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

Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Sanger Sequencing01:57

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
Nucleic Acid Structure01:25

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 has a double-helix structure. The...
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...

You might also read

Related Articles

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

Sort by
Same author

Smooth constrained block matching algorithm for the evaluation of diaphragm deformation in speckle-tracking ultrasound.

Frontiers in medicine·2026
Same author

DNA Methylation Regulates CDK5R1 and NRBP1 to Exert Effects on Alcohol Dependence: Insights From Mendelian Randomization.

Addiction biology·2026
Same author

Analysis Model for Infant Incubator Adverse Events Using Retrieval-Augmented Generation Combined With Dual-Adapter Fine-Tuning: Development and Evaluation Study.

JMIR medical informatics·2026
Same author

AI-Driven Medical Device Risk Management: A New Paradigm Integrating Large Language Models and Prompt Engineering for Standard-Risk Knowledge Graph Construction and Application.

Risk management and healthcare policy·2026
Same author

Elucidation of the Structure Determinants for the Delivery Process of Phospholipid-Based Nanomaterials Using a Combinatorial Nanoparticle Library Approach.

ACS applied materials & interfaces·2026
Same author

Coherent control of photonic spin Hall effect in a cavity.

Optics express·2025

Related Experiment Video

Updated: Jul 3, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

An AFM/rotaxane molecular reading head for sequence-dependent DNA structures.

Brian A Ashcroft1, Quinn Spadola, Shahid Qamar

  • 1Biodesign Institute, Arizona State University, PO Box 875601 Tempe, AZ 85287, USA.

Small (Weinheim an Der Bergstrasse, Germany)
|August 6, 2008
PubMed
Summary
This summary is machine-generated.

DNA secondary structures like hairpins present challenges for nanopore sequencing. A novel "tape reader" nanomechanical device requires significantly more force to unfold DNA hairpins within a nanopore.

More Related Videos

CD Spectroscopy to Study DNA-Protein Interactions
06:48

CD Spectroscopy to Study DNA-Protein Interactions

Published on: February 10, 2022

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Related Experiment Videos

Last Updated: Jul 3, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

CD Spectroscopy to Study DNA-Protein Interactions
06:48

CD Spectroscopy to Study DNA-Protein Interactions

Published on: February 10, 2022

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Area of Science:

  • Nanotechnology
  • Molecular Biology
  • Biophysics

Background:

  • DNA secondary structures, such as hairpins, can impede DNA processing by enzymes and hinder DNA passage through nanopores.
  • Nanopore sequencing is a novel technology that relies on the translocation of DNA through a small aperture.

Purpose of the Study:

  • To investigate the mechanical forces required to unfold DNA secondary structures within a confined nanopore geometry.
  • To assess the feasibility of a nanomechanical molecular "tape reader" for DNA analysis.

Main Methods:

  • Assembled a nanomechanical molecular "tape reader" by threading a nanopore over DNA.
  • Utilized an atomic force microscope to pull the DNA through the nanopore.
  • Studied the force required to open DNA hairpins under these specific geometric constraints.

Main Results:

  • Unfolding DNA hairpins within a 0.7-nm-diameter nanopore required 40 times more force compared to pulling DNA from its ends.
  • Kinetic analysis indicated that less strain is needed to destabilize the double helix in this confined geometry.
  • Significant force is necessary to provide the free energy for hairpin unfolding in the nanopore.

Conclusions:

  • DNA secondary structures pose a substantial obstacle for DNA translocation through nanopores.
  • The nanomechanical "tape reader" configuration significantly increases the force required to overcome DNA secondary structures.
  • Further research is needed to optimize nanopore designs for efficient DNA sequencing.