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Series GSE14547 Query DataSets for GSE14547
Status Public on Mar 01, 2009
Title The effects of mismatches on hybridization in DNA microarrays: determination of nearest neighbor parameters
Organism synthetic construct
Experiment type Other
Summary 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
 
Overall design 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.
 
Contributor(s) Hooyberghs J, Van Hummelen P, Carlon E
Citation(s) 19270064
Submission date Jan 23, 2009
Last update date Mar 20, 2012
Contact name Jef Hooyberghs
Organization name VITO nv
Street address Boeretang 200
City Mol
ZIP/Postal code 2400
Country Belgium
 
Platforms (4)
GPL8106 Agilent 8x15k synthetic construct custom array experiment 1
GPL8107 Agilent 8x15k synthetic construct custom array experiment 2
GPL8108 Agilent 8x15k synthetic construct custom array experiment 3
Samples (32)
GSM363880 experiment 1, oligo1a, 50PM, fragmentation performed
GSM363881 experiment 1, oligo1a, 100PM, fragmentation performed
GSM363882 experiment 1, oligo1a, 500PM, fragmentation performed
Relations
BioProject PRJNA111641

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE14547_RAW.tar 61.5 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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