Hybridization to oligonucleotides

Southern EM (1996) DNA chips analyzing sequence by hybridization to oligonucleotides on a large scale. Trends Genet 12 110-115... 

The highly radioactive end-labeled oligonucleotides should not be used for more than 1 week after preparation because they are subject to radiochemical degradation. Labeled probes not used immediately are stored at — 20°. We routinely prepare several groups of slot blots and perform the hybridization to oligonucleotide probes on the day they are labeled. 

Southern, E.M. (1996) DNA Chips Analyzing Sequence by Hybridization to Oligonucleotides on a Large Scale, Trends Genet. 12,110-115. 

The amplicons prepared are subsequently analyzed by a variety of methods. They can be hybridized to oligonucleotide probes in reverse or forward dot-blot assays. The panel of probes is chosen to cover critical polymorphic positions in the HLA gene tested. The pattern of reactivity of the panel can then be analyzed to assign allele identities. ... 

Furdon, P. J., Dominski, Z., and Kole, R. (1989) RNase II cleavage of RNA hybridized to oligonucleotides containing methylphosphonate, phosphoro-thioate and phosphodiester bonds. Nucl Acids Res,ll, 9193-9204. 

The oligonucleotide population is then hybridized to single-stranded DNA and primed synthesis is carried out as described above. 

Fig. 3.46. " Sn image of Sn-labeled DNA hybridized to six oligonucleotide spots three complimentary and three non-comple-mentary.

Antisense therapy means the selective, sequence-specific inhibition of gene expression by single-stranded DNA oligonucleotides. By hybridizing to the target mRNA, which results in a subsequent double-helix formation, gene expression is blocked. This process can occur at any point between the conclusion of transcription and initiation of translation or even possibly during translation. 

Egholm M., Buchardt O., Christensen L., Behrens C., Ereier S.M., Driver D.A., Berg, R. H., Kim, S.K., Nor-DEN B., Nielsen, P.E. PNA hybridizes to complementary oligonucleotides obeying the Watson—Crick hydrogen-bonding rules. Nature 1993, 365 566-568. 

Liebermann T, Knoll W (2003) Parallel multispot detection of target hybridization to surface-bound probe oligonucleotides of different base mismatch by surface-plasmon field-enhanced fluorescence microscopy. Langmuir 9 1567-1572... 

It s also possible to select your DNA before you put it in the vector. If you know the sequence (or even part of it), DNA pieces (from genomic DNA or cDNA) with this sequence can be purified on a gel and identified by hybridization to an oligonucleotide using a Southern blot. Alternatively, if you know the sequence of the ends of your DNA, you can amplify it specifically by the polymerase chain reaction. There are lots of clever ways to find your DNA. 

The presence of the chimeric construct in each ars-transformant was verified by PCR using an upstream oligonucleotide that hybridizes to the hydA promoter fragment and a downstream oligonucleotide that hybridizes to the ars gene asindicated with black arrows at the bottom. 

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