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Please use this identifier to cite or link to this item: https://dspace.lboro.ac.uk/2134/11316

Title: Array-based evolution of DNA aptamers allows modelling of an explicit sequence-fitness landscape
Authors: Knight, Christopher G.
Platt, Mark
Rowe, William
Wedge, David C.
Khan, Farid
Day, Philip J.R.
McShea, Andy
Knowles, Joshua
Kell, Douglas B.
Issue Date: 2009
Publisher: Oxford University Press (© The Authors)
Citation: KNIGHT, C.G., PLATT, M., ROWE, W. ... et al, 2009. Array-based evolution of DNA aptamers allows modelling of an explicit sequence-fitness landscape. Nucleic Acids Research, 37 (1), e6.
Abstract: Mapping the landscape of possible macromolecular polymer sequences to their fitness in performing biological functions is a challenge across the biosciences. A paradigm is the case of aptamers, nucleic acids that can be selected to bind particular target molecules. We have characterized the sequence-fitness landscape for aptamers binding allophycocyanin (APC) protein via a novel Closed Loop Aptameric Directed Evolution (CLADE) approach. In contrast to the conventional SELEX methodology, selection and mutation of aptamer sequences was carried out in silico, with explicit fitness assays for 44 131 aptamers of known sequence using DNA microarrays in vitro. We capture the landscape using a predictive machine learning model linking sequence features and function and validate this model using 5500 entirely separate test sequences, which give a very high observed versus predicted correlation of 0.87. This approach reveals a complex sequence-fitness mapping, and hypotheses for the physical basis of aptameric binding; it also enables rapid design of novel aptamers with desired binding properties. We demonstrate an extension to the approach by incorporating prior knowledge into CLADE resulting in some of the tightest binding sequences.
Description: Copyright 2009 Author(s). This article is distributed under a Creative Commons Attribution 3.0 Unported License.
Version: Published
DOI: 10.1093/nar/gkn899
URI: https://dspace.lboro.ac.uk/2134/11316
Publisher Link: http://dx.doi.org/10.1093/nar/gkn899
ISSN: 0305-1048
Appears in Collections:Published Articles (Chemistry)

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