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Analysis of a complete DNA-protein affinity landscape
journal contribution
posted on 2013-01-02, 12:11 authored by William Rowe, Mark PlattMark Platt, David C. Wedge, Philip J.R. Day, Douglas B. Kell, Joshua KnowlesProperties 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.
History
School
- Science
Department
- 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.Publisher
© Royal Society of ChemistryVersion
- NA (Not Applicable or Unknown)
Publication date
2010Notes
This article is closed access.ISSN
1742-5689Publisher version
Language
- en