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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
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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
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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.
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Contributor(s) |
Hooyberghs J, Van Hummelen P, Carlon E |
Citation(s) |
19270064 |
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Submission date |
Jan 23, 2009 |
Last update date |
Mar 20, 2012 |
Contact name |
Jef Hooyberghs |
Organization name |
VITO nv
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Street address |
Boeretang 200
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City |
Mol |
ZIP/Postal code |
2400 |
Country |
Belgium |
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Platforms (4)
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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 |
GPL8109 |
Agilent 8x15k synthetic construct custom array experiment 4 |
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Samples (32)
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GSM363880 |
experiment 1, oligo1a, 50PM, fragmentation performed |
GSM363881 |
experiment 1, oligo1a, 100PM, fragmentation performed |
GSM363882 |
experiment 1, oligo1a, 500PM, fragmentation performed |
GSM363883 |
experiment 1, oligo1a, 1000PM, fragmentation performed |
GSM363884 |
experiment 1, oligo1a, 2500PM, fragmentation performed |
GSM363885 |
experiment 1, oligo1a, 5000PM, fragmentation performed |
GSM363886 |
experiment 1, oligo1a, 7500PM, fragmentation performed |
GSM363887 |
experiment 1, oligo1a, 10000PM, fragmentation performed |
GSM363888 |
experiment 2, oligo2a, 50PM, fragmentation performed |
GSM363889 |
experiment 2, oligo2a, 1000PM, fragmentation performed |
GSM363890 |
experiment 2, oligo2a, 5000PM, fragmentation performed |
GSM363891 |
experiment 2, oligo2a, 10000PM, fragmentation performed |
GSM363892 |
experiment 2, oligo2b, 50PM, fragmentation performed |
GSM363893 |
experiment 2, oligo2b, 1000PM, fragmentation performed |
GSM363894 |
experiment 2, oligo2b, 5000PM, fragmentation performed |
GSM363895 |
experiment 2, oligo2b, 10000PM, fragmentation performed |
GSM363896 |
experiment 3, oligo3a, 50PM, no fragmentation |
GSM363897 |
experiment 3, oligo3a, 1000PM, no fragmentation |
GSM363898 |
experiment 3, oligo3a, 5000PM, no fragmentation |
GSM363899 |
experiment 3, oligo3a, 10000PM, no fragmentation |
GSM363900 |
experiment 3, oligo3b, 50PM, no fragmentation |
GSM363901 |
experiment 3, oligo3b, 1000PM, no fragmentation |
GSM363902 |
experiment 3, oligo3b, 5000PM, no fragmentation |
GSM363903 |
experiment 3, oligo3b, 10000PM, no fragmentation |
GSM363904 |
experiment 4, oligo4a, 50PM, no fragmentation |
GSM363905 |
experiment 4, oligo4a, 100PM, no fragmentation |
GSM363906 |
experiment 4, oligo4a, 500PM, no fragmentation |
GSM363907 |
experiment 4, oligo4a, 1000PM, no fragmentation |
GSM363908 |
experiment 4, oligo4b, 50PM, no fragmentation |
GSM363909 |
experiment 4, oligo4b, 100PM, no fragmentation |
GSM363910 |
experiment 4, oligo4b, 500PM, no fragmentation |
GSM363911 |
experiment 4, oligo4b, 1000PM, no fragmentation |
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Relations |
BioProject |
PRJNA111641 |
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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