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Nucleic Acids Research, 2003, Vol. 31, No. 6 e30
© 2003 Oxford University Press

Analyzing partially randomized nucleic acid pools: straight dope on doping

Rob Knight and Michael Yarus

Department of Molecular, Cellular and Developmental Biology, Campus Box 347, University of Colorado, Boulder, CO 80309, USA

*To whom correspondence should be addressed. Tel: +1 303 492 7108; Fax: +1 303 492 7744; Email: rob{at}spot.colorado.edu

Partially randomized (doped) pools are important for optimizing activities initially isolated by selection-amplification or SELEX, and for locating nucleotides critical for function. Here we present a method for calculating the number of unique sequences in a pool, and the expected copy number of each unique sequence with a specified number of changes from the original sequence. Surprisingly, small differences in doping can have large consequences for the number of copies of sequences with certain numbers of changes from the original sequence. We demonstrate the effects of pool size, percentage doping, length of the random region and taking aliquots from the original pool on the exploration of sequence space in a doped reselection experiment. A web form is provided for customized calculations.


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