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

Nucleic Acid Structure01:25

Nucleic Acid Structure

7.2K
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...
7.2K

You might also read

Related Articles

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

Sort by
Same author

Theoretical Examination on the Chiral Separation Mechanism of Ibuprofen on Cellulose Tris(4-methylbenzoate).

Molecules (Basel, Switzerland)·2025
Same author

Theoretical analysis of the Norrish reaction mechanism in aliphatic polyamide.

Physical chemistry chemical physics : PCCP·2025
Same author

Application of Elongation Method-Based Alternating Property Optimization: (Hyper)polarizability of Substituted Polyfuran.

Molecules (Basel, Switzerland)·2025
Same author

Mechanistic Study of Substituent Effect on Photoinduced O-C Bond Activation in Polycarbonate.

Molecules (Basel, Switzerland)·2025
Same author

Through-Space/Through-Bond Energy Decomposition Analysis Clarifies the Mechanism of Transition Mutation in DNA Containing O6-Methylguanine Lesion.

Journal of computational chemistry·2025
Same author

Elongation Method-Based Alternating Multi-Directional Automated Property Optimization Process and Its Application.

Journal of computational chemistry·2025
Same journal

DNA conformation determines the size of DNA-histone H1 nanoscale clusters.

The Journal of chemical physics·2026
Same journal

Confinement-controlled phase behavior of charged colloids under gravity.

The Journal of chemical physics·2026
Same journal

Dissociation line of tetrahydrofuran hydrates from NPH molecular dynamics simulations.

The Journal of chemical physics·2026
Same journal

Development of a magnetic interatomic potential for cubic antiferromagnets: The case of NiO.

The Journal of chemical physics·2026
Same journal

Simulations of solvent effects on excited state dynamics of p-DAPA, a red single benzene-based fluorophore.

The Journal of chemical physics·2026
Same journal

Rotational excitation of thioformaldehyde (H2CS) in collisions with molecular hydrogen.

The Journal of chemical physics·2026
See all related articles

Related Experiment Video

Updated: Sep 21, 2025

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

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

20.7K

Local electronic structure analysis by ab initio elongation method: A benchmark using DNA block polymers.

Yuuichi Orimoto1, Keisuke Hisama2, Yuriko Aoki1

  • 1Department of Material Sciences, Faculty of Engineering Sciences, Kyushu University, 6-1 Kasuga-Park, Fukuoka 816-8580, Japan.

The Journal of Chemical Physics
|June 1, 2022
PubMed
Summary
This summary is machine-generated.

The ab initio elongation method enables accurate, linear-scaling electronic structure calculations for large molecules. This approach efficiently detects unique local electronic structures in DNA polymers, paving the way for future applications.

More Related Videos

DNA Nanotubes as a Versatile Tool to Study Semiflexible Polymers
08:00

DNA Nanotubes as a Versatile Tool to Study Semiflexible Polymers

Published on: October 25, 2017

7.0K
Studying DNA Looping by Single-Molecule FRET
11:27

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

15.5K

Related Experiment Videos

Last Updated: Sep 21, 2025

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

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

20.7K
DNA Nanotubes as a Versatile Tool to Study Semiflexible Polymers
08:00

DNA Nanotubes as a Versatile Tool to Study Semiflexible Polymers

Published on: October 25, 2017

7.0K
Studying DNA Looping by Single-Molecule FRET
11:27

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

15.5K

Area of Science:

  • Computational chemistry
  • Quantum chemistry
  • Materials science

Background:

  • Accurate electronic structure calculations are crucial for understanding molecular properties.
  • Scaling challenges limit traditional methods for large, aperiodic systems like DNA polymers.
  • The ab initio elongation (ELG) method offers a linear-scaling approach.

Purpose of the Study:

  • To evaluate the effectiveness of the ELG method for local electronic structure analysis in DNA block polymers.
  • To demonstrate the method's capability for efficient detection of singular electronic structures.
  • To explore the potential for high-throughput analysis and integration with machine learning.

Main Methods:

  • Sequential elongation of electronic structures using region-localized molecular orbitals (RLMOs).
  • Partial self-consistent-field calculations within an interaction space.
  • Analysis of canonical molecular orbitals (CMOs) and local orbital energies.

Main Results:

  • The ELG method successfully performed linear-scaling electronic structure calculations for DNA block polymers.
  • Local site information, including HOMO/LUMO, was efficiently obtained.
  • The method demonstrated effectiveness in identifying unique local electronic structures.

Conclusions:

  • The ELG method is a feasible and accurate approach for large-scale electronic structure calculations.
  • This method facilitates efficient detection of singular electronic structures in complex systems.
  • Combining ELG with machine learning offers a promising strategy for high-throughput analysis and discovery.