dorsal/arxiv
View SchemaBrush Effects on DNA Chips: Thermodynamics, Kinetics and Design Guidlines
| Authors | A. Halperin, A. Buhot, E. B. Zhulina |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0504002 |
| URL | https://arxiv.org/abs/q-bio/0504002 |
| DOI | 10.1529/biophysj.105.063479 |
Abstract
In biology experiments, oligonucleotide microarrays are contacted with a solution of long nucleic acid (NA) targets. The hybridized probes thus carry long tails. When the surface density of the oligonucleotide probes is high enough, the progress of hybridization leads to the formation of a polyelectrolyte brush due to mutual crowding of the NA tails. The free energy penalty associated with the brush modifies both the hybridization isotherms and the rate equations: the attainable hybridization is lowered significantly as is the hybridization rate. While the equilibrium hybridization fraction, $x_{eq}$, is low, the hybridization follows a Langmuir type isotherm, $x_{eq}/(1-x_{eq}) = c_t K$ where $c_t$ is the target concentration and $K$ is the equilibrium constant smaller than its bulk value by a factor $(n/N)^{2/5}$ due to wall effects where $n$ and $N$ denote the number of bases in the probe and the target. At higher $x_{eq}$, when the brush is formed, the leading correction is $x_{eq}/(1-x_{eq}) = c_t K \exp [ - const' (x_{eq}^{2/3} - x_B^{2/3})]$ where $x_B$ corresponds to the onset of the brush regime. The denaturation rate constant in the two regimes are identical. However, the hybridization rate constant in the brush regime is lower, the leading correction being $\exp [- const' (x^{2/3} - x_B^{2/3})]$.
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"abstract": "In biology experiments, oligonucleotide microarrays are contacted with a\nsolution of long nucleic acid (NA) targets. The hybridized probes thus carry\nlong tails. When the surface density of the oligonucleotide probes is high\nenough, the progress of hybridization leads to the formation of a\npolyelectrolyte brush due to mutual crowding of the NA tails. The free energy\npenalty associated with the brush modifies both the hybridization isotherms and\nthe rate equations: the attainable hybridization is lowered significantly as is\nthe hybridization rate. While the equilibrium hybridization fraction, $x_{eq}$,\nis low, the hybridization follows a Langmuir type isotherm, $x_{eq}/(1-x_{eq})\n= c_t K$ where $c_t$ is the target concentration and $K$ is the equilibrium\nconstant smaller than its bulk value by a factor $(n/N)^{2/5}$ due to wall\neffects where $n$ and $N$ denote the number of bases in the probe and the\ntarget. At higher $x_{eq}$, when the brush is formed, the leading correction is\n$x_{eq}/(1-x_{eq}) = c_t K \\exp [ - const\u0027 (x_{eq}^{2/3} - x_B^{2/3})]$ where\n$x_B$ corresponds to the onset of the brush regime. The denaturation rate\nconstant in the two regimes are identical. However, the hybridization rate\nconstant in the brush regime is lower, the leading correction being $\\exp [-\nconst\u0027 (x^{2/3} - x_B^{2/3})]$.",
"arxiv_id": "q-bio/0504002",
"authors": [
"A. Halperin",
"A. Buhot",
"E. B. Zhulina"
],
"categories": [
"q-bio.GN",
"cond-mat.soft",
"q-bio.QM"
],
"doi": "10.1529/biophysj.105.063479",
"title": "Brush Effects on DNA Chips: Thermodynamics, Kinetics and Design Guidlines",
"url": "https://arxiv.org/abs/q-bio/0504002"
},
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