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

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...
DNA Bacteriophages01:26

DNA Bacteriophages

Bacteriophages, or phages, are viruses that specifically infect bacteria, utilizing their genetic material to hijack host cellular machinery for replication. DNA bacteriophages employ single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) genomes. These phages exhibit diverse replication strategies and host interactions, influencing their ecological roles and applications in biotechnology and medicine.ssDNA BacteriophagesssDNA phages, with their small genomes, utilize unique strategies to...
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...
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
DNA Isolation01:24

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...

You might also read

Related Articles

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

Sort by
Same author

Collective memory and mental health: Limitations, provocations, possibilities.

Current opinion in psychology·2026
Same author

Complete genome sequences of five <i>Variovorax</i> strains isolated from the <i>Populus</i> rhizosphere and endosphere.

Microbiology resource announcements·2025
Same author

Modifying Methylene-Tetrahydrofolate Reductase to Disrupt Electron Bifurcation in Clostridium autoethanogenum.

Biotechnology journal·2025
Same author

BONCAT-Live for isolation and cultivation of active environmental bacteria.

mBio·2025
Same author

Addendum: Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale.

Nature biotechnology·2025
Same author

BONCAT-Live for isolation and cultivation of active environmental microbes.

bioRxiv : the preprint server for biology·2025
Same journal

Epidemiological characteristics of amebiasis in Japan from 2001 to 2022.

PloS one·2026
Same journal

Longitudinal associations of academic stress with eating related patterns, nutrition, somatic indicators, and depressive symptoms in university students: A study protocol.

PloS one·2026
Same journal

Pollution removal efficiency enhancement by agricultural biomass additions in constructed wetlands: A framework integrating meta-analysis with explainable machine learning.

PloS one·2026
Same journal

Insulation failure mapping on power transformer bushing using FRA and electrostatic simulation.

PloS one·2026
Same journal

Enhancing medical Q&A systems with multimodal knowledge graphs and dual-layer attention mechanisms.

PloS one·2026
Same journal

UAMP: Consistent video object segmentation with uncertainty-aware memory propagation.

PloS one·2026
See all related articles

Related Experiment Video

Updated: May 19, 2026

Generating Transposon Insertion Libraries in Gram-Negative Bacteria for High-Throughput Sequencing
08:19

Generating Transposon Insertion Libraries in Gram-Negative Bacteria for High-Throughput Sequencing

Published on: July 7, 2020

Sequencing intractable DNA to close microbial genomes.

Richard A Hurt1, Steven D Brown, Mircea Podar

  • 1Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America.

Plos One
|August 4, 2012
PubMed
Summary
This summary is machine-generated.

Researchers developed a novel DNA sequencing method to close intractable gaps in microbial genomes caused by GC-rich secondary structures. This advancement improves genome finishing and accurate gene annotation for microbial sequencing projects.

More Related Videos

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing
10:00

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

Published on: May 23, 2018

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Related Experiment Videos

Last Updated: May 19, 2026

Generating Transposon Insertion Libraries in Gram-Negative Bacteria for High-Throughput Sequencing
08:19

Generating Transposon Insertion Libraries in Gram-Negative Bacteria for High-Throughput Sequencing

Published on: July 7, 2020

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing
10:00

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

Published on: May 23, 2018

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Area of Science:

  • Genomics
  • Microbiology
  • Molecular Biology

Background:

  • High-throughput DNA sequencing has increased microbial genome projects.
  • Intractable regions with sequence gaps are common in deposited microbial genomes.
  • GC-rich secondary structures impede sequencing of these problematic regions.

Purpose of the Study:

  • To develop a procedure for sequencing intractable regions in microbial genomes.
  • To close sequence gaps in Desulfovibrio desulfuricans ND132 and Desulfovibrio africanus genomes.
  • To provide a step-wise method for efficient genome finishing.

Main Methods:

  • Utilized strand-displacing DNA polymerases.
  • Implemented a novel ramped PCR extension cycle.
  • Targeted GC-rich secondary structures within intractable genomic regions.

Main Results:

  • Successfully amplified and closed all intractable gap regions in both target genomes.
  • Demonstrated the effectiveness of the developed procedure on Desulfovibrio genomes.
  • Enabled accurate gene annotation in previously problematic regions.

Conclusions:

  • The developed procedure effectively overcomes challenges in sequencing GC-rich regions.
  • This method reduces the effort required for microbial genome finishing.
  • Facilitates more complete and accurate microbial genome datasets.