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Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/14416

Title: Probing hybridization parameters from microarray experiments: nearest-neighbor model and beyond
Authors: Hadiwikarta, W. W.
Walter, J. -C.
Carlon, E.
Issue Date: 2012
Citation: NUCLEIC ACIDS RESEARCH, 40 (18), p. e138
Abstract: In this article, it is shown how optimized and dedicated microarray experiments can be used to study the thermodynamics of DNA hybridization for a large number of different conformations in a highly parallel fashion. In particular, free energy penalties for mismatches are obtained in two independent ways and are shown to be correlated with values from melting experiments in solution reported in the literature. The additivity principle, which is at the basis of the nearest-neighbor model, and according to which the penalty for two isolated mismatches is equal to the sum of the independent penalties, is thoroughly tested. Additivity is shown to break down for a mismatch distance below 5 nt. The behavior of mismatches in the vicinity of the helix edges, and the behavior of tandem mismatches are also investigated. Finally, some thermodynamic outlying sequences are observed and highlighted. These sequences contain combinations of GA mismatches. The analysis of the microarray data reported in this article provides new insights on the DNA hybridization parameters and can help to increase the accuracy of hybridization-based technologies.
Notes: [Hadiwikarta, W. W.; Walter, J. -C.; Carlon, E.] KULeuven, Inst Theoret Phys, B-3001 Louvain, Belgium. [Hooyberghs, J.] Hasselt Univ, Dept WNI, B-3590 Diepenbeek, Belgium. [Hadiwikarta, W. W.; Hooyberghs, J.] VITO, Flemish Inst Technol Res, B-2400 Mol, Belgium. enrico.carlon@fys.kuleuven.be
URI: http://hdl.handle.net/1942/14416
DOI: 10.1093/nar/gks475
ISI #: 000309927100002
ISSN: 0305-1048
Category: A1
Type: Journal Contribution
Validation: ecoom, 2013
Appears in Collections: Research publications

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