A Software Tool for Generating Non-crosshybridizing Libraries of DNA Oligonucleotides View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2003-01-16

AUTHORS

Russell Deaton , Junghuei Chen , Hong Bi , John A. Rose

ABSTRACT

Under an all or nothing hybridization model, the problem of finding a library of non-crosshybridizing DNA oligonucleotides is shown to be equivalent to finding an independent set of vertices in a graph. Individual oligonucleotides or Watson-Crick pairs are represented as vertices. Indicating a hybridization, an edge is placed between vertices (oligonucleotides or pairs) if the minimum free energy of hybridization, according to the nearest-neighbor model of duplex thermal stability, is less than some threshold value. Using this equivalence, an algorithm is implemented to find maximal libraries. Sequence designs were generated for a test of a modified PCR protocol. The results indicated that the designed structures formed as planned, and that there was little to no secondary structure present in the single-strands. In addition, simulations to find libraries of 10-mers and 20-mers were done, and the base composition of the non-crosshybridizing libraries was found to be 2/3 A-T and 1/3 G-C under high salt conditions, and closer to uniform for lower salt concentrations. More... »

PAGES

252-261

Book

TITLE

DNA Computing

ISBN

978-3-540-00531-5
978-3-540-36440-5

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/3-540-36440-4_22

DOI

http://dx.doi.org/10.1007/3-540-36440-4_22

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1022065278


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