Thermodynamics of RNA/DNA hybridization in high-density oligonucleotide microarrays

Carlon, Enrico; Heim, Thomas M.

doi:10.1016/j.physa.2005.09.067

Cited by 56 publications

(150 citation statements)

References 17 publications

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“…R-loops are formed on the transcribed strand, leaving the nontranscribed strand in ssDNA formation at higher frequency than its complementary strand (Li and Manley 2005;Ronai et al 2007). Using a biophysical model (Carlon and Heim 2006) we calculated the differences between the free-energy levels of RNA/DNA hybrids and DNA/DNA (i.e., dsDNA) structures in various distances of the TSS for genes in our data set. According to this model, for most genes the RNA/DNA hybrid in the first 200 bp downstream from the TSS is more stable than DNA/DNA confirmation (Supplemental Fig.…”

Section: Localization Of Mutationsmentioning

confidence: 99%

“…S13). The predicted higher stability can be attributed to higher GC content and the GC skew near the TSS of human genes, since GpG dinucleotides are the main contributors to the energetic difference between RNA/DNA hybrids and DNA/DNA structures (Carlon and Heim 2006). It is important to note that until now it was not fully understood what the conditions for R-loops formations were.…”

Section: Localization Of Mutationsmentioning

confidence: 99%

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Transcription induces strand-specific mutations at the 5′ end of human genes

Polak¹,

Arndt²

2008

Genome Res.

105

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A regional analysis of nucleotide substitution rates along human genes and their flanking regions allows us to quantify the effect of mutational mechanisms associated with transcription in germ line cells. Our analysis reveals three distinct patterns of substitution rates. First, a sharp decline in the deamination rate of methylated CpG dinucleotides, which is observed in the vicinity of the 5Ј end of genes. Second, a strand asymmetry in complementary substitution rates, which extends from the 5Ј end to 1 kbp downstream from the 3Ј end, associated with transcription-coupled repair. Finally, a localized strand asymmetry, an excess of C→T over G→A substitution in the nontemplate strand confined to the first 1-2 kbp downstream of the 5Ј end of genes. We hypothesize that higher exposure of the nontemplate strand near the 5Ј end of genes leads to a higher cytosine deamination rate. Up to now, only the somatic hypermutation (SHM) pathway has been known to mediate localized and strand-specific mutagenic processes associated with transcription in mammalia. The mutational patterns in SHM are induced by cytosine deaminase, which just targets single-stranded DNA. This DNA conformation is induced by R-loops, which preferentially occur at the 5Ј ends of genes. We predict that R-loops are extensively formed in the beginning of transcribed regions in germ line cells.

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Section: Localization Of Mutationsmentioning

confidence: 99%

Section: Localization Of Mutationsmentioning

confidence: 99%

Transcription induces strand-specific mutations at the 5′ end of human genes

Polak¹,

Arndt²

2008

Genome Res.

105

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“…[2][3][4][5][6][7][8][9][10][11][12] The tacit assumption behind the use of these models is that hybridization in typical microarray experiments is sufficiently long (usually 15 − 17h), so that thermal equilibrium can be considered to be attained.…”

Section: Resultsmentioning

confidence: 99%

Nonequilibrium Effects in DNA Microarrays: A Multiplatform Study

et al. 2011

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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 ∆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 ∆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. 16,20 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.

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“…It was shown that this biological process is controlled by some key parameters. Each of these parameters have been studied and defined in the literature: The environmental parameters such as temperature assessed from the chemical proprieties of the solution and the DNA sequence [10] using the Nearest Neighbor model [11], the ionic composition of the solution, especially salt concentration, and the intrinsic DNA parameters such as the DNA sequence composition [10] and its length [12].…”

Section: Dna As Bio-bond For Self-assemblymentioning

confidence: 99%

Characterization of DNA bio-bonds for meso-scale self-assembly

Abbaci

Daunay

Haliyo

et al. 2008

2008 30th Annual International Conference of the IEEE Engineering in Medicine and Biology Society

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Abstract-In this paper, we have investigated the use of DNA hybridization as the basis for the production of new mesoscale components. AFM experimental results are studied and compared to two theoretical approaches: molecular and thermodynamic. We explain how and why DNA hybridization process can provide a good bond to self assemble components, and how molecular modelling methods allow further understanding of the physical mechanism of this process. Furthermore, the strength interaction of DNA complementary strands is measured and analyzed using statistical tools. These results are then compared to the theoretical approaches.

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Thermodynamics of RNA/DNA hybridization in high-density oligonucleotide microarrays

Cited by 56 publications

References 17 publications

Transcription induces strand-specific mutations at the 5′ end of human genes

Transcription induces strand-specific mutations at the 5′ end of human genes

Nonequilibrium Effects in DNA Microarrays: A Multiplatform Study

Characterization of DNA bio-bonds for meso-scale self-assembly

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