Nucleic Acids Research Advance Access originally published online on March 6, 2009
Nucleic Acids Research 2009 37(7):e53; doi:10.1093/nar/gkp109
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2009, Vol. 37, No. 7 e53
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Methods Online |
The effects of mismatches on hybridization in DNA microarrays: determination of nearest neighbor parameters
1Institute for Theoretical Physics, Katholieke Universiteit Leuven, Celestijnenlaan 200D, B-3001 Leuven, 2Flemish Institute for Technological Research (VITO), Boeretang 200, B-2400 Mol and 3MicroArray Facility, VIB, Herestraat 49, B-3000 Leuven, Belgium
*To whom correspondence should be addressed. Tel: +32 14 33 5277; Fax: +32 14 58 2657; Email: jef.hooyberghs{at}vito.be
Received October 15, 2008. Revised February 3, 2009. Accepted February 3, 2009.
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.
The microarray data discussed in this publication have been deposited in NCBI's; Gene Expression Omnibus and are accessible through GEO Series accession number GSE14547 [NCBI GEO] . (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14547)