602 research outputs found
Thermodynamic behavior of short oligonucleotides in microarray hybridizations can be described using Gibbs free energy in a nearest-neighbor model
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 concerning oligo length, overall similarity, and continuous
stretches, the final behavior is difficult to predict. The aim of this study
was to investigate the effect of well-defined mismatches on hybridization
specificity using CodeLink Activated Slides, and to study quantitatively the
relation between hybridization intensity and Gibbs free energy (Delta G),
taking the mismatches into account. Our data clearly showed a correlation
between the hybridization intensity and Delta G of the oligos over three orders
of magnitude for the hybridization intensity, which could be described by the
Langmuir model. As Delta G was calculated according to the nearest-neighbor
model, using values related to DNA hybridizations in solution, this study
clearly shows that target-probe hybridizations on microarrays with a
three-dimensional coating are in quantitative agreement with the corresponding
reaction in solution. These results can be interesting for some practical
applications. The correlation between intensity and Delta G can be used in
quality control of microarray hybridizations by designing probes and
corresponding RNA spikes with a range of Delta G values. Furthermore, this
correlation might be of use to fine-tune oligonucleotide design algorithms in a
way to improve the prediction of the influence of mismatching targets on
microarray hybridizations.Comment: 32 pages on a single pdf fil
Electric-field control of interfering transport pathways in a single-molecule anthraquinone transistor
It is understood that molecular conjugation plays an important role in charge
transport through single-molecule junctions. Here, we investigate electron
transport through an anthraquinone based single-molecule three-terminal device.
With the use of an electric-field induced by a gate electrode, the molecule is
reduced resulting into a ten-fold increase in the off-resonant differential
conductance. Theoretical calculations link the change in differential
conductance to a reduction-induced change in conjugation, thereby lifting
destructive interference of transport pathways.Comment: Nano Letters (2015
Thermodynamic scaling behavior in genechips
Abstract Background Affymetrix Genechips are characterized by probe pairs, a perfect match (PM) and a mismatch (MM) probe differing by a single nucleotide. Most of the data preprocessing algorithms neglect MM signals, as it was shown that MMs cannot be used as estimators of the non-specific hybridization as originally proposed by Affymetrix. The aim of this paper is to study in detail on a large number of experiments the behavior of the average PM/MM ratio. This is taken as an indicator of the quality of the hybridization and, when compared between different chip series, of the quality of the chip design. Results About 250 different GeneChip hybridizations performed at the VIB Microarray Facility for Homo sapiens, Drosophila melanogaster, and Arabidopsis thaliana were analyzed. The investigation of such a large set of data from the same source minimizes systematic experimental variations that may arise from differences in protocols or from different laboratories. The PM/MM ratios are derived theoretically from thermodynamic laws and a link is made with the sequence of PM and MM probe, more specifically with their central nucleotide triplets. Conclusion The PM/MM ratios subdivided according to the different central nucleotides triplets follow qualitatively those deduced from the hybridization free energies in solution. It is shown also that the PM and MM histograms are related by a simple scale transformation, in agreement with what is to be expected from hybridization thermodynamics. Different quantitative behavior is observed on the different chip organisms analyzed, suggesting that some organism chips have superior probe design compared to others.</p
Exciton and Hole-Transfer Dynamics in Polymer:Fullerene Blends
Ultrafast hole transfer dynamics from fullerene derivative to polymer in bulk heterojunction blends are studied with visible-pump – IR-probe spectroscopy. The hole transfer process is found to occur in 50/300 fs next to the interface, while a longer 15-ps time is attributed to exciton diffusion towards interface in PC71BM domains. High polaron generation efficiency in P3HT blends indicates excellent intercalation between the polymer and the fullerene even at highest PC71BM concentration thereby yielding a valuable information on the blend morphology
Synthesis and Photophysical Properties of Novel Fullerene Derivatives as Model Compounds for Bulk-Heterojunction PV Cells
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
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