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oligonucleotide fingerprinting


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Any technique which produces a “fingerprint” consisting of a distinct oligonucleotide (q.v.) pattern representing nucleic acids from a particular source. In the simplest example, the genomes of different strains of an organism may be compared by enzymatic digestion of their genomic DNA (or RNA) to generate oligonucleotide fragments, which, when resolved on a gel by electrophoresis (q.v.), produce banding patterns representing fingerprints unique to each strain. A relatively more complex technique uses fingerprints generated by hybridization of oligonucleotides to cDNA (q.v.) or genomic libraries to characterize expressed genes at the genome-wide scale, to compare different cDNA libraries, and to select shotgun clones for sequencing. In this method, hundreds of labeled, synthetic oligonucleotides of known sequences, usually 6–10 bp in length, are hybridized to PCR-amplified cDNA or genomic library sequences that have been spotted on parallel DNA microarrays. Each oligonucleotide probe (q.v.) is used in a separate hybridization experiment. The extent of hybridization across microarray filters is recorded by a laser scanner and image analysis software. This produces a unique fingerprint of each arrayed DNA fragment, based on the extent of similarity to each oligonucleotide sequence. Using this approach, hundreds of thousands of individual library fragments can be comparatively examined. cDNAs with similar fingerprints are grouped into clusters, and this provides information about the number of expressed genes and their relative expression levels. Individual fingerprints are used for database searches for sequence matches to known genes or to identify new genes. DNA fragments having maximum dissimilarity in their fingerprints (i.e., minimum sequence overlap) are used for genomic sequencing with reduced redundancy. See DNA fingerprint technique, DNA microarray technology, genomic library, polymerase chain reaction.

Subjects: Genetics and Genomics.


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