title: Constrained Multistate Sequence Design for Nucleic Acid Reaction Pathway Engineering.
abstract: We describe a framework for designing the sequences of multiple nucleic acid strands intended to hybridize in solution via a prescribed reaction pathway. Sequence design is formulated as a multistate optimization problem using a set of target test tubes to represent reactant, intermediate, and product states of the system, as well as to model crosstalk between components. Each target test tube contains a set of desired "on-target" complexes, each with a target secondary structure and target concentration, and a set of undesired "off-target" complexes, each with vanishing target concentration. Optimization of the equilibrium ensemble properties of the target test tubes implements both a positive design paradigm, explicitly designing for on-pathway elementary steps, and a negative design paradigm, explicitly designing against off-pathway crosstalk. Sequence design is performed subject to diverse user-specified sequence constraints including composition constraints, complementarity constraints, pattern prevention constraints, and biological constraints. Constrained multistate sequence design facilitates nucleic acid reaction pathway engineering for diverse applications in molecular programming and synthetic biology. Design jobs can be run online via the NUPACK web application.
authors.affiliation: Division of Biology & Biological Engineering, California Institute of Technology , Pasadena, California 91125, United States.
authors.forename: Brian R
authors.initials: BR
authors.lastname: Wolfe
authors.affiliation: Division of Chemistry & Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Porubsky
authors.affiliation: Division of Biology & Biological Engineering, California Institute of Technology , Pasadena, California 91125, United States.
authors.forename: Joseph N
authors.initials: JN
authors.lastname: Zadeh
authors.affiliation: Division of Biology & Biological Engineering, California Institute of Technology , Pasadena, California 91125, United States.
authors.forename: Robert M
authors.initials: RM
authors.lastname: Dirks
authors.affiliation: Division of Biology & Biological Engineering, California Institute of Technology , Pasadena, California 91125, United States.|Division of Engineering & Applied Science, California Institute of Technology , Pasadena, California 91125, United States.|Weatherall Institute of Molecular Medicine, University of Oxford , Oxford OX3 9DS, United Kingdom.
authors.forename: Niles A
authors.identifier: 0000-0003-2367-4406
authors.initials: NA
authors.lastname: Pierce
mesh_terms: D000465:Algorithms; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000138:chemical synthesis* / Q000737:chemistry
chemical_list: D009696:Nucleic Acids