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Short Oligonucleotides (short + oligonucleotide)

Distribution by Scientific Domains

Chemistry	60%

Selected Abstracts

Electrochemical Biosensor for the Detection of Interaction Between Arsenic Trioxide and DNA Based on Guanine Signal

ELECTROANALYSIS, Issue 7 2003
Mehmet Ozsoz
Abstract The interaction of arsenic trioxide (As2O3) with calf thymus double-stranded DNA (dsDNA), calf thymus single-stranded DNA (ssDNA) and also 17-mer short oligonucleotide (Probe,A) was studied electrochemically by using differential pulse voltammetry (DPV) with carbon paste electrode (CPE) at the surface and also in solution. Potentiometric stripping analysis (PSA) was employed to monitor the interaction of As2O3 with dsDNA in solution phase by using a renewable pencil graphite electrode (PGE). The changes in the experimental parameters such as the concentration of As2O3, and the accumulation time of As2O3 were studied by using DPV; in addition, the reproducibility data for the interaction between DNA and As2O3 was determined by using both electrochemical techniques. After the interaction of As2O3 with dsDNA, the DPV signal of guanine was found to be decreasing when the accumulation time and the concentration of As2O3 were increased. Similar DPV results were also found with ssDNA and oligonucleotide. PSA results observed at a low DNA concentration such as 1,ppm and a different working electrode such as PGE showed that there could be damage to guanine bases. The partition coefficients of As2O3 after interaction with dsDNA and ssDNA in solution by using CPE were calculated. Similarly, the partition coefficients (PC) of As2O3 after interaction with dsDNA in solution was also calculated by PSA at PGE. The features of this proposed method for the detection of DNA damage by As2O3 are discussed and compared with those methods previously reported for the other type of DNA targeted agents in the literature. [source]

Genetic diversity contribution to errors in short oligonucleotide microarray analysis

PLANT BIOTECHNOLOGY JOURNAL, Issue 5 2006
Matias Kirst
Summary DNA arrays based on short oligonucleotide (, 25-mer) probes are being developed for many species, and are being applied to quantify transcript abundance variation in species with high genetic diversity. To define the parameters necessary to design short oligo arrays for maize (Zea mays L.), a species with particularly high nucleotide (single nucleotide polymorphism, SNP) and insertion-deletion (indel) polymorphism frequencies, we analysed gene expression estimates generated for four maize inbred lines using a custom Affymetrix DNA array, and identified biases associated with high levels of polymorphism between lines. Statistically significant interactions between probes and maize inbreds were detected, affecting five or more probes (out of 30 probes per transcript) in the majority of cases. SNPs and indels were identified by re-sequencing; they are the primary source of probe-by-line interactions, affecting probeset level estimates and reducing the power of detecting transcript level variation between maize inbreds. This analysis identified 36 196 probes in 5118 probesets containing markers that may be used for genotyping in natural and segregating populations for association gene analysis and genetic mapping. [source]

Parallel separations of oligonucleotides with optically gated sample introduction on multi-channel microchips

JOURNAL OF SEPARATION SCIENCE, JSS, Issue 1-2 2004
Hongwei Xu
Abstract With the release of the human genome sequence, there has been increasing attention given to other genetic analyses, including the detection of genetic variations and fast sequencing of multiple samples for pharmacogenomics studies. Rapid injections of samples in multiplexed separation channels by optically gated sample introduction are shown here for DNA separation. Serial separations of four amino acids are shown in less than four seconds on a microchip with four multiplexed channels. Five short oligonucleotides have also been rapidly separated in 2% LPA with four channels using this technique. In addition, multiple unique samples have been simultaneously separated and five-base resolution has been demonstrated. [source]

Mixture Modeling for Genome-Wide Localization of Transcription Factors

BIOMETRICS, Issue 1 2007
Sündüz Kele
Summary Chromatin immunoprecipitation followed by DNA microarray analysis (ChIP-chip methodology) is an efficient way of mapping genome-wide protein,DNA interactions. Data from tiling arrays encompass DNA,protein interaction measurements on thousands or millions of short oligonucleotides (probes) tiling a whole chromosome or genome. We propose a new model-based method for analyzing ChIP-chip data. The proposed model is motivated by the widely used two-component multinomial mixture model of de novo motif finding. It utilizes a hierarchical gamma mixture model of binding intensities while incorporating inherent spatial structure of the data. In this model, genomic regions belong to either one of the following two general groups: regions with a local protein,DNA interaction (peak) and regions lacking this interaction. Individual probes within a genomic region are allowed to have different localization rates accommodating different binding affinities. A novel feature of this model is the incorporation of a distribution for the peak size derived from the experimental design and parameters. This leads to the relaxation of the fixed peak size assumption that is commonly employed when computing a test statistic for these types of spatial data. Simulation studies and a real data application demonstrate good operating characteristics of the method including high sensitivity with small sample sizes when compared to available alternative methods. [source]

Multiscale modeling of nucleic acids: Insights into DNA flexibility

BIOPOLYMERS, Issue 9 2008
Yannick J. Bomble
Abstract The elastic rod theory is used together with all-atom normal mode analysis in implicit solvent to characterize the mechanical flexibility of duplex DNA. The bending, twisting, stretching rigidities extracted from all-atom simulations (on linear duplexes from 60 to 150 base pairs in length and from 94-bp minicircles) are in reasonable agreement with experimental results. We focus on salt concentration and sequence effects on the overall flexibility. Bending persistence lengths are about 20% higher than most experimental estimates, but the transition from low-salt to high-salt behavior is reproduced well, as is the dependence of the stretching modulus on salt (which is opposite to that of bending). CTG and CGG trinucleotide repeats, responsible for several degenerative disorders, are found to be more flexible than random DNA, in agreement with several recent studies, whereas poly(dA).poly(dT) is the stiffest sequence we have encountered. The results suggest that current all-atom potentials, which were parameterized on small molecules and short oligonucleotides, also provide a useful description of duplex DNA at much longer length scales. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 722,731, 2008. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source]