Biotechnology and bioengineering publish this investigation article

January 1^st, 2018

Synthetic DNA design needs to harness the many information layers embedded in a DNA string. We previously developed the Evolutionary Landscape Painter (ELP), an algorithm that exploits the degeneracy of the code to increase protein evolvability. Here, we have used ELP to recode the integron integrase gene (intI1) in two alternative alleles. Although synonymous, both alleles yielded less IntI1 protein and were less active in recombination assays than intI1. We spliced the three alleles and mapped the activity decrease to the beginning of alternative sequences. Mfold predicted the presence of more stable secondary structures in the alternative genes. Using synonymous mutations, we decreased their stability and recovered full activity. Following a design-build-test approach, we have now updated ELP to consider such structures and provide streamlined alternative sequences. Our results support the possibility of modulating gene activity through the ad hoc design of 5` secondary structures in synthetic genes. This article is protected by copyright. All rights reserved

Escudero JA., Nivina A., Cambray G., Lopez-Igual R., Loot C. and Mazel D.

Recoding of synonymous genes to expand evolutionary landscapes requires control of secondary structure affecting translation

Recoding of synonymous genes to expand evolutionary landscapes requires control of secondary structure affecting translation

	Department of Genomes and Genetics. Institut Pasteur.
	Centre National de la Recherche Scientifique (CNRS).
	Departamento de Sanidad Animal. Facultad de Veterinaria. Universidad Complutense (UCM).
	Servicio de Zoonosis de Transmisión Alimentaria y Resistencia a Antimicrobianos (ZTA). Centro de Vigilancia Sanitaria Veterinaria (VISAVET). Universidad Complutense (UCM).
	Université Sorbonne Paris Descartes.
	Institut National de la Recherche Agronomique (INRA).