14,357 research outputs found
Paradigms for computational nucleic acid design
The design of DNA and RNA sequences is critical for many endeavors, from DNA nanotechnology, to PCR‐based applications, to DNA hybridization arrays. Results in the literature rely on a wide variety of design criteria adapted to the particular requirements of each application. Using an extensively studied thermodynamic model, we perform a detailed study of several criteria for designing sequences intended to adopt a target secondary structure. We conclude that superior design methods should explicitly implement both a positive design paradigm (optimize affinity for the target structure) and a negative design paradigm (optimize specificity for the target structure). The commonly used approaches of sequence symmetry minimization and minimum free‐energy satisfaction primarily implement negative design and can be strengthened by introducing a positive design component. Surprisingly, our findings hold for a wide range of secondary structures and are robust to modest perturbation of the thermodynamic parameters used for evaluating sequence quality, suggesting the feasibility and ongoing utility of a unified approach to nucleic acid design as parameter sets are refined further. Finally, we observe that designing for thermodynamic stability does not determine folding kinetics, emphasizing the opportunity for extending design criteria to target kinetic features of the energy landscape
Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins
Using self-organized polymer models, we predict mechanical unfolding and
refolding pathways of ribo-zymes, and the green fluorescent protein. In
agreement with experiments, there are between six and eight unfolding
transitions in the Tetrahymena ribozyme. Depending on the loading rate, the
number of rips in the force-ramp unfolding of the Azoarcus ribozymes is between
two and four. Force-quench refolding of the P4-P6 subdomain of the Tetrahymena
ribozyme occurs through a compact intermediate. Subsequent formation of
tertiary contacts between helices P5b-P6a and P5a/P5c-P4 leads to the native
state. The force-quench refolding pathways agree with ensemble experiments. In
the dominant unfolding route, the N-terminal a helix of GFP unravels first,
followed by disruption of the N terminus b strand. There is a third
intermediate that involves disruption of three other strands. In accord with
experiments, the force-quench refolding pathway of GFP is hierarchic, with the
rate-limiting step being the closure of the barrel.Comment: 33 pages 7 figure
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