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

DNA Base Pairing02:27

DNA Base Pairing

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,

You might also read

Related Articles

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

Sort by
Same author

[Interactions of caffeine with DNA double helix fragments. Molecular mechanics simulation].

Biofizika·2005
Same author

[Possible configuration of dimers of Gua-Cyt bases. Computation by molecular mechanic models and density functional theory].

Biofizika·2003
Same author

Methodologies for determining capture efficiencies in surface treatment tanks.

AIHA journal : a journal for the science of occupational and environmental health and safety·2003
Same author

Results of kidney transplantation in recipients over 70 years of age: experience at a single center.

Transplantation proceedings·2003
Same author

Helical computed tomography angiography is the most efficient test to assess vascular calcifications in the iliac arterial sector in renal transplant candidates.

Transplantation proceedings·2003
Same author

Visualization of airflows in push-pull ventilation systems applied to surface treatment tanks.

AIHA journal : a journal for the science of occupational and environmental health and safety·2003

Related Experiment Video

Updated: Jul 14, 2026

Free Radicals in Chemical Biology: from Chemical Behavior to Biomarker Development
14:22

Free Radicals in Chemical Biology: from Chemical Behavior to Biomarker Development

Published on: April 15, 2013

[Interaction of caffeine with basic nucleic acids my a molecular mechanic method].

T I Grokhlina1, N A Polteva, E Gonzalez

  • 1Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia.

Biofizika
|October 30, 2003
PubMed
Summary

Caffeine (CAF) interactions with DNA were studied using computational methods. The most significant binding occurs when caffeine and DNA molecules are nearly perpendicular, suggesting a key role in DNA duplex interactions.

More Related Videos

Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC (Crosslinking of Small Molecules to Isolate Chromatin)
10:05

Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC (Crosslinking of Small Molecules to Isolate Chromatin)

Published on: January 20, 2016

Caffeine Extraction, Enzymatic Activity and Gene Expression of Caffeine Synthase from Plant Cell Suspensions
09:11

Caffeine Extraction, Enzymatic Activity and Gene Expression of Caffeine Synthase from Plant Cell Suspensions

Published on: October 2, 2018

Related Experiment Videos

Last Updated: Jul 14, 2026

Free Radicals in Chemical Biology: from Chemical Behavior to Biomarker Development
14:22

Free Radicals in Chemical Biology: from Chemical Behavior to Biomarker Development

Published on: April 15, 2013

Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC (Crosslinking of Small Molecules to Isolate Chromatin)
10:05

Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC (Crosslinking of Small Molecules to Isolate Chromatin)

Published on: January 20, 2016

Caffeine Extraction, Enzymatic Activity and Gene Expression of Caffeine Synthase from Plant Cell Suspensions
09:11

Caffeine Extraction, Enzymatic Activity and Gene Expression of Caffeine Synthase from Plant Cell Suspensions

Published on: October 2, 2018

Area of Science:

  • Computational chemistry
  • Molecular biology
  • Biophysics

Context:

  • Caffeine is a widely consumed stimulant with known biological effects.
  • Understanding caffeine's interaction with DNA is crucial for elucidating its biological mechanisms.
  • Previous studies have explored caffeine-DNA interactions, but detailed energetic analyses of specific binding modes are limited.

Purpose:

  • To computationally investigate the interaction energies between caffeine and DNA bases/basepairs.
  • To identify stable binding configurations and their relative stabilities.
  • To determine the preferred modes of caffeine interaction with DNA monomers, single-stranded fragments, and double helices.

Summary:

  • Calculations revealed three types of stable caffeine-DNA arrangements based on interaction energy minima.
  • One stable arrangement involves molecular stacking, relevant for single-stranded DNA interactions.
  • Two other arrangements involve hydrogen bonding, with a perpendicular molecular orientation showing the most favorable interaction energies for DNA duplexes.

Impact:

  • Identifies specific molecular arrangements critical for caffeine-DNA binding.
  • Provides a quantitative basis for understanding caffeine's influence on DNA structure and function.
  • Suggests that hydrogen-bonded, perpendicular interactions are most significant for caffeine's effect on the DNA double helix.