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Title: Analysis of a complete DNA-protein affinity landscape
Authors: Rowe, William
Platt, Mark
Wedge, David C.
Day, Philip J.R.
Kell, Douglas B.
Knowles, Joshua
Keywords: Fitness landscapes
Issue Date: 2010
Publisher: © Royal Society of Chemistry
Citation: ROWE, W., PLATT, M., WEDGE, D.C. ... et al, 2010. Analysis of a complete DNA-protein affinity landscape. Journal of the Royal Society Interface, 7 (44), pp.397-408.
Abstract: Properties of biological fitness landscapes are of interest to a wide sector of the life sciences, from ecology to genetics to synthetic biology. For biomolecular fitness landscapes, the information we currently possess comes primarily from two sources: sparse samples obtained from directed evolution experiments; and more fine-grained but less authentic information from ‘in silico’ models (such as NK-landscapes). Here we present the entire protein-binding profile of all variants of a nucleic acid oligomer 10 bases in length, which we have obtained experimentally by a series of highly parallel on-chip assays. The resulting complete landscape of sequence-binding pairs, comprising more than one million binding measurements in duplicate, has been analysed statistically using a number of metrics commonly applied to synthetic landscapes. These metrics show that the landscape is rugged, with many local optima, and that this arises from a combination of experimental variation and the natural structural properties of the oligonucleotides.
Description: This article is closed access.
Version: Closed access
DOI: 10.1098/rsif.2009.0193
URI: https://dspace.lboro.ac.uk/2134/11321
Publisher Link: http://dx.doi.org/10.1098/rsif.2009.0193
ISSN: 1742-5689
Appears in Collections:Closed Access (Chemistry)

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