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 Concept Videos

Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

47.4K
Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
47.4K
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

5.5K
5.5K
Nucleic Acid Structure01:25

Nucleic Acid Structure

9.6K
The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA...
9.6K
Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

20.0K
Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
20.0K
Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

2.9K
2.9K
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

1.3K
At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
1.3K

You might also read

Related Articles

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

Sort by
Same author

5-Formylcytosine is an activating epigenetic mark for RNA Pol III during zygotic reprogramming.

Cell·2024
Same author

Nanostructured lipopeptide-based membranomimetics for stabilizing bacteriorhodopsin.

Biomaterials science·2024
Same author

Combining Complementarity and Binding Energetics in the Assessment of Protein Interactions: EnCPdock-A Practical Manual.

Journal of computational biology : a journal of computational molecular cell biology·2024
Same author

Base pair compositional variability influences DNA structural stability and tunes hydration thermodynamics and dynamics.

The Journal of chemical physics·2023
Same author

EnCPdock: a web-interface for direct conjoint comparative analyses of complementarity and binding energetics in inter-protein associations.

Journal of molecular modeling·2023
Same author

Slower diffusion and anomalous association of R453W lamin A protein alter nuclear architecture in AD-EDMD.

RSC advances·2022

Related Experiment Video

Updated: Feb 22, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

21.3K

Intrinsic structural variability in GNRA-like tetraloops: insight from molecular dynamics simulation.

Debasish Mukherjee1, Dhananjay Bhattacharyya2

  • 1Computational Science Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India.

Journal of Molecular Modeling
|October 2, 2017
PubMed
Summary

MicroRNA hairpin loops, crucial for biogenesis, were analyzed using molecular dynamics. We quantified interbase stacking preferences in tetraloops, revealing structural insights into RNA interactions.

Keywords:
Fraying effectPre-miRNAPseudo-torsion angleStacking overlapStem-loop structuresSugar pucker

More Related Videos

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

16.1K
Design and Synthesis of a Reconfigurable DNA Accordion Rack
07:44

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Published on: August 15, 2018

7.5K

Related Experiment Videos

Last Updated: Feb 22, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

21.3K
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

16.1K
Design and Synthesis of a Reconfigurable DNA Accordion Rack
07:44

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Published on: August 15, 2018

7.5K

Area of Science:

  • Structural biology
  • Molecular dynamics
  • RNA biophysics

Background:

  • Hairpin loops in RNA, including pre-microRNAs, are vital for biological interactions and microRNA biogenesis.
  • Previous studies noted hairpin loops of varying sequences in RNA structures, often comprising four residues (tetraloops).

Purpose of the Study:

  • To analyze the structural and functional characteristics of six unexplored tetraloops and canonical GNRA tetraloops.
  • To quantify loop stability through base-base stacking, hydrogen bonding, and backbone variability.
  • To determine interbase stacking preferences within single-stranded hairpin loop bases.

Main Methods:

  • Molecular dynamics simulations were employed to analyze tetraloop structures.
  • Analyses included quantifying base-base stacking, base-sugar and base-phosphate hydrogen bonding, and backbone variability.
  • Interbase stacking preferences of unpaired bases in hairpin loops were specifically quantified.

Main Results:

  • Distinct interbase stacking preferences were identified for single-stranded bases within hairpin loops.
  • Some non-GNRA loop sequences exhibited canonical GNRA structural properties.
  • Loop stability was assessed through various quantitative measures.

Conclusions:

  • The study provides novel quantification of interbase stacking preferences in RNA tetraloops.
  • Structural insights into hairpin loop interactions and their role in RNA function are elucidated.
  • Findings contribute to understanding the diversity and properties of RNA hairpin loops.