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

Related Concept Videos

Nucleic Acid Structure

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...

You might also read

Related Articles

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

Sort by

Same author

Dynamic Covalent Programming at DNA Base-Pairing Interfaces.

Journal of the American Chemical Society·2026

Same author

A non-equilibrium oscillatory starch derivative driven by thermally induced phase separation: Application in dynamic anti-counterfeiting and wastewater treatment.

Carbohydrate polymers·2026

Same author

Artificial intelligence powered voice assistants: A revolution in operating room interactions.

Digital health·2026

Same author

Effectiveness of Bleeding Control Methods in Rhinoplasty: A Systematic Review and Meta-Analysis.

Archives of plastic surgery·2026

Same author

Epigenetic reprogramming for ocular aging and disease: Mechanisms, biomarkers, and the road to the clinic.

Progress in retinal and eye research·2026

Same author

Genome-wide association studies and genomic selection for leaf-related traits in maize.

Frontiers in plant science·2025

Search research articles

Related Experiment Video

Updated: Jul 30, 2025

Efficient Purification and LC-MS/MS-based Assay Development for Ten-Eleven Translocation-2 5-Methylcytosine Dioxygenase

Efficient Purification and LC-MS/MS-based Assay Development for Ten-Eleven Translocation-2 5-Methylcytosine Dioxygenase

Published on: October 15, 2018

A Bright and Ionizable Cytosine Mimic for i-Motif Structures.

Ashkan Karimi^1,2, Kaixiang Wang¹, Kaleena Basran¹

¹Department of Chemistry, McGill University, Montreal, Quebec H3A-0B8, Canada.

Bioconjugate Chemistry

|May 17, 2023

Summary

A novel fluorescent cytosine analog, ^tsC, enables real-time tracking of DNA structural changes. This bright probe mimics cytosine's properties, aiding in understanding DNA folding and i-motif formation.

More Related Videos

Ensemble Force Spectroscopy by Shear Forces

Ensemble Force Spectroscopy by Shear Forces

Published on: July 26, 2022

Sequence-specific Labeling of Nucleic Acids and Proteins with Methyltransferases and Cofactor Analogues

Sequence-specific Labeling of Nucleic Acids and Proteins with Methyltransferases and Cofactor Analogues

Published on: November 22, 2014

Related Experiment Videos

Last Updated: Jul 30, 2025

Efficient Purification and LC-MS/MS-based Assay Development for Ten-Eleven Translocation-2 5-Methylcytosine Dioxygenase

Efficient Purification and LC-MS/MS-based Assay Development for Ten-Eleven Translocation-2 5-Methylcytosine Dioxygenase

Published on: October 15, 2018

Ensemble Force Spectroscopy by Shear Forces

Ensemble Force Spectroscopy by Shear Forces

Published on: July 26, 2022

Sequence-specific Labeling of Nucleic Acids and Proteins with Methyltransferases and Cofactor Analogues

Sequence-specific Labeling of Nucleic Acids and Proteins with Methyltransferases and Cofactor Analogues

Published on: November 22, 2014

Area of Science:

Biophysical Chemistry
Molecular Biology
Nucleic Acid Chemistry

Background:

Understanding DNA structural dynamics, including i-motif formation, is crucial for various biological processes.
Existing fluorescent probes often lack the specific acid-base properties or fluorescence characteristics needed for real-time monitoring of DNA conformational changes.

Purpose of the Study:

To synthesize and characterize a new fluorescent cytosine analog, ^tsC, for monitoring DNA structures.
To investigate the utility of ^tsC in tracking dynamic conversions between single-stranded, double-stranded, and i-motif DNA structures.
To explore the formation of hemiprotonated base pairs in DNA structures.

Main Methods:

Chemical synthesis of the fluorescent cytosine analog ^tsC.
Incorporation of ^tsC into DNA sequences, specifically human telomeric repeat sequences.
Spectroscopic analysis, including fluorescence emission and circular dichroism, to monitor protonation and structural changes.
Ratiometric analysis of ^tsC fluorescence to track real-time structural conversions.

Main Results:

^tsC was successfully synthesized, exhibiting bright and red-shifted fluorescence upon protonation.
^tsC accurately mimics the acid-base properties of cytosine (pKa ≈ 4.3).
Ratiometric fluorescence measurements allowed real-time tracking of reversible DNA structural transitions (single-stranded, double-stranded, i-motif).
Evidence suggests the formation of hemiprotonated C⁺:C base pairs in partially folded single-stranded DNA, even without global i-motif formation at pH 6.0.

Conclusions:

^tsC serves as a valuable tool for real-time monitoring of DNA structural dynamics due to its fluorescence properties and cytosine-like acid-base behavior.
The study provides insights into the formation and stability of hemiprotonated base pairs in DNA.
^tsC facilitates the investigation of DNA folding pathways and the conditions favoring i-motif formation.