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Biophys J, August 2000, p. 680-685, Vol. 79, No. 2

Optimization of Nucleic Acid Sequences

Ingrid Lafontaine and Richard Lavery

Laboratoire de Biochimie Théorique UPR 9080 Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Paris 75005, France

Base sequence influences the structure, mechanics, dynamics, and interactions of nucleic acids. However, studying all possible sequences for a given fragment leads to a number of base combinations that increases exponentially with length. We present here a novel methodology based on a multi-copy approach enabling us to determine which base sequence favors a given structural change or interaction via a single energy minimization. This methodology, termed ADAPT, has been implemented starting from the JUMNA molecular mechanics program by adding special nucleotides, "lexides," containing all four bases, whose contribution to the energy of the system is weighted by continuously variable coefficients. We illustrate the application of this approach in the case of double-stranded DNA by determining the optimal sequences satisfying structural (B-Z transition), mechanical (intrinsic curvature), and interaction (ligand-binding) properties.

Biophys J, August 2000, p. 680-685, Vol. 79, No. 2
© 2000 by the Biophysical Society   0006-3495/00/08/680/06  $2.00


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