High-density arrays and insights into genome function

DNA-arrays with electrical detection: A label-free low cost technology for routine use in life sciences and diagnostics

Fast and highly parallel DNA analysis are essential for improved biomedical research and development. Currently fluorescence-based methods are state of the art in DNA microarray analysis. The necessity to modify the target DNA with labels is costly, laborious and requires skilled personnel. Moreover, false positive calls from unspecific adsorption are possible and it is difficult to discriminate perfect matching target sequences from those with a single mismatch. In this paper a new and simple electrochemical approach for hybridisation detection without the need of labelling the target DNA is described. The EDDA (Electrically Detected Displacement Assay) method uses a solution of short redox-labelled signalling oligonucleotides (oligonucleotides carrying a covalently attached redox active compound like ferrocene) to characterize the hybridisation state of label-free capture probe DNA immobilised on gold electrodes. The number of capture probes associated with signalling oligonucleotides is determined by chronocoulometry. This technique allows to separate the electrochemical response of capture probe associated signal probes from the response of freely diffusing signalling probes. In the absence of the complementary target sequences the redox-labelled signalling probes at the surface give rise to an instantaneous increase of the detection signal, while freely diffusing signalling probes show a significantly delayed response. Hybridisation with targets complementary to the capture probe displace the loosely associated signalling probes thereby decreasing the instantaneous signal. Besides an introduction to the EDDA technology, data validating the method for biological material will be presented and an outlook to the detection of single nucleotide polymorphisms (SNPs) is given.

Empirical analysis of transcriptional activity in the Arabidopsis genome

Functional analysis of a genome requires accurate gene structure information and a complete gene inventory. A dual experimental strategy was used to verify and correct the initial genome sequence annotation of the reference plant Arabidopsis. Sequencing full-length cDNAs and hybridizations using RNA populations from various tissues to a set of high-density oligonucleotide arrays spanning the entire genome allowed the accurate annotation of thousands of gene structures. We identified 5817 novel transcription units, including a substantial amount of antisense gene transcription, and 40 genes within the genetically defined centromeres. This approach resulted in completion of approximately 30% of the Arabidopsis ORFeome as a resource for global functional experimentation of the plant proteome.

Dissecting the architecture of a quantitative trait locus in yeast

Most phenotypic diversity in natural populations is characterized by differences in degree rather than in kind. Identification of the actual genes underlying these quantitative traits has proved difficult. As a result, little is known about their genetic architecture. The failures are thought to be due to the different contributions of many underlying genes to the phenotype and the ability of different combinations of genes and environmental factors to produce similar phenotypes. This study combined genome-wide mapping and a new genetic technique named reciprocal-hemizygosity analysis to achieve the complete dissection of a quantitative trait locus (QTL) in Saccharomyces cerevisiae. A QTL architecture was uncovered that was more complex than expected. Functional linkages both in cis and in trans were found between three tightly linked quantitative trait genes that are neither necessary nor sufficient in isolation. This arrangement of alleles explains heterosis (hybrid vigour), the increased fitness of the heterozygote compared with homozygotes. It also demonstrates a deficiency in current approaches to QTL dissection with implications extending to traits in other organisms, including human genetic diseases.

Denaturing high-performance liquid chromatography: A review

Denaturing high-performance liquid chromatography (DHPLC) compares two or more chromosomes as a mixture of denatured and reannealed PCR amplicons, revealing the presence of a mutation by the differential retention of homo- and heteroduplex DNA on reversed-phase chromatography supports under partial denaturation. Temperature determines sensitivity, and its optimum can be predicted by computation. Single-nucleotide substitutions, deletions, and insertions have been detected successfully by on-line UV or fluorescence monitoring within 2-3 minutes in unpurified amplicons as large as 1.5 Kb. Sensitivity and specificity of DHPLC consistently exceed 96%. These features and its low cost make DHPLC one of the most powerful tools for the re-sequencing of the human and other genomes. Aside from its application to the mutational analysis of candidate genes, DHPLC has proven instrumental in elucidating human evolution and in the mapping of genes. Employing completely denaturing conditions, the utility of DHPLC has been extended to the genotyping of known polymorphisms by utilizing the ability of poly(styrene-divinylbenzene) to resolve single-stranded DNA molecules of identical size that differ in a single base. Under completely denaturing conditions, it is thus possible to resolve all possible base substitutions with the single exception of C-->G transversions. Improvements in throughput became feasible with the recent introduction of monolithic poly(styrene-divinylbenzene) capillaries that lend themselves to the fabrication of arrays connected to a multi-color laser induced fluorescence scanner or a mass spectrometer.