Thermodynamics of RNA/DNA hybridization in high density oligonucleotide microarrays

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 versus the hybridization free energy of RNA/DNA duplexes in solution, for perfect matching and mismatching probes. Both values tend to align on a single master curve in good agreement with Langmuir adsorption theory, provided one takes into account the decrease of the effective target concentration due to target-target hybridization in solution. We give an example of a deviation from the expected thermodynamical behavior for the probe set 1091\_at due to annotation problems, i.e. the surface-bound probe is not the exact complement of the target RNA sequence, because of errors present in public databases at the time when the array was designed. We show that the parametrization of the experimental data with RNA/DNA free energy improves the quality of the fits and enhances the stability of the fitting parameters compared to previous studies.Comment: 11 pages, 16 figures - final version as publishe

Sensitivity, Specificity and the Hybridization Isotherms of DNA Chips

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 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 $c_{50}$s 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.Comment: 18 pages and 7 figures. To be published in Biophys.

Free energy of DNA duplex formation on short oligonucleotide microarrays

DNA/DNA duplex formation is the basic mechanism that is used in genome tiling arrays and SNP arrays manufactured by Affymetrix. However, detailed knowledge of the physical process is still lacking. In this study, we show a free energy analysis of DNA/DNA duplex formation these arrays based on the positional-dependent nearest-neighbor (PDNN) model, which was developed previously for describing DNA/RNA duplex formation on expression microarrays. Our results showed that the two ends of a probe contribute less to the stability of the duplexes and that there is a microarray surface effect on binding affinities. We also showed that free energy cost of a single mismatch depends on the bases adjacent to the mismatch site and obtained a comprehensive table of the cost of a single mismatch under all possible combination of adjacent bases. The mismatch costs were found to be correlated with those determined in aqueous solution. We further demonstrate that the DNA copy number estimated from the SNP array correlates negatively with the target length; this is presumably caused by inefficient PCR amplification for long fragments. These results provide important insights into the molecular mechanisms of microarray technology and have implications for microarray design and the interpretation of observed data

The effects of mismatches on hybridization in DNA microarrays: determination of nearest neighbor parameters

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 nearest-neighbor model, which estimates the hybridization free energy of a given sequence as a sum of dinucleotide terms. Compared with its solution counterparts, hybridization in DNA microarrays may be hindered due to the presence of a solid surface and of a high density of DNA strands. We present here a study aimed at the determination of hybridization free energies in DNA microarrays. Experiments are performed on custom Agilent slides. The solution contains a single oligonucleotide. The microarray contains spots with a perfect matching complementary sequence and other spots with one or two mismatches: in total 1006 different probe spots, each replicated 15 times per microarray. The free energy parameters are directly fitted from microarray data. The experiments demonstrate a clear correlation between hybridization free energies in the microarray and in solution. The experiments are fully consistent with the Langmuir model at low intensities, but show a clear deviation at intermediate (non-saturating) intensities. These results provide new interesting insights for the quantification of molecular interactions in DNA microarrays.Comment: 31 pages, 5 figure

Explaining differences in saturation levels for Affymetrix GeneChip® arrays

The experimental spike-in studies of microarray hybridization conducted by Affymetrix demonstrate a nonlinear response of fluorescence intensity signal to target concentration. Several theoretical models have been put forward to explain these data. It was shown that the Langmuir adsorption isotherm recapitulates a general trend of signal response to concentration. However, this model fails to explain some key properties of the observed signal. In particular, according to the simple Langmuir isotherm, all probes should saturate at the same intensity level. However, this effect was not observed in the publicly available Affymetrix spike-in data sets. On the contrary, it was found that the saturation intensities vary greatly and can be predicted based on the probe sequence composition. In our experimental study, we attempt to account for the unexplained variation in the observed probe intensities using customized fluidics scripts. We explore experimentally the effect of the stringent wash, target concentration and hybridization time on the final microarray signal. The washing effect is assessed by scanning chips both prior to and after the stringent wash. Selective labeling of both specific and non-specific targets allows the visualization and investigation of the washing effect for both specific and non-specific signal components. We propose a new qualitative model of the probe-target hybridization mechanism that is in agreement with observed hybridization and washing properties of short oligonucleotide microarrays. This study demonstrates that desorption of incompletely bound targets during the washing cycle contributes to the observed difference in saturation levels

Washout policies in long-term indwelling urinary catheterisation in adults

Background  People requiring long-term bladder draining with an indwelling catheter can experience catheter blockage. Regimens involving different solutions can be used to wash out catheters with the aim of preventing blockage. This is an update of a review published in 2010.  Objectives  To determine if certain washout regimens are better than others in terms of effectiveness, acceptability, complications, quality of life and critically appraise and summarise economic evidence for the management of long-term indwelling urinary catheterisation in adults.  Search methods  We searched the Cochrane Incontinence Group Specialised Trials Register, which contains trials identified from the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, MEDLINE In-Process, MEDLINE Epub Ahead of Print, CINAHL, ClinicalTrials.gov, WHO ICTRP and handsearching of journals and conference proceedings to 23 May 2016. We also examined all reference lists of identified trials and contacted manufacturers and researchers in the field.  Selection criteria  All randomised and quasi-randomised trials comparing catheter washout policies (e.g. washout versus no washout, different washout solutions, frequency, duration, volume, concentration, method of administration) in adults (aged 16 years and above) in any setting (i.e. hospital, nursing/residential home, community) with an indwelling urethral or suprapubic catheter for more than 28 days.  Data collection and analysis  Two review authors independently extracted data. Disagreements were resolved by discussion. Data were assessed and analysed as described in theCochrane Handbook. If data in trials were not fully reported, clarification was sought from the study authors. For categorical outcomes, the numbers reporting an outcome were related to the numbers at risk in each group to derive a risk ratio (RR). For continuous outcomes, means and standard deviations were used to derive mean differences (MD).  Main results  We included seven trials involving a total of 349 participants, 217 of whom completed the studies. Three were cross-over and four were parallel-group randomised controlled trials (RCTs). Of these, two trials were added for this update (one parallel-group RCT with 40 participants and one cross-over RCT with 67 participants). Analyses of three cross-over trials yielded suboptimal results because they were based on between-group differences rather than individual participants' differences for sequential interventions. Two parallel-group trials had limited clinical value: one combined results for suprapubic and urethral catheters and the other provided data for only four participants. Only one trial was free of significant methodological limitations, but there were difficulties with recruitment and maintaining participants in this study.  The included studies reported data on six of the nine primary and secondary outcome measures. None of the trials addressed: number of catheters used, washout acceptability measures (including patient satisfaction, patient discomfort, pain and ease of use), or health status/measures of psychological health; very limited data were collected for health economic outcomes. Trials assessed only three of the eight intervention comparisons identified. Two trials reported in more than one comparison group.  Four trials compared washout (either saline or acidic solution) with no washout. We are uncertain if washout solutions (saline or acidic), compared to no washout solutions, has an important effect on the rate of symptomatic urinary tract infection or length of time each catheter was in situ because the results are imprecise.  Four trials compared different types of washout solution; saline versus acidic solutions (2 trials); saline versus acidic solution versus antibiotic solution (1 trial); saline versus antimicrobial solution (1 trial). We are uncertain if type of washout solution has an important effect on the rate of symptomatic urinary tract infection or length of time each catheter was in situ because the results are imprecise.  One trial compared different compositions of acidic solution (stronger versus weaker solution). We are uncertain if different compositions of acidic solutions has an important effect on the rate of symptomatic urinary tract infection or length of time each catheter was in situ because only 14 participants (of 25 who were recruited) completed this 12 week, three arm trial.  Four studies reported on possible harmful effects of washout use, such as blood in the washout solution, changes in blood pressure and bladder spasms.  There were very few small trials that met the review inclusion criteria. The high risk of bias of the included studies resulted in the evidence being graded as low or very low quality.  Authors' conclusions  Data from seven trials that compared different washout policies were limited, and generally, of poor methodological quality or were poorly reported. The evidence was not adequate to conclude if washouts were beneficial or harmful. Further rigorous, high quality trials that are adequately powered to detect benefits from washout being performed as opposed to no washout are needed. Trials comparing different washout solutions, washout volumes, and frequencies or timings are also needed

Kinetics and thermodynamics of DNA hybridization on gold nanoparticles

Hybridization of single-stranded DNA immobilized on the surface of gold nanoparticles (GNPs) into double stranded DNA and its subsequent dissociation into ssDNA were investigated. Melting curves and rates of dissociation and hybridization were measured using fluorescence detection based on hybridization-induced fluorescence change. Two distribution functions, namely the state distribution and the rate distribution, were proposed in order to take interfacial heterogeneity into account and to quantitatively analyze the data. Reaction and activation enthalpies and entropies of DNA hybridization and dissociation on GNPs were derived and compared with the same quantities in solution. Our results show that the interaction between GNPs and DNA reduces the energetic barrier and accelerates the dissociation of adhered DNA. At low surface densities of ssDNA adhered to GNP surface, the primary reaction pathway is that ssDNA in solution first adsorbs onto the GNP, and then diffuses along the surface until hybridizing with an immobilized DNA. We also found that the secondary structure of a DNA hairpin inhibits the interaction between GNPs and DNA and enhances the stability of the DNA hairpin adhered to GNPs

Random-Matrix Theory of Quantum Size Effects on Nuclear Magnetic Resonance in Metal Particles

The distribution function of the local density of states is computed exactly for the Wigner-Dyson ensemble of random Hamiltonians. In the absence of time-reversal symmetry, precise agreement is obtained with the "supersymmetry" theory by Efetov and Prigodin of the NMR lineshape in disordered metal particles. Upon breaking time-reversal symmetry, the variance of the Knight shift in the smallest particles is reduced by a universal factor of 2/3. ***To be published in Physical Review B.****Comment: 4 pages, REVTeX-3.0, 1 postscript figure, INLO-PUB-940819; [2017: figure included in text

Nonequilibrium effects in DNA microarrays: a multiplatform study

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.Comment: 27 pages, 9 figures, 1 tabl

Non-linear analysis of GeneChip arrays

The application of microarray hybridization theory to Affymetrix GeneChip data has been a recent focus for data analysts. It has been shown that the hyperbolic Langmuir isotherm captures the shape of the signal response to concentration of Affymetrix GeneChips. We demonstrate that existing linear fit methods for extracting gene expression measures are not well adapted for the effect of saturation resulting from surface adsorption processes. In contrast to the most popular methods, we fit background and concentration parameters within a single global fitting routine instead of estimating the background before obtaining gene expression measures. We describe a non-linear multi-chip model of the perfect match signal that effectively allows for the separation of specific and non-specific components of the microarray signal and avoids saturation bias in the high-intensity range. Multimodel inference, incorporated within the fitting routine, allows a quantitative selection of the model that best describes the observed data. The performance of this method is evaluated on publicly available datasets, and comparisons to popular algorithms are presented