Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

RNA secondary structure design.

Bernd Burghardt1, Alexander K Hartmann

  • 1Institut für Theoretische Physik, Universität Göttingen, Friedrich-Hund-Platz 1, D-37077 Göttingen, Germany. burghard@physik.uni-goe.de

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
|March 16, 2007
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Numerical estimation of limiting large-deviation rate functions.

Physical review. E·2026
Same author

Rare events of host switching for diseases using a susceptible-infected-recovered model with mutations.

Physical review. E·2026
Same author

Distribution of the Number of Paths in Two-Dimensional Directed Percolation.

Entropy (Basel, Switzerland)·2025
Same author

Diffusion with stochastic resetting on a lattice.

Physical review. E·2025
Same author

Nonuniversality for crossword puzzle percolation.

Physical review. E·2025
Same author

Resetting by rescaling: Exact results for a diffusing particle in one dimension.

Physical review. E·2024
Same journal

Tension on dsDNA bound to ssDNA-RecA filaments may play an important role in driving efficient and accurate homology recognition and strand exchange.

Physical review. E, Statistical, nonlinear, and soft matter physics·2016
Same journal

Publisher's Note: Amplitude-phase coupling drives chimera states in globally coupled laser networks [Phys. Rev. E 91, 040901(R) (2015)].

Physical review. E, Statistical, nonlinear, and soft matter physics·2016
Same journal

Erratum: Shapes of sedimenting soft elastic capsules in a viscous fluid [Phys. Rev. E 92, 033003 (2015)].

Physical review. E, Statistical, nonlinear, and soft matter physics·2016
Same journal

Erratum: Attenuation of excitation decay rate due to collective effect [Phys. Rev. E 90, 022142 (2014)].

Physical review. E, Statistical, nonlinear, and soft matter physics·2016
Same journal

Publisher's Note: Role of connectivity and fluctuations in the nucleation of calcium waves in cardiac cells [Phys. Rev. E 92, 052715 (2015)].

Physical review. E, Statistical, nonlinear, and soft matter physics·2016
Same journal

Publisher's Note: Lattice Boltzmann approach for complex nonequilibrium flows [Phys. Rev. E 92, 043308 (2015)].

Physical review. E, Statistical, nonlinear, and soft matter physics·2016
See all related articles

Designing RNA secondary structures is possible, with the natural four-letter alphabet significantly increasing sequence designability compared to smaller alphabets. This research explores RNA designability and algorithmic complexity.

Area of Science:

  • Computational Biology
  • Bioinformatics
  • RNA Structure Prediction

Background:

  • The inverse-folding problem seeks RNA sequences for specific secondary structures.
  • Structure designability is crucial for understanding RNA function and engineering novel RNAs.
  • Previous methods lacked exhaustive search capabilities for designability.

Purpose of the Study:

  • To determine the designability of RNA secondary structures across different alphabet sizes.
  • To implement and analyze an exact algorithm for RNA inverse folding.
  • To investigate the relationship between RNA designability and algorithmic complexity.

Main Methods:

  • Developed a branch-and-bound algorithm for exhaustive search in RNA sequence space.
  • Utilized dynamic programming to calculate bounds for the branch-and-bound algorithm.

Related Experiment Videos

  • Evaluated designability for 2, 3, and 4-letter alphabets using random structure ensembles.

    • Main Results:

    • RNA secondary structures are largely undesignable with 2-letter alphabets.
    • Designability improves with 3-letter alphabets, but many structures remain undesignable.
    • In the natural 4-letter case, most structures are designable, with undesignable structures being rare.
    • High undesignability correlates with increased algorithmic complexity.
    • Algorithmic complexity is highest for naturally occurring RNA structures in the 4-letter case.

    Conclusions:

    • The natural 4-letter RNA alphabet significantly enhances secondary structure designability.
    • Algorithmic complexity in RNA inverse folding is linked to structure designability.
    • This work provides a framework for exact RNA inverse folding and designability assessment.