Journal: Nucleic Acids Research

Article Title: Array-based evolution of DNA aptamers allows modelling of an explicit sequence-fitness landscape

doi: 10.1093/nar/gkn899

Figure Lengend Snippet: Schematic of the CLADE approach. CLADE as utilized in this study starts at the top of the schematic with an initial choice of DNA sequences. These sequences may be generated entirely in silico , or optionally, as with some of the sequences here, utilizing prior knowledge generated in vitro . These sequences are synthesized on a custom microarray and bound with the chosen ligand, here the APC protein. Analysis of binding intensities gives a distribution of fitnesses; the frequency distribution of Generation 1 binding to APC protein is shown by way of example. Some of these sequences are selected in silico , based on the in vitro score distribution, here using tournament selection (see Materials and methods section). These sequences are then mutated in silico to generate a new sequence set which can then be synthesised in vitro , and so on round the cycle as often as is required. The final aptamer set offers a greatly increased binding affinity to the ligand.

Article Snippet: Image analysis used Combimatrix Microarray Imager ( https://webapps.combimatrix.com/customarray/customarrayHome.jsp ).

Techniques: Generated, In Silico, In Vitro, Synthesized, Microarray, Protein Binding, Binding Assay, Selection, Sequencing