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 conformational sampling. I. Single-nucleotide loop closure.

C H Mak1

  • 1Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, USA. cmak@usc.edu

Journal of Computational Chemistry
|October 30, 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

Idiopathic Internal Thoracic Artery (ITA) Pseudoaneurysm treated with Endovascular Embolization.

The Medical journal of Malaysia·2017
Same author

RNA Conformational Sampling: II. Arbitrary Length Multinucleotide Loop Closure.

Journal of chemical theory and computation·2015
Same author

Ions and RNAs: Free Energies of Counterion-Mediated RNA Fold Stabilities.

Journal of chemical theory and computation·2015
Same author

The sign problem in real-time path integral simulations: using the cumulant action to implement multilevel blocking.

The Journal of chemical physics·2009
Same author

Path integral studies of the rotations of methane and its heavier isotopomers in 4He nanoclusters.

The journal of physical chemistry. A·2009
Same author

Cloning and differential expression of manganese superoxide dismutase (Mn-SOD) of Trichinella pseudospiralis.

Parasitology research·2007
Same journal

How Do DICER1 Syndrome Mutations Disrupt Catalysis? Unveiling Dicer Metal Binding Architecture and Mechanism of Action Using MD Simulations and QM/MM Calculations.

Journal of computational chemistry·2026
Same journal

Quadruple Bonding of Alkaline Earth Atoms in AeCLi<sub>4</sub> (Ae = Be - Ba) Complexes.

Journal of computational chemistry·2026
Same journal

From SMILES Codes for Reactants and Products to Transition States With VeloxChem.

Journal of computational chemistry·2026
Same journal

Electric-Field Effects on Structure and Conductance in a Cytochrome b<sub>562</sub> Junction.

Journal of computational chemistry·2026
Same journal

Quantum Chemistry Study of Luminescence Quenching in the Eu<sup>3+</sup>@UiO-67 Sensor Induced by Ag<sup>+</sup> Ions.

Journal of computational chemistry·2026
Same journal

Projection-Modified Direct Inversion in the Iterative Subspace: A Memory-Efficient Convergence Method for the Extended Molecular Ornstein-Zernike Theory.

Journal of computational chemistry·2026
See all related articles

This study introduces an efficient algorithm for closing single-nucleotide loops in nucleic acids. The novel R-representation simplifies calculations, accurately regenerating native RNA structures.

Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • The loop-closure problem is crucial for understanding nucleic acid structure and dynamics.
  • Existing methods for modeling nucleic acid loops can be computationally intensive.

Purpose of the Study:

  • To develop an efficient numerical algorithm for closing single-nucleotide loops in nucleic acids.
  • To introduce a new representation (R-representation) simplifying nucleotide conformation analysis.

Main Methods:

  • Utilized six new internal coordinates (R-representation) to define nucleotide conformation.
  • Reduced the degrees of freedom for loop closure from six to four per nucleotide.
  • Employed simple numerical techniques to solve loop-closure equations.

Related Experiment Videos

Main Results:

  • Successfully regenerated native torsion angles for over 7000 nucleotides in RNA test sets without exception.
  • Demonstrated the transformation of conformational probability density using the R-representation.
  • Provided statistical evidence for coupling between delta and nu(2) torsion angles and its impact on conformation.

Conclusions:

  • The developed algorithm offers an efficient and accurate solution for nucleic acid loop closure.
  • The R-representation simplifies conformational analysis and reveals insights into torsion angle coupling.
  • The algorithm is applicable to both nucleic acid backbones and ribose ring closure.