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 Topoisomerases02:02

DNA Topoisomerases

36.4K
Topoisomerases are enzymes that relax overwound DNA molecules during various cell processes, including DNA replication and transcription. These enzymes regulate positive and negative DNA supercoiling without changing the nucleotide sequence. DNA overwinding in a clockwise direction results in positively supercoiled DNA, whereas underwinding in a counterclockwise direction produces negatively supercoiled DNA.
Types and Mechanism of action
Topoisomerases are divided into two main types. ...
36.4K
DNA Helicases00:55

DNA Helicases

24.5K
DNA unwinding helicase enzymes are a type of motor protein. Motor proteins can translocate along filaments or polymers using energy generated from ATP hydrolysis. Helicases are involved in all the important cellular processes where DNA unwinding is required, such as DNA replication, repair, recombination, and transcription. They are present in all living organisms, but vary in their structure, function, and mechanism of action. For example, in prokaryotes, DnaB helicase binds and translocates...
24.5K
Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

17.0K
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...
17.0K
DNA as a Genetic Template02:05

DNA as a Genetic Template

28.2K
Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
28.2K
The DNA Replication Fork01:02

The DNA Replication Fork

41.6K
An organism’s genome needs to be duplicated in an efficient and error-free manner for its growth and survival. The replication fork is a Y-shaped active region where two strands of DNA are separated and replicated continuously. The coupling of DNA unzipping and complementary strand synthesis is a characteristic feature of a replication fork.   Organisms with small circular DNA, such as E. coli, often have a single origin of replication; therefore, they have only two replication...
41.6K
The DNA Replication Fork01:02

The DNA Replication Fork

18.8K
18.8K

You might also read

Related Articles

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

Sort by
Same author

Register-Shifted Structures in Uracil:Adenine and Uracil:Guanine Base-Paired DNA.

Biochemistry·2026
Same author

PME Switching in Confinement Simulations of Charged Solutes.

The journal of physical chemistry. A·2024
Same author

CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.

The journal of physical chemistry. B·2024
Same author

Conformational Free-Energy Differences of Large Solvated Systems with the Focused Confinement Method.

Journal of chemical theory and computation·2020
Same author

Rational discovery of antimetastatic agents targeting the intrinsically disordered region of MBD2.

Science advances·2019
Same author

Calculation of Conformational Free Energies with the Focused Confinement Method.

Journal of chemical theory and computation·2019

Related Experiment Video

Updated: Feb 26, 2026

Studying DNA Looping by Single-Molecule FRET
11:27

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

15.9K

Free Energy Coupling between DNA Bending and Base Flipping.

Ning Ma1, Arjan van der Vaart1

  • 1Department of Chemistry, University of South Florida , 4202 East Fowler Avenue CHE 205, Tampa, Florida 33620, United States.

Journal of Chemical Information and Modeling
|July 12, 2017
PubMed
Summary

DNA bending and thymine base flipping are energetically coupled, influenced by neighboring bases and DNA damage. Bending facilitates flipping, especially towards the major groove, in both normal and damaged DNA.

More Related Videos

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
Stretching Short Sequences of DNA with Constant Force Axial Optical Tweezers
08:48

Stretching Short Sequences of DNA with Constant Force Axial Optical Tweezers

Published on: October 13, 2011

13.6K

Related Experiment Videos

Last Updated: Feb 26, 2026

Studying DNA Looping by Single-Molecule FRET
11:27

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

15.9K
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
Stretching Short Sequences of DNA with Constant Force Axial Optical Tweezers
08:48

Stretching Short Sequences of DNA with Constant Force Axial Optical Tweezers

Published on: October 13, 2011

13.6K

Area of Science:

  • Molecular Biology
  • Biophysics
  • Computational Chemistry

Background:

  • DNA base flipping is crucial for various biological processes.
  • Understanding the energetic interplay between DNA conformation and base accessibility is key.

Purpose of the Study:

  • To investigate the free energy landscape of thymine base flipping in double-stranded DNA.
  • To determine the influence of DNA bending and neighboring base pairs on base flipping energetics.
  • To compare base flipping in undamaged DNA versus DNA with photoproducts.

Main Methods:

  • Free energy simulations were employed to model DNA systems.
  • Energetic costs associated with base flipping were calculated.
  • Structural analyses of protein-DNA complexes were used for verification.

Main Results:

  • Base flipping energetics are sequence-dependent, with certain base pairs increasing the cost.
  • DNA bending generally aids base flipping, particularly at higher bending angles.
  • Flipping of 6-4 pyrimidine-pyrimidone photoproducts is energetically more favorable than in undamaged DNA.
  • Major groove flipping is preferred for both undamaged and damaged DNA.

Conclusions:

  • DNA bending and base flipping are coupled processes, with bending priming the system for flipping.
  • DNA damage, specifically 6-4 photoproducts, significantly alters the energetics of base flipping and DNA bending.
  • Computational findings are consistent with structural observations in protein-DNA complexes.