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

The DNA Helix01:16

The DNA Helix

Overview
¹H NMR: Complex Splitting01:13

¹H NMR: Complex Splitting

A proton M that is coupled to a proton X results in doublet signals for M. However, NMR-active nuclei can be simultaneously coupled to more than one nonequivalent nucleus. When M is coupled to a second proton A, such as in styrene oxide, each peak in the doublet is split into another doublet.
Splitting diagrams or splitting tree diagrams are routinely used to depict such complex couplings. While drawing splitting diagrams, the splitting with the larger coupling constant is usually applied first.
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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...
The DNA Helix01:07

The DNA Helix

Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most viruses. DNA is composed of two strands of nucleotides that wind around each other to form a spring-like structure called a double helix. However, the double helix is not perfectly symmetrical. Instead, there are regularly occurring grooves in the structure. The major groove occurs where the sugar-phosphate backbones are relatively far apart. This space...
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
Nucleic Acid Structure01:25

Nucleic Acid Structure

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 has a double-helix structure. The...

You might also read

Related Articles

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

Sort by
Same author

A new NMR protocol for estimating protein side chain rotameric preferences using <sup>1</sup>H relaxation and J couplings.

Journal of magnetic resonance (San Diego, Calif. : 1997)·2026
Same author

The NMR Exchange Format (NEF): Specification and Applications.

bioRxiv : the preprint server for biology·2026
Same author

Development of an optimized parameter set for monovalent ions in the reference interaction site model of solvation.

The Journal of chemical physics·2026
Same author

The scientific legacy of Martin Karplus from the perspective of his collaborators.

Biophysical journal·2026
Same author

Validated ligand geometries for macromolecular refinement restraints and molecular-mechanics force fields.

Acta crystallographica. Section D, Structural biology·2026
Same author

Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0].

Living journal of computational molecular science·2026

Related Experiment Video

Updated: Jul 20, 2026

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

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

NMR structure of a cyclic polyamide-DNA complex.

Qing Zhang1, Tammy J Dwyer, Vickie Tsui

  • 1Department of Chemistry, University of California, Berkeley, California 94720-1460, USA.

Journal of the American Chemical Society
|June 24, 2004
PubMed
Summary

This study reveals the structure of a cyclic polyamide bound to DNA using NMR and molecular dynamics. The ligand binds tightly, showing DNA flexibility despite structural alterations.

More Related Videos

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles
10:23

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles

Published on: May 8, 2015

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
14:55

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

Related Experiment Videos

Last Updated: Jul 20, 2026

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

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles
10:23

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles

Published on: May 8, 2015

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
14:55

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

Area of Science:

  • Structural Biology
  • Biochemistry
  • Molecular Biophysics

Background:

  • Cyclic polyamides are investigated as DNA-binding agents.
  • Understanding ligand-DNA interactions is crucial for drug design.

Purpose of the Study:

  • To determine the solution structure of a cyclic polyamide complexed with a specific DNA oligomer.
  • To analyze the binding interactions and dynamics of the polyamide-DNA complex.

Main Methods:

  • Nuclear Magnetic Resonance (NMR) spectroscopy was used to obtain 2D (1)H NMR data.
  • Distance restraints were derived from NOESY cross-peak intensities using MARDIGRAS.
  • Restrained molecular dynamics calculations with a solvent model were performed to generate structures.

Main Results:

  • The solution structure of the cyclic polyamide (cyclo-gamma-ImPyPy-gamma-PyPyPy-) complexed to a DNA duplex was determined.
  • The ligand exhibits nanomolar dissociation constant for DNA binding.
  • Structures showed some DNA distortion and altered ligand ring stacking due to cyclization, yet maintained similar DNA interactions compared to unlinked complexes.
  • Slow ligand dissociation and reduced DNA opening fluctuations were observed.

Conclusions:

  • The cyclic polyamide binds stably to DNA, inducing minor structural changes.
  • Cyclization affects ligand conformation but not overall DNA interaction profile.
  • The ligand-DNA complex demonstrates a dynamic interplay between ligand binding and DNA flexibility.