Hybridization at a surface: the role of spacers in DNA microarrays.
Flexible spacer chains are utilized to enhance the hybridization of terminally anchored oligonucleotide probes of DNA microarrays. A polymer physics approach identifies an underlying mechanism and yields guidelines for the optimal spacer length in terms of the effect on the equilibrium state. For low grafting densities, the dominant effect arises because of the decimation in the number of accessible chain configurations due to the impenetrable surface. Opposing trends are found for long targets and for short targets. At higher grafting densities, different brush regimes introduce an extra hybridization penalty. A novel brush regime is obtained for long neutral spacers and short targets at intermediate ionic strength where the chain stretching is due to the electrostatic interactions between the probes.
Halperin
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Structures et Propriétés d'Architectures Moléculaires, UMR 5819 (CEA, CNRS, UJF), DRFMC/SPrAM, CEA-Grenoble, 38054 Grenoble Cedex 9, France.
Buhot
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A
Zhulina
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EB
D008956:Models, Chemical; D009693:Nucleic Acid Hybridization / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D015345:Oligonucleotide Probes / Q000737:chemistry*
D015345:Oligonucleotide Probes