Biology – Quantitative Biology – Biomolecules
Scientific paper
2011-07-08
J. Phys. Chem. B, 2011, 115 (20), pp 6732--6739
Biology
Quantitative Biology
Biomolecules
27 pages, 9 figures, 1 table
Scientific paper
10.1021/jp2014034
It has recently been shown that in some DNA microarrays the time needed to reach thermal equilibrium may largely exceed the typical experimental time, which is about 15h in standard protocols (Hooyberghs et al. Phys. Rev. E 81, 012901 (2010)). In this paper we discuss how this breakdown of thermodynamic equilibrium could be detected in microarray experiments without resorting to real time hybridization data, which are difficult to implement in standard experimental conditions. The method is based on the analysis of the distribution of fluorescence intensities I from different spots for probes carrying base mismatches. In thermal equilibrium and at sufficiently low concentrations, log I is expected to be linearly related to the hybridization free energy $\Delta G$ with a slope equal to $1/RT_{exp}$, where $T_{exp}$ is the experimental temperature and R is the gas constant. The breakdown of equilibrium results in the deviation from this law. A model for hybridization kinetics explaining the observed experimental behavior is discussed, the so-called 3-state model. It predicts that deviations from equilibrium yield a proportionality of $\log I$ to $\Delta G/RT_{eff}$. Here, $T_{eff}$ is an effective temperature, higher than the experimental one. This behavior is indeed observed in some experiments on Agilent arrays. We analyze experimental data from two other microarray platforms and discuss, on the basis of the results, the attainment of equilibrium in these cases. Interestingly, the same 3-state model predicts a (dynamical) saturation of the signal at values below the expected one at equilibrium.
Carlon Enrico
Hooyberghs Jef
Kroll Myriam K.
Walter Jean-Charles
No associations
LandOfFree
Nonequilibrium effects in DNA microarrays: a multiplatform study does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.
If you have personal experience with Nonequilibrium effects in DNA microarrays: a multiplatform study, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Nonequilibrium effects in DNA microarrays: a multiplatform study will most certainly appreciate the feedback.
Profile ID: LFWR-SCP-O-222442