Enhanced high density oligonucleotide array-based sequence analysis using modified nucleoside triphosphates

Enhanced high density oligonucleotide array-based sequence analysis using modified nucleoside triphosphates.

Pairs of high density oligonucleotide arrays (DNA chips) consisting of >96 000 oligonucleotides were designed to screen the entire 5.53 kb coding region of the hereditary breast and ovarian cancer BRCA1 gene for all possible sequence changes in the homozygous and heterozygous states. Single-stranded RNA targets were generated by PCR amplification of individual BRCA1 exons using primers containi...

From features to expression: High-density oligonucleotide array analysis revisited

One of the most popular tools for large scale gene expression studies are highdensity oligonucleotide (GeneChip R ) arrays. These currently have 16-20 small probes (“features”) for evaluating the transcript abundance of each gene. In addition, each probe is accompanied by a mismatched probe (MM) designed as a control for non-specificity. An algorithm is presented to compute comparative expressi...

From features to expression: High-density oligonucleotide array analysis revisited.

Algorithms for high-density oligonucleotide array.

As a global gene expression-monitoring tool, high-density oligonucleotide arrays (HDAs), accelerate biological and drug discovery processes. Computational considerations affect several key issues, from array design and accurate gene expression level determination to various aspects of the biological analysis of cell functions and gene networks. This review highlights recent progress in ideas an...

Modified Nucleoside Triphosphates for In-vitro Selection Techniques

The development of SELEX (Selective Enhancement of Ligands by Exponential Enrichment) provides a powerful tool for the search of functional oligonucleotides with the ability to bind ligands with high affinity and selectivity (aptamers) and for the discovery of nucleic acid sequences with diverse enzymatic activities (ribozymes and DNAzymes). This technique has been extensively applied to the se...