2008
DOI: 10.1186/1471-2105-9-509
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Position dependent mismatch discrimination on DNA microarrays – experiments and model

Abstract: Background: The propensity of oligonucleotide strands to form stable duplexes with complementary sequences is fundamental to a variety of biological and biotechnological processes as various as microRNA signalling, microarray hybridization and PCR. Yet our understanding of oligonucleotide hybridization, in particular in presence of surfaces, is rather limited. Here we use oligonucleotide microarrays made in-house by optically controlled DNA synthesis to produce probe sets comprising all possible single base mi… Show more

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Cited by 42 publications
(55 citation statements)
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“…Oligoarrays represent a mature technology; however, all issues associated with the broad applications of oligoarrays have not been fully elucidated, as a plethora of recent studies have indicated (25,27,29). In this study, we used complete genomic sequences of several tester strains to validate microarray results and to obtain quantitative assessments of the performance of oligoarrays for whole-genome DNA-DNA competitive hybridization.…”
Section: Discussionmentioning
confidence: 99%
“…Oligoarrays represent a mature technology; however, all issues associated with the broad applications of oligoarrays have not been fully elucidated, as a plethora of recent studies have indicated (25,27,29). In this study, we used complete genomic sequences of several tester strains to validate microarray results and to obtain quantitative assessments of the performance of oligoarrays for whole-genome DNA-DNA competitive hybridization.…”
Section: Discussionmentioning
confidence: 99%
“…Given the high quality of the 3 completed genomes and 11 draft genomes used in our analyses, we were able to combine sequence comparisons and syntenic relationships to determine gene orthologs and observed that, compared to NAP1 references, the members of the NAP7-NAP8 group displayed a higher level of genetic diversity, with an average of 97% identity. We believe that in comparative genome hybridization (CGH) studies, for example, where probe mismatches can affect hybridization (41,49) and where NAP1 or strain 630 genomes have been used as the reference, even a very low number of mismatches between the probe and target DNA can increase the false-negative rate (34,58). This leads us to suggest that the C. difficile CGH arrays, which were designed using either strain 630 (R group) or NAP1 isolate QCD-32g58, may produce numerous falsenegative hybridizations when tested using more a more distantly related strain (e.g., NAP7) and have resulted in the calculation of a smaller core genome size.…”
Section: Discussionmentioning
confidence: 99%
“…For example, DNA microarray assays consist of DNA 'probes' which are tethered to a surface, and 'target' molecules which diffuse through solution. 69,70 With the advent of DNA origami, experimentalists are now able to localize isolated reactants at will. 71 Figure 6 illustrates such a localisation for a generic system.…”
Section: G Theory Of Localising a Single Reactant Speciesmentioning
confidence: 99%