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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

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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
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Sanger Sequencing01:57

Sanger Sequencing

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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...
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RNA-seq03:21

RNA-seq

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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. 
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Maxam-Gilbert Sequencing01:05

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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.
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Updated: Sep 9, 2025

Nanopore DNA Sequencing for Metagenomic Soil Analysis
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Write and Read: Harnessing Synthetic DNA Modifications for Nanopore Sequencing.

Uri Bertocchi1,2, Assaf Grunwald1, Gal Goldner1

  • 1School of Chemistry, Tel Aviv University, Tel Aviv-Yafo, 6997801, Israel.

Biorxiv : the Preprint Server for Biology
|September 5, 2025
PubMed
Summary
This summary is machine-generated.

This study introduces a novel nanopore sequencing method to detect DNA modifications like methylation and hydroxymethylation. This "write-and-read" framework uses chemical tags to create unique electrical signals for identifying altered nucleotides.

Keywords:
5-hydroxymethylcytosine (5hmC)5-methylcytosine (5mC)DNA taggingEpigeneticsMethyltransferase (Mtase)Nanopore sequencingβ-glucosyltransferase (BGT)

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Last Updated: Sep 9, 2025

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biotechnology

Background:

  • Nanopore sequencing offers multi-omic data capture on single DNA molecules.
  • Nucleotide modifications like DNA methylation can be detected via nanopore electrical signals.
  • Encoding genomic information requires chemical modification of DNA.

Purpose of the Study:

  • To develop a versatile "write-and-read" framework for nanopore sequencing.
  • To demonstrate direct detection of chemically modified nucleotides using nanopore electrical signatures.
  • To explore bio-orthogonal DNA labeling for expanded sequence detection.

Main Methods:

  • Chemo-enzymatic DNA labeling with synthetic tags.
  • Nanopore sequencing to record electrical fingerprints of modified DNA.
  • Proof-of-concept: DNA glucosylation of 5-hydroxymethylcytosine (5hmC) with glucose or glucose-azide.
  • Enzymatic alkylation for N6-adenine modification.

Main Results:

  • Chemically modified nucleotides generate distinct and reproducible electrical shifts in nanopore signals.
  • Successful direct detection of 5hmC with glucose or glucose-azide adducts.
  • Enzymatic alkylation of adenine produces characteristic signal shifts, differentiating modified from native bases.
  • Demonstrated distinct electrical fingerprints for modified nucleotides.

Conclusions:

  • The
  • write-and-read
  • framework enables direct detection of DNA modifications via nanopore sequencing.
  • Programmable chemical modifications expand the detectable "alphabet" of DNA.
  • This approach facilitates simultaneous multi-omic analysis on individual molecules, advancing genetic research.