Related papers: Brush Effects on DNA Chips: Thermodynamics, Kineti…
Competitve 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…
We analyze a series of publicly available controlled experiments (Latin square) on Affymetrix high density oligonucleotide microarrays using a simple physical model of the hybridization process. We plot for each gene the signal intensity…
High-density oligonucleotide arrays are among the most rapidly expanding technologies in biology today. In the {\sl GeneChip} system, the reconstruction of the target concentration depends upon the differential signal generated from…
We investigate the effects of crowding on the conformations and assembly of confined, highly charged, and thick polyelectrolyte brushes in the osmotic regime. Particle tracking experiments on increasingly dense suspensions of colloids…
Test experiments of hybridization in DNA microarrays show systematic deviations from the equilibrium isotherms. We argue that these deviations are due to the presence of a partially hybridized long-lived state, which we include in a kinetic…
The hybridization and dehybridization of DNA subject to tension is relevant to fundamental genetic processes and to the design of DNA-based mechanobiology assays. While strong tension accelerates DNA melting and decelerates DNA annealing,…
While designing oligonucleotide-based microarrays, cross-hybridization between surface-bound oligos and non-intended labeled targets is probably the most difficult parameter to predict. Although literature describes rules-of-thumb…
Recent experiments have shown that trivalent ion, spermidine$^{3+}$, can provoke lateral microphase segregation in DNA brushes. Using molecular simulations and simple theoretical arguments, we explore the effects of trivalent counterions on…
Quantifying interactions in DNA microarrays is of central importance for a better understanding of their functioning. Hybridization thermodynamics for nucleic acid strands in aqueous solution can be described by the so-called…
The effect of target molecule depletion from the supernatant solution is incorporated into a physico-chemical model of hybridisation on oligonucleotide microarrays. Two possible regimes are identified: local depletion, in which depletion by…
Microarray-based genotyping is based on the high discrimination capability of oligonucleotide probes. For detection of Single Nucleotide Polymorphisms (SNPs) single-base discrimination is required. We investigate how various…
Background: Diagnostic DNA arrays for detection of point mutations as markers for cancer usually function in the presence of a large excess of wild type DNA. This excess can give rise to false positives due to competitive hybridization of…
We experimentally and theoretically consider highly condensed planar brushes made of charged polymers. Using x-ray reflectivity on polyelectrolytes which are anchored at the water-air interface, it is shown that such strongly stretched…
The lack of specificity in microarray experiments due to non-specific hybridization raises a serious problem for the analysis of microarray data because the residual chemical background intensity is not related to the expression degree of…
Gene expression analysis by means of microarrays is based on the sequence specific binding of mRNA to DNA oligonucleotide probes and its measurement using fluorescent labels. The binding of RNA fragments involving other sequences than the…
Protein brushes not only play a key role in the functionality of neurofilaments but also have wide applications in biomedical materials. Here, we investigate the effect of ionic strength on the morphology of protein brushes using a…
Understanding the effect of inhomogeneity on the charge regulation and dielectric properties, and how it depends on the conformational characteristics of the macromolecules is a long-standing problem. In order to address this problem, we…
We investigate polyelectrolyte brushes in the osmotic regime using both theoretical analysis and molecular dynamics simulation techniques. In the simulations at moderate Bjerrum length, we observe that the brush height varies weakly with…
Despite the success and popularity of oligonucleotide arrays as a high-throughput technique for measuring mRNA expression levels, quantitative calibration studies have until now been limited. The main reason is that suitable data was not…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…