Chip Technology by Springer-Verlag, Jorg Hoheisel

By Springer-Verlag, Jorg Hoheisel

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55 A Study of the Secondary Structure of Nucleic Acids with Modified Bases . . . . . . . . . . . . . . 55 5 Concluding Remarks . . . . . . . . . . . . . 56 6 References . . . . . . . . . . . . . . . . 56 1 Introduction Scanning arrays are made by combinatorial in situ synthesis of a large number of oligonucleotides on a solid support in a spatially addressable fashion. They comprise sets of oligonucleotides of various lengths in which a series of oligonucleotides, complementary to the target RNA or DNA, is made by sequential coupling of nucleotides to a solid substrate (such as glass or polypropylene) that has been modified to allow oligonucleotide synthesis.

Golub et al. [31] went on to address the issue of class discovery, that is, the identification of new cancer classes. The statistical tool called self-organizing maps was employed to determine whether the original data set could be subdivided beyond the ALL-AML categories. The AML samples again clustered together, but the ALL samples were now split into two groups that were subsequently shown by immunotyping to be of B-cell or T-cell origin. Although this ALL subdivision was previously known, the clustering analysis would have discovered it even if it had not been known.

CY5) and hybridised to a scanning array. The choice of label depends on the application. For example, when studying folding of a target nucleic acid, it may be more appropriate to label it with a radioisotope rather than CY5 because the bulky CY5 groups may interfere with or alter the folding of the labeled compound. The labeled product is generated by the standard in vitro transcription in the presence of a labeled precursor (such as [α-33P]UTP or [α-32P]UTP or CY5UTP), using an appropriate DNA template.

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