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Maxam-Gilbert Sequencing

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...

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Related Experiment Video

Updated: May 28, 2026

In Vitro Chemical Mapping of G-Quadruplex DNA Structures by Bis-3-Chloropiperidines

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Published on: May 12, 2023

Small-molecule-based CUT&RUN for G-quadruplex DNA using a cyclic naphthalene diimide-copper complex.

Yukina Sanada¹, Satoshi Fujii², Shigeori Takenaka¹

¹Department of Applied Chemistry, Kyushu Institute of Technology, 1-1 Sensui-cho, Tobata-ku, Kitakyushu-shi, Fukuoka, 804-8550, Japan.

Analytical Sciences : the International Journal of the Japan Society for Analytical Chemistry

|May 26, 2026

Summary

Researchers developed a small molecule that targets G-quadruplex (G4) DNA structures. This molecule selectively binds and cleaves G4 DNA in chromatin, offering a new method for genomic analysis.

Keywords:

CUT&RUN Cu–ATCUN motif G-quadruplex DNA (G4)G4 DNA cleavage G4-targeted chromatin analysis cyclicnaphthalene diimide

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Last Updated: May 28, 2026

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Published on: September 19, 2017

Area of Science:

Biochemistry
Molecular Biology
Genomics

Background:

G-quadruplex (G4) DNA structures are prevalent in crucial genomic regions, influencing gene regulation and stability.
Experimental identification of G4 sites within chromatin presents significant challenges.

Purpose of the Study:

To develop a novel small-molecule ligand for selective G4 DNA recognition and cleavage.
To demonstrate the utility of this ligand for analyzing G4 sites in chromatin.

Main Methods:

Synthesis and characterization of the multifunctional small-molecule ligand cNDI-CuGGHE.
Spectroscopic analysis to determine G4 binding affinity and selectivity.
In vitro DNA cleavage assays using gel electrophoresis.
Application of a cNDI-CuGGHE-based CUT&RUN-like assay in HeLa cells followed by quantitative PCR.

Main Results:

cNDI-CuGGHE exhibits preferential binding to various G4 structures with high affinity (10⁶ M⁻¹), stabilizing them against duplex DNA.
The ligand efficiently mediates structure-dependent DNA cleavage at G4 sites in vitro.
Analysis of chromatin DNA shows reduced amplification of G4-containing regions, indicating targeted cleavage in cells.

Conclusions:

The small molecule cNDI-CuGGHE effectively targets and cleaves G-quadruplex DNA in chromatin.
This approach offers a viable alternative to antibody-enzyme conjugates for G4-targeted chromatin analysis.