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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 complementary sequence and other spots with one or two mismatches: 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. Keywords: experiment to assess technical aspects of hybridization in microarrays The study consists of four experiments. Each experiments consists of one slide with eight identical microarrays which were hybridized with an identical solution but at a different concentration. Per experiment a single target sequence in solution was used for hybridization: target1 to target4 (Table 1 main manuscript or description of samples below). Each target oligo was bought in duplicate, referred to as oligos a and b. In experiment 1 and 2 a fragmentation step (f) was applied. More details can be found in the main manuscript especially Table 3.

ORGANISM(S): synthetic construct

SUBMITTER: Paul Van Hummelen

PROVIDER: E-GEOD-14547 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The effects of mismatches on hybridization in DNA microarrays: determination of nearest neighbor parameters.

Hooyberghs J J Van Hummelen P P Carlon E E

Nucleic acids research 20090306 7

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 o ...[more]

PMID: 19270064

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Project description:This series represents the data set from the paper Assembly of microarrays for genome-wide measurement of DNA copy number appearing in Nat Genet 2001 Nov;29(3):263-4 and it's web supplement. Specimen procurement, labeling, hybridization and imaging protocols from Nat Genet 2001 Nov;29(3):263-4 web supplement: Specimens. We obtained GM03563, GM00143, GM05296, GM07408, GM01750, GM03134, GM13330, GM03576, GM01535, GM07081, GM02948, GM04435, GM10315, GM13031 and GM01524 cell strains from the NIGMS Human Genetics Cell Repository (Coriell Institute for Medical Research), and cultured them under the recommended conditions. We cultured cell lines BT474, HCT116, T47D, MPE600, COLO320, SW837, MDA-MB-231, MDA-MB-453 and HT29 under the recommended conditions. 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The effects of mismatches on hybridization in DNA microarrays: determination of nearest neighbor parameters

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The effects of mismatches on hybridization in DNA microarrays: determination of nearest neighbor parameters.

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