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

Nucleic Acid Structure01:25

Nucleic Acid Structure

6.3K
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...
6.3K
Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

14.8K
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...
14.8K
Protein Organization01:24

Protein Organization

6.8K
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
6.8K

You might also read

Related Articles

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

Sort by
Same author

Predicting Single-Stranded DNA Oligonucleotides 3D Structures: An Open Issue.

Computational and structural biotechnology journal·2026
Same author

Borrelia surface proteins: new horizons in Lyme disease diagnosis.

Applied microbiology and biotechnology·2025
Same author

Synthetic Peptide Antibodies via a Rational Approach Based on Disulfide-Stabilized α-Helical Peptides, for the Recognition of the Intrinsically Disordered Protein NUPR1.

Macromolecular bioscience·2025
Same author

Selection and characterization of DNA aptamers targeting the surface Borrelia protein CspZ with high-throughput cross-over SELEX.

Communications biology·2025
Same author

Production, purification, and quality assessment of borrelial proteins CspZ from Borrelia burgdorferi and FhbA from Borrelia hermsii.

Applied microbiology and biotechnology·2024
Same author

The functionality of a therapeutic antibody candidate restored by a single mutation from proline to threonine in the variable region.

Human vaccines & immunotherapeutics·2023
Same journal

conMItion: an R package adjusting confounding factors for associations in multi-omics.

Bioinformatics (Oxford, England)·2026
Same journal

SpaMFG: a Spatial Multi-omics Integration Method based on Feature Grouping.

Bioinformatics (Oxford, England)·2026
Same journal

CSCN: Inference of Cell-Specific Causal Networks Using Single-Cell RNA-Seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

Sparse CCA-Based Mediation Analysis with High-Dimensional Exposures and Mediators.

Bioinformatics (Oxford, England)·2026
Same journal

Enhancing Cross-Context Generalization in Drug Perturbation Prediction with a Multimodal Conditional Diffusion Framework.

Bioinformatics (Oxford, England)·2026
Same journal

Primer Design through Submodular Function Estimation.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: Aug 19, 2025

The ITS2 Database
16:17

The ITS2 Database

Published on: March 12, 2012

31.0K

AptaMat: a matrix-based algorithm to compare single-stranded oligonucleotides secondary structures.

Thomas Binet1, Bérangère Avalle1, Miraine Dávila Felipe2

  • 1Université de technologie de Compiègne, UPJV, CNRS, Enzyme and Cell Engineering, Centre de recherche Royallieu, CS 60 319 - 60 203, Compiègne Cedex, France.

Bioinformatics (Oxford, England)
|November 28, 2022
PubMed
Summary
This summary is machine-generated.

AptaMat is a new algorithm that accurately compares single-stranded nucleic acid secondary structures. It outperforms existing methods in distinguishing similar structures and classifying RNA families.

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

20.7K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

68.8K

Related Experiment Videos

Last Updated: Aug 19, 2025

The ITS2 Database
16:17

The ITS2 Database

Published on: March 12, 2012

31.0K
Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

20.7K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

68.8K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Comparing single-stranded nucleic acid (ssNA) secondary structures is crucial for understanding their function, evolution, and the impact of mutations.
  • Existing comparison metrics are often too complex or lack the sensitivity to differentiate closely related ssNA structures.

Purpose of the Study:

  • To develop a simple yet sensitive algorithm for comparing ssNA secondary structures.
  • To introduce AptaMat, a novel method that utilizes matrix representations and Manhattan distance for ssNA structure comparison.

Main Methods:

  • Developed AptaMat algorithm using matrix representations of ssNA secondary structures.
  • Employed Manhattan distance metric for quantitative comparison of these matrices.
  • Compared AptaMat's performance against Hamming distance, RNAdistance, and an image-based approach.

Main Results:

  • AptaMat demonstrated superior ability to discriminate between similar ssNA secondary structures compared to existing metrics.
  • The algorithm successfully classified 14 RFAM families within a clustering procedure, highlighting its practical utility.
  • AptaMat offers a more sensitive and less elaborate approach to ssNA structure comparison.

Conclusions:

  • AptaMat provides a significant advancement in the field of ssNA secondary structure comparison.
  • The algorithm's simplicity and high sensitivity make it a valuable tool for researchers in molecular biology and bioinformatics.
  • AptaMat's performance suggests its potential for broader applications in genomic analysis and drug discovery.