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

DNA as a Genetic Template

DNA as a Genetic Template

DNA Topoisomerases

DNA Topoisomerases

Topoisomerases are enzymes that relax overwound DNA molecules during various cell processes, including DNA replication and transcription. These enzymes regulate positive and negative DNA supercoiling without changing the nucleotide sequence. DNA overwinding in a clockwise direction results in positively supercoiled DNA, whereas underwinding in a counterclockwise direction produces negatively supercoiled DNA.
Types and Mechanism of action
Topoisomerases are divided into two main types. ...

DNA Agarose Gel Electrophoresis

DNA Agarose Gel Electrophoresis

Agarose gel electrophoresis is a laboratory technique commonly used to separate DNA fragments by size. However, it can also be used to isolate and purify DNA fragments using a gel extraction protocol.
Gel extraction follows five major steps: running gel electrophoresis to separate fragments, isolating the individual bands, extracting DNA from those bands, and removing the dye and salts from the extracted mixture to obtain pure DNA.
In cloning experiments, both the insert and vector DNA...

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

Error characterization and error correction approaches in combinatorial DNA-based storage.

Scientific reports·2026

Same author

Efficiency of Digital Photolithographic Synthesis of Large, High-Quality DNA Libraries and Microarrays using a Guanine O<sup>6</sup> Dephosphitylation Strategy.

Communications chemistry·2025

Same author

The zettabyte era is in our DNA.

Nature computational science·2024

Same author

GradHC: highly reliable gradual hash-based clustering for DNA storage systems.

Bioinformatics (Oxford, England)·2024

Same author

Reconstruction algorithms for DNA-storage systems.

Scientific reports·2024

Same author

Design of optimal labeling patterns for optical genome mapping via information theory.

Bioinformatics (Oxford, England)·2023

Same journal

OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.

BMC bioinformatics·2026

Same journal

NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.

BMC bioinformatics·2026

Same journal

SurvGME: an R package for survival analysis with graphical and measurement error models.

BMC bioinformatics·2026

Same journal

SimMapNet: a Bayesian framework for gene regulatory network inference using gene ontology similarities as external hint.

BMC bioinformatics·2026

Same journal

Dual channel drug-drug interactions extraction based on cross attention.

BMC bioinformatics·2026

Same journal

FeSseqdb: a curated sequence-level database and interpretable machine learning framework for identifying iron-sulfur proteins.

BMC bioinformatics·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Sep 12, 2025

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Published on: August 15, 2018

Dna-storalator: a computational simulator for DNA data storage.

Gadi Chaykin¹, Omer Sabary², Nili Furman¹

¹Henry and Marilyn Taub Faculty of Computer Science, Technion - Israel Institute of Technology, 3200003, Haifa, Israel.

BMC Bioinformatics

|August 5, 2025

Summary

This summary is machine-generated.

DNA data storage offers dense, durable data archiving. A new simulator, DNA-Storalator, models biological processes and coding techniques to overcome DNA storage errors like insertions and deletions.

Keywords:

DNA data storage DNA sequencing errors DNA storage simulator DNA synthesis errors DNA-based data storage.clustering algorithms reconstruction algorithms

More Related Videos

Analyzing and Building Nucleic Acid Structures with 3DNA

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation

DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation

Published on: December 29, 2021

Related Experiment Videos

Last Updated: Sep 12, 2025

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Design and Synthesis of a Reconfigurable DNA Accordion Rack

Published on: August 15, 2018

Analyzing and Building Nucleic Acid Structures with 3DNA

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation

DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation

Published on: December 29, 2021

Area of Science:

Biotechnology
Computer Science
Data Storage

Background:

DNA data storage leverages DNA molecules for extremely dense and durable data archiving.
Insertion, deletion, and substitution errors are inherent challenges in DNA storage systems.
Novel algorithmic and coding solutions are crucial for reliable DNA data storage.

Purpose of the Study:

To introduce DNA-Storalator, a cross-platform software tool for simulating DNA data storage processes.
To provide an accessible platform for researchers to study DNA-based storage technologies.
To facilitate the development of new coding techniques and algorithms for DNA storage.

Main Methods:

Simulates biological stages: synthesis, PCR amplification, and sequencing, including error injection based on real-world rates.
Employs clustering algorithms to group noisy DNA strands and state-of-the-art reconstruction algorithms for data recovery.
Integrates with external error-correcting codes and other encoding/decoding techniques.

Main Results:

DNA-Storalator emulates biological and computational aspects of DNA data storage.
The simulator injects biologically relevant errors (insertions, deletions, substitutions) with customizable rates.
It enables control over amplification and strand copy distribution, aiding in error analysis and model creation.

Conclusions:

The DNA-Storalator provides a comprehensive and accessible computational tool for advancing DNA data storage research.
It supports the examination of new biological technologies, coding strategies, and algorithms.
Facilitates innovation in both current and future DNA storage systems.