Skip Navigation



Nucleic Acids Research Advance Access published online on March 6, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp109
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (1773K) Freely available
Right arrow Screen PDF (1792K) Freely available
Right arrow Supplementary Data
Right arrow All Versions of this Article:
37/7/e53    most recent
gkp109v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Hooyberghs, J.
Right arrow Articles by Carlon, E.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Hooyberghs, J.
Right arrow Articles by Carlon, E.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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

J. Hooyberghs1,2,*, P. Van Hummelen3 and E. Carlon1

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 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. (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14547)

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.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.