. The solution contains a single oligonucleotide. The microarray contains spots with a perfect matching (PM) complementary sequence and other spots with one or two mismatches (MM) : in total 1006 different probe spots, each replicated 15 times per microarray. The free energy parameters are directly fitted from microarray data. The experiments demonstrate a clear correlation between hybridization free energies in the microarray and in solution. The experiments are fully consistent with the Langmuir model at low intensities, but show a clear deviation at intermediate (non-saturating) intensities. These results provide new interesting insights for the quantification of molecular interactions in DNA microarrays.
authors.affiliation: Institute for Theoretical Physics, Katholieke Universiteit Leuven, Leuven, Belgium. jef.hooyberghs@vito.be
authors.forename: J
authors.initials: J
authors.lastname: Hooyberghs
authors.forename: P
authors.initials: P
authors.lastname: Van Hummelen
authors.forename: E
authors.initials: E
authors.lastname: Carlon
mesh_terms: D020137:Base Pair Mismatch; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards; D015345:Oligonucleotide Probes / Q000737:chemistry; D011786:Quality Control; D013816:Thermodynamics
chemical_list: D015345:Oligonucleotide Probes