help button home button Biophys. J.
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
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 Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Halperin, A.
Right arrow Articles by Zhulina, E.B.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Halperin, A.
Right arrow Articles by Zhulina, E.B.
Biophysical Journal 86:718-730 (2004)
© 2004 The Biophysical Society

Sensitivity, Specificity, and the Hybridization Isotherms of DNA Chips

A. Halperin *, A. Buhot * and E.B. Zhulina {dagger}

* Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique, Université Joseph Fourier, Grenoble, France and {dagger} Institute of Macromolecular Compounds of the Russian Academy of Sciences, St. Petersburg, Russia

Correspondence: Address reprint requests to Dr. Avraham S. Halperin, CNRS, SPrAM, DRFMC-SI3M/CEA-Grenoble, 17 rue des Martyrs, Grenoble 38054, France. Tel.: 33-47-644-0696; E-mail: ahalperin{at}cea.fr.

Competitive hybridization, at the surface and in the bulk, lowers the sensitivity of DNA chips. Competitive surface hybridization occurs when different targets can hybridize with the same probe. Competitive bulk hybridization takes place when the targets can hybridize with free complementary chains in the solution. The effects of competitive hybridization on the thermodynamically attainable performance of DNA chips are quantified in terms of the hybridization isotherms of the spots. These relate the equilibrium degree of the hybridization to the bulk composition. The hybridization isotherm emerges as a Langmuir isotherm modified for electrostatic interactions within the probe layer. The sensitivity of the assay in equilibrium is directly related to the slope of the isotherm. A simpler description is possible, in terms of c50 values specifying the bulk composition corresponding to 50% hybridization at the surface. The effects of competitive hybridization are important for the quantitative analysis of DNA chip results, especially when used to study point mutations.




This article has been cited by other articles:


Home page
 BioinformaticsHome page
N. Ono, S. Suzuki, C. Furusawa, T. Agata, A. Kashiwagi, H. Shimizu, and T. Yomo
An improved physico-chemical model of hybridization on high-density oligonucleotide microarrays
Bioinformatics, May 15, 2008; 24(10): 1278 - 1285.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
P. Gong and R. Levicky
DNA surface hybridization regimes
PNAS, April 8, 2008; 105(14): 5301 - 5306.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
J. Bishop, A. M. Chagovetz, and S. Blair
Kinetics of Multiplex Hybridization: Mechanisms and Implications
Biophys. J., March 1, 2008; 94(5): 1726 - 1734.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
M. I. Glazer, J. A. Fidanza, G. H. McGall, M. O. Trulson, J. E. Forman, and C. W. Frank
Kinetics of Oligonucleotide Hybridization to DNA Probe Arrays on High-Capacity Porous Silica Substrates
Biophys. J., September 1, 2007; 93(5): 1661 - 1676.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
E. B. Zhulina and F. A. M. Leermakers
Effect of the Ionic Strength and pH on the Equilibrium Structure of a Neurofilament Brush
Biophys. J., September 1, 2007; 93(5): 1452 - 1463.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
J. B. Fiche, A. Buhot, R. Calemczuk, and T. Livache
Temperature Effects on DNA Chip Experiments from Surface Plasmon Resonance Imaging: Isotherms and Melting Curves
Biophys. J., February 1, 2007; 92(3): 935 - 946.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
J. Bishop, C. Wilson, A. M. Chagovetz, and S. Blair
Competitive Displacement of DNA during Surface Hybridization
Biophys. J., January 1, 2007; 92(1): L10 - L12.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. Abdueva, D. Skvortsov, and S. Tavare
Non-linear analysis of GeneChip arrays
Nucleic Acids Res., September 10, 2006; 34(15): e105 - e105.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
J. Bishop, S. Blair, and A. M. Chagovetz
A Competitive Kinetic Model of Nucleic Acid Surface Hybridization in the Presence of Point Mutants
Biophys. J., February 1, 2006; 90(3): 831 - 840.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
G. A. Held, G. Grinstein, and Y. Tu
Relationship between gene expression and observed intensities in DNA microarrays--a modeling study.
Nucleic Acids Res., January 1, 2006; 34(9): e70 - e70.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
A. Halperin, A. Buhot, and E. B. Zhulina
Brush Effects on DNA Chips: Thermodynamics, Kinetics, and Design Guidelines
Biophys. J., August 1, 2005; 89(2): 796 - 811.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
H. Binder and S. Preibisch
Specific and Nonspecific Hybridization of Oligonucleotide Probes on Microarrays
Biophys. J., July 1, 2005; 89(1): 337 - 352.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Chem.Home page
A. Halperin, A. Buhot, and E. B. Zhulina
Hybridization Isotherms of DNA Microarrays and the Quantification of Mutation Studies
Clin. Chem., December 1, 2004; 50(12): 2254 - 2262.
[Abstract] [Full Text] [PDF]


HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
Copyright © 2004 by the Biophysical Society.