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 Isolation

DNA Isolation

DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further processing. For example, plasmid DNA extraction is a bit more complicated than genomic DNA extraction because of the need for an appropriate lysis method to separate plasmid DNA from gDNA during isolation. However, for specific applications, such as long-range DNA sequencing that require a good yield of high- quality DNA samples, we need to follow...

Next-generation Sequencing

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....

Long-patch Base Excision Repair

Long-patch Base Excision Repair

Since the discovery of the two BER pathways, there has been a debate about how a cell chooses one pathway over the other and the factors determining this selection. Numerous in vitro experiments have pointed out multiple determinants for the sub-pathway selection. These are:

You might also read

Related Articles

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

Sort by

Same author

Topology-Aware Generation and Activity-Based Filtering: A Computational-Experimental Framework for Data-Scarce Quaternary Ammonium Compound Discovery.

Journal of chemical information and modeling·2026

Same author

DyVarMap: Integrating Conformational Dynamics and Interpretable Machine Learning for Cancer-Associated Missense Variant Classification in FGFR2.

Bioengineering (Basel, Switzerland)·2026

Same author

Predicting epistasis across proteins by structural logic.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same author

Contribution of DNA breathing to physical interactions with transcription factors.

bioRxiv : the preprint server for biology·2025

Same author

DNA breathing integration with deep learning foundational model advances genome-wide binding prediction of human transcription factors.

Nucleic acids research·2024

Same author

In the twilight zone of protein sequence homology: do protein language models learn protein structure?

Bioinformatics advances·2024

Same journal

Layered social competition coordinates reproductive hierarchy formation in ants.

bioRxiv : the preprint server for biology·2026

Same journal

Combination epigenetic-targeted therapy increases the immunogenicity of poorly immunogenic sarcomas.

bioRxiv : the preprint server for biology·2026

Same journal

Loss of LanC-like proteins delays post-injury regeneration of aging skeletal muscles.

bioRxiv : the preprint server for biology·2026

Same journal

Integrative Transfer Network: Deep Transfer Learning Across Populations and Prediction Targets.

bioRxiv : the preprint server for biology·2026

Same journal

Confidence-supported label-free metabolic imaging with FPhaS phase autofluorescence microscopy.

bioRxiv : the preprint server for biology·2026

Same journal

Sequence-encoded autoinhibition couples mRNA decapping activity to phase separation.

bioRxiv : the preprint server for biology·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jun 4, 2025

An Efficient Strategy for Generating Tissue-specific Binary Transcription Systems in Drosophila by Genome Editing

An Efficient Strategy for Generating Tissue-specific Binary Transcription Systems in Drosophila by Genome Editing

Published on: September 19, 2018

Efficient High-Throughput DNA Breathing Features Generation Using Jax-EPBD.

Toki Tahmid Inan^1,2, Anowarul Kabir^1,2, Kim Rasmussen¹

¹Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM.

Biorxiv : the Preprint Server for Biology

|December 23, 2024

Summary

This summary is machine-generated.

JAX-EPBD accelerates DNA breathing dynamics simulations by 30x, improving transcription factor binding predictions and revealing sequence-specific bubble dynamics linked to gene regulation.

More Related Videos

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA

Published on: October 1, 2017

In Vitro Selection of Engineered Transcriptional Repressors for Targeted Epigenetic Silencing

In Vitro Selection of Engineered Transcriptional Repressors for Targeted Epigenetic Silencing

Published on: May 5, 2023

Related Experiment Videos

Last Updated: Jun 4, 2025

An Efficient Strategy for Generating Tissue-specific Binary Transcription Systems in Drosophila by Genome Editing

An Efficient Strategy for Generating Tissue-specific Binary Transcription Systems in Drosophila by Genome Editing

Published on: September 19, 2018

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA

A Simple, Robust, and High Throughput Single Molecule Flow Stretching Assay Implementation for Studying Transport of Molecules Along DNA

Published on: October 1, 2017

In Vitro Selection of Engineered Transcriptional Repressors for Targeted Epigenetic Silencing

In Vitro Selection of Engineered Transcriptional Repressors for Targeted Epigenetic Silencing

Published on: May 5, 2023

Area of Science:

Computational Biology
Molecular Dynamics
Genomics

Background:

DNA breathing dynamics, transient base-pair openings, are crucial for DNA-templated processes.
Existing models like EPBD face computational limits for analyzing long DNA sequences.

Purpose of the Study:

Introduce JAX-EPBD, a GPU-accelerated framework for high-throughput DNA breathing simulations.
Enhance the scalability and speed of analyzing DNA dynamics for genome-scale applications.

Main Methods:

Developed JAX-EPBD using JAX for GPU acceleration, enabling Langevin molecular dynamics.
Achieved up to 30x speedup and improved scalability over traditional C-based EPBD.
Applied JAX-EPBD to predict transcription factor binding affinity and analyze promoter dynamics.

Main Results:

JAX-EPBD efficiently captures time-dependent DNA breathing behaviors like bubble lifetimes and base flipping kinetics.
Incorporating DNA breathing features improved transcription factor binding affinity predictions.
Observed sequence-specific bubble dynamics in the AAV P5 promoter correlating with transcriptional activity.

Conclusions:

JAX-EPBD is a powerful, scalable tool for studying DNA breathing dynamics.
The framework facilitates understanding DNA breathing's role in gene regulation and TF binding.
Enables genome-scale analyses of DNA dynamics for biological insights.