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

Computer modeling 16 S ribosomal RNA.

J M Hubbard1, J E Hearst

  • 1Department of Chemistry, University of California, Berkeley 94720.

Journal of Molecular Biology
|October 5, 1991
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

Optimizing biologic sequencing in metastatic colorectal cancer: first line and beyond.

Current oncology (Toronto, Ont.)·2019
Same author

Determination of the average orientation of DNA in the octopus sperm Eledone cirrhossa through polarized light scattering.

Applied optics·2010
Same author

Current activity guidelines for CABG patients are too restrictive: comparison of the forces exerted on the median sternotomy during a cough vs. lifting activities combined with valsalva maneuver.

The Thoracic and cardiovascular surgeon·2008
Same author

Killed but metabolically active microbes: a new vaccine paradigm for eliciting effector T-cell responses and protective immunity.

Nature medicine·2005
Same author

Recombinational and mutagenic repair of psoralen interstrand cross-links in Saccharomyces cerevisiae.

The Journal of biological chemistry·2001
Same author

The crystal structures of psoralen cross-linked DNAs: drug-dependent formation of Holliday junctions.

Journal of molecular biology·2001
Same journal

UPF3A and UPF3B shape the transcriptome cooperatively yet oppose cell function.

Journal of molecular biology·2026
Same journal

Antibody-secreting cells integrate efficient NMD with non‑canonical UPR signaling to maintain proteostasis and support massive immunoglobulin synthesis.

Journal of molecular biology·2026
Same journal

Small molecule stabilization of diverse amyloidogenic immunoglobulin light chains revealed by hydrogen-deuterium exchange mass spectrometry.

Journal of molecular biology·2026
Same journal

UPF1 at Work: Structural and Mechanistic Insights Into a Master Regulator of Nonsense-Mediated mRNA Decay.

Journal of molecular biology·2026
Same journal

Structural basis for the pro-amyloidogenic action and ligand binding of a novel W72R variant of human apolipoprotein A-I.

Journal of molecular biology·2026
Same journal

Cryo-EM Structure of the C. elegans Septin Tetramer Reveals a Revised Architecture and Conserved Positional Orthology.

Journal of molecular biology·2026
See all related articles

A novel computational protocol objectively generates a 3D structure for 16S ribosomal RNA (rRNA). This method uses distance geometry and cross-linking data, improving upon traditional modeling for RNA structure analysis.

Area of Science:

  • Computational Biology
  • Structural Biology
  • Molecular Biology

Background:

  • Accurate three-dimensional (3D) modeling of ribosomal RNA (rRNA) is crucial for understanding its function.
  • Traditional modeling techniques can be subjective and lack reproducibility.
  • Existing models often lack the resolution required for detailed analysis.

Purpose of the Study:

  • To develop an objective and reproducible computational protocol for generating a 3D structure of 16S rRNA.
  • To improve upon existing RNA modeling techniques by incorporating distance geometry.
  • To create a high-resolution model of 16S rRNA structure suitable for broader research use.

Main Methods:

  • A novel computer protocol utilizing distance geometry to objectively fold the 16S rRNA molecule.

Related Experiment Videos

  • The protocol models RNA as linked double-stranded helices and flexible single-strands.
  • Constraints derived from chemical cross-linking studies and phylogenetic data were employed.

    • Main Results:

    • A 3D model of 16S rRNA was generated without human intervention, achieving high resolution.
    • The model's dimensions (245 x 190 x 140 Å) are compatible with the 30S ribosomal subunit.
    • The model's radius of gyration (76 Å) is consistent with folded 16S rRNA, and computer graphics facilitate interpretation.

    Conclusions:

    • The developed protocol provides an objective and reproducible method for 3D RNA structure determination.
    • The generated 16S rRNA model offers a resolution comparable to preliminary X-ray crystallography.
    • The model's format enhances accessibility for researchers in ribosomal structure and function studies.