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

Atomic Force Microscopy01:08

Atomic Force Microscopy

4.3K
Atomic force microscopy (AFM) is a type of scanning probe microscopy that can analyze topographic details of various specimens like ceramics, glass, polymers, and biological samples. AFM offers over 1000 times more resolution than the optical imaging system. Images generated from AFM are three-dimensional surface profiles, offering an advantage over the flat, two-dimensional images from other imaging techniques.
The AFM Probe
The probe is regarded as the heart of any AFM setup and comprises the...
4.3K

You might also read

Related Articles

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

Sort by
Same author

The Viral Immunoshadow: Early Adenovirus Strategies for Cloaking Innate Immunity with E1A, E4orf1, and Beyond.

Cells·2026
Same author

C11orf54 catalyzes L-xylulose formation in human metabolism.

Proceedings of the National Academy of Sciences of the United States of America·2025
Same author

Activity of Membrane-Permeabilizing Lpt Peptides.

Biomolecules·2024
Same author

Adenovirus small E1A directs activation of Alu transcription at YAP/TEAD- and AP-1-bound enhancers through interactions with the EP400 chromatin remodeler.

Nucleic acids research·2024
Same author

TFIIIC as a Potential Epigenetic Modulator of Histone Acetylation in Human Stem Cells.

International journal of molecular sciences·2023
Same author

Beyond the Interface: Improved Pulmonary Surfactant-Assisted Drug Delivery through Surface-Associated Structures.

Pharmaceutics·2023

Related Experiment Video

Updated: Jan 2, 2026

High-Speed Atomic Force Microscopy Imaging of DNA Three-Point-Star Motif Self Assembly Using Photothermal Off-Resonance Tapping
08:59

High-Speed Atomic Force Microscopy Imaging of DNA Three-Point-Star Motif Self Assembly Using Photothermal Off-Resonance Tapping

Published on: March 22, 2024

762

A New Strategy to Investigate RNA:DNA Triplex Using Atomic Force Microscopy.

Giovanni Merici1, Davide Amidani1, Giorgio Dieci1

  • 1Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy.

International Journal of Molecular Sciences
|March 13, 2024
PubMed
Summary
This summary is machine-generated.

Long non-coding RNAs (lncRNAs) regulate genes by binding DNA. Atomic force microscopy visualized RNA:DNA triplex formation, a key regulatory mechanism, offering new insights into gene regulation.

Keywords:
RNA:DNA triplexatomic force microscopylncRNA

More Related Videos

Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids
09:04

Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids

Published on: September 21, 2017

9.5K
Nanomanipulation of Single RNA Molecules by Optical Tweezers
06:59

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Published on: August 20, 2014

14.8K

Related Experiment Videos

Last Updated: Jan 2, 2026

High-Speed Atomic Force Microscopy Imaging of DNA Three-Point-Star Motif Self Assembly Using Photothermal Off-Resonance Tapping
08:59

High-Speed Atomic Force Microscopy Imaging of DNA Three-Point-Star Motif Self Assembly Using Photothermal Off-Resonance Tapping

Published on: March 22, 2024

762
Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids
09:04

Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids

Published on: September 21, 2017

9.5K
Nanomanipulation of Single RNA Molecules by Optical Tweezers
06:59

Nanomanipulation of Single RNA Molecules by Optical Tweezers

Published on: August 20, 2014

14.8K

Area of Science:

  • Molecular Biology
  • Genetics
  • Biophysics

Background:

  • Long non-coding RNAs (lncRNAs) are crucial regulators of gene expression and genome organization.
  • LncRNA-DNA interactions occur via protein binding or direct sequence-specific RNA:DNA triplex formation.
  • Understanding these interactions is vital for deciphering gene regulatory mechanisms.

Purpose of the Study:

  • To develop and validate a novel atomic force microscopy (AFM) strategy for characterizing RNA:DNA triplex formation.
  • To visualize and study the specific RNA:DNA triplex formed between Khps1 lncRNA and the SPHK1 gene enhancer.
  • To investigate the influence of environmental conditions (pH, temperature) on triplex stability.

Main Methods:

  • Utilized atomic force microscopy (AFM) for high-resolution visualization of molecular interactions.
  • Focused on the Khps1 lncRNA and its interaction with the SPHK1 enhancer region.
  • Performed experiments under varying pH and temperature conditions to assess triplex formation robustness.

Main Results:

  • Successfully visualized the formation of RNA:DNA triplexes between Khps1 lncRNA and the SPHK1 enhancer using AFM.
  • Demonstrated stable triplex formation across a range of pH and temperature conditions.
  • Identified challenges in distinguishing triplexes from R-loops, highlighting the need for refined analytical approaches.

Conclusions:

  • Atomic force microscopy provides an effective strategy for visualizing lncRNA:DNA triplex formation at the single-molecule level.
  • The study confirms the formation and stability of RNA:DNA triplexes involving Khps1 lncRNA and the SPHK1 enhancer.
  • This AFM-based approach offers new perspectives for studying lncRNA-mediated gene regulation.