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

Conserved Binding Sites01:49

Conserved Binding Sites

4.2K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.2K
Nucleic Acid Structure01:25

Nucleic Acid Structure

6.0K
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...
6.0K
Improving Translational Accuracy02:07

Improving Translational Accuracy

9.1K
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
9.1K
Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

13.9K
For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
13.9K
DNA Base Pairing02:27

DNA Base Pairing

27.0K
Erwin Chargaff’s rules on DNA equivalence paved the way for the discovery of base pairing in DNA. Chargaff’s rules state that in a double-stranded DNA molecule,
27.0K
Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

49.1K
Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
49.1K

You might also read

Related Articles

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

Sort by
Same author

Assessing the contribution of rare DNA states to cancer mutational signatures using sequence-specific conformational fingerprinting.

Nature communications·2026
Same author

Thermodynamic prediction of RNA cellular activity from sequence via conformational ensembles.

Cell·2026
Same author

Revealing hidden protonated conformational states in RNA dynamic ensembles.

Nucleic acids research·2025
Same author

Probing rare and short-lived conformational states in nucleic acids using off-resonance carbonyl and guanidino carbon R<sub>1ρ</sub> relaxation dispersion.

Journal of magnetic resonance (San Diego, Calif. : 1997)·2025
Same author

Kinetic Dissection of Proton-Coupled Conformational Transitions in Nucleic Acids by Integrating pH-Dependent NMR and Chemical Modifications.

Journal of the American Chemical Society·2025
Same author

Insight into the Conformational Ensembles Formed by U-U and T-T Mismatches in RNA and DNA Duplexes From a Structure-based Survey, NMR, and Molecular Dynamics Simulations.

Journal of molecular biology·2025

Related Experiment Video

Updated: Jun 7, 2025

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

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

20.5K

Conformational penalties: New insights into nucleic acid recognition.

Ainan Geng1, Rohit Roy2, Hashim M Al-Hashimi3

  • 1Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA.

Current Opinion in Structural Biology
|November 10, 2024
PubMed
Summary

Understanding the energy cost of nucleic acid structural changes during binding is key. Recent advances allow measurement of these conformational penalties, revealing their critical role in molecular recognition and cellular function.

Keywords:
BindingConformational ensemblesFoldingNucleic acid recognition

More Related Videos

Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids
09:04

Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids

Published on: September 21, 2017

9.5K
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.2K

Related Experiment Videos

Last Updated: Jun 7, 2025

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

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

20.5K
Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids
09:04

Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids

Published on: September 21, 2017

9.5K
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.2K

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Thermodynamics

Background:

  • Nucleic acid structure and function are central to molecular biology.
  • Binding affinity and specificity are crucial for biological processes.
  • The energetic costs of structural rearrangements in nucleic acids are often overlooked.

Purpose of the Study:

  • To review recent advancements in measuring conformational penalties in nucleic acids.
  • To determine the contribution of these penalties to nucleic acid recognition, folding, and regulation.
  • To highlight the thermodynamic basis of nucleic acid-protein interactions.

Main Methods:

  • Development of methods to measure and characterize low-populated conformational states.
  • High-throughput techniques for obtaining ensemble information.
  • Application of methods in large macromolecular assemblies and cellular environments.
  • Creation of quantitative thermodynamic models.

Main Results:

  • Progress in characterizing transient and rare nucleic acid conformations.
  • Ensemble data acquisition is now feasible for complex systems.
  • Thermodynamic models successfully link conformational penalties to biological activity.
  • Conformational energy costs significantly impact nucleic acid recognition.

Conclusions:

  • Conformational penalties are a critical thermodynamic factor in nucleic acid binding.
  • Accurate measurement and modeling of these penalties are essential for understanding nucleic acid function.
  • Future research should continue to explore the role of dynamics in nucleic acid-protein interactions.