Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Search research articles

Related Experiment Videos

Sequence dependence in base flipping: experimental and computational studies.

Lauren L O'Neil¹, Olaf Wiest

¹Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, 46556-5670, USA.

Organic & Biomolecular Chemistry

|January 26, 2008

Summary

This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

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

Sort by

Same author

Organic Chemistry as a Catalyst for AI Innovation: Challenges, Methods, and Emerging Paradigms.

Chemical reviews·2026

Same author

A Lactone-Enabled Approach to Metronidazole-Based Scaffolds.

The Journal of organic chemistry·2026

Same author

Rapid FF Generation via Hessian-Informed Initial Parameters and Automated Refinement.

Journal of chemical theory and computation·2025

Same author

Conformation Dependent Features of Bisphosphine Ligands.

The Journal of organic chemistry·2025

Same author

Variants of the Ebola virus matrix protein VP40 have differential effects on oligomerization and plasma membrane interactions.

The Journal of biological chemistry·2025

Same author

Synthesis of Caged HMG-CoA Reductase Substrates for the Elucidation of Cellular Pathways.

The Journal of organic chemistry·2024

Same journal

Catalytic synthesis of saturated azacycles using transborylation.

Organic & biomolecular chemistry·2026

Same journal

Pyridines with adamantane fragments and their 1,2,4-triazine analogues as anti-quorum-sensing agents, synthesis and molecular docking.

Organic & biomolecular chemistry·2026

Same journal

Synthesis of polymethylene-linked bis(cyclobutane-fused chromanones) mediated by gold photocatalysis.

Organic & biomolecular chemistry·2026

Same journal

Palladium-catalyzed chelation-assisted C-H functionalization of quinoline aldehydes to esters with mechanistic insights.

Organic & biomolecular chemistry·2026

Same journal

One-pot metal-free access to uracil-benzofuran bis-heterocycles: synthesis and DFT insights.

Organic & biomolecular chemistry·2026

Same journal

Transition-metal-free three-component synthesis of α-tertiary trifluoromethyl phosphonates from CF<sub>3</sub> diazo compounds.

Organic & biomolecular chemistry·2026

See all related articles

Base flipping in DNA, the movement of a base out of its stacked position, is energetically costly for undamaged DNA. However, this study explored base flipping in DNA with abasic sites using a novel assay.

Area of Science:

Molecular Biology
Biochemistry
Structural Biology

Background:

Base flipping involves moving a DNA base from an intrahelical, stacked position to an extrahelical, solvent-exposed state.
Favorable intrahelical interactions (hydrogen bonding, base stacking) make base flipping energetically unfavorable in undamaged DNA duplexes.
Damaged DNA bases may exhibit a lower energetic cost for base flipping.

Purpose of the Study:

To investigate the sequence dependence of base flipping in DNA containing an abasic site.
To quantify the energetic parameters associated with base flipping in damaged DNA.
To compare base flipping behavior in single- and double-stranded DNA.

Main Methods:

Development and application of a selective, non-covalent assay for detecting base flipping.

Related Experiment Videos

Determination of dissociation constants for a zinc-cyclen complex binding to DNA.

Measurement of equilibrium constants for base flipping.

Utilizing molecular dynamics simulations to analyze zinc-cyclen complex interactions with DNA.

Main Results:

The study determined sequence-dependent dissociation and equilibrium constants for base flipping in DNA with abasic sites.
Molecular dynamics simulations provided insights into the binding of the zinc-cyclen complex to single- and double-stranded DNA.
Differences in dissociation constants between single- and double-stranded DNA systems were rationalized.

Conclusions:

The energetic cost of base flipping is significantly influenced by DNA sequence, particularly in the presence of abasic sites.
The zinc-cyclen complex serves as a useful tool for studying base flipping dynamics.
Understanding base flipping mechanisms is crucial for DNA repair and other biological processes.