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Updated: Jan 20, 2026

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules
Published on: April 12, 2019
Optimizing the fold stability of the circularly permuted Trp-cage motif
Katherine A Graham1, Aimee Byrne1, Micheal Mason1
1Department of Chemistry, University of Washington, Seattle, Washington, United States of America.
Abstract:
Through optimization of the linker region and key stabilizing mutations, it has been possible to improve the stability of the circularly permuted (cp) Trp-cage miniprotein. However, even the most stable Trp-cage circular permutants are still less stable than the analogous standard topology (std) Trp-cages. Extending mutational studies of Trp-cage fold stability to cp-species, including analogs lacking chain terminal charges, has uncovered and quantitated some additional stabilizing and destabilizing interactions. Upon protonation, the circular permutants are destabilized to a much greater extent than the standard topology series. End effects, particularly Coulombic interactions, appear to be more important for the cp-series while the Y10/P4 interaction in the cp-series is not as significant a stabilizing feature as the corresponding Y3/P19 in the standard topology series.
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Repressible Operon: trp Operon