Analysis of a complete DNA - protein affinity landscape

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    Properties of biological .tness 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 pro.le 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. © 2009 The Royal Society.
    Original languageEnglish
    Pages (from-to)397-408
    Number of pages11
    JournalJournal of the Royal Society Interface
    Issue number44
    Publication statusPublished - 6 Mar 2010


    • Allophycocyanin
    • Aptamer
    • NK-landscape
    • Tness landscapes


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