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Updated: Dec 26, 2025

Studying DNA Looping by Single-Molecule FRET

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

DNA looping by two 5-methylcytosine-binding proteins quantified using nanofluidic devices.

Ming Liu¹, Saeid Movahed¹, Saroj Dangi¹

¹Department of Physics, North Carolina State University, Raleigh, NC, 27695-8202, USA.

Epigenetics & Chromatin

|March 18, 2020

Summary

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Methyl-CpG-binding domain protein 2 (MeCP2) compacts DNA by forming bridges and loops, unlike MBD2. ATTO 565-labeled MBD2 shows potential for epigenetic mapping.

Area of Science:

Molecular Biology
Epigenetics
Biophysics

Background:

MeCP2 and MBD2 are proteins binding 5-methylcytosine in CpG sites.
These proteins interact with others to influence DNA packing.
Nanofluidic channels enable probing protein-induced DNA compaction.

Purpose of the Study:

To investigate the DNA compaction mechanisms of MeCP2 and MBD2.
To compare the effects of these related proteins on DNA structure.
To evaluate MBD2 as a potential epigenetic mapping agent.

Main Methods:

DNA stretching in nanofluidic channels.
Atomic Force Microscopy (AFM) for structural analysis.
Utilizing ATTO 565-labeled MBD2.

Keywords:

DNA compaction DNA methylation MBD2 MeCP2

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Related Experiment Videos

Last Updated: Dec 26, 2025

Studying DNA Looping by Single-Molecule FRET

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules

Published on: April 12, 2019

Single-Molecule Imaging of EWS-FLI1 Condensates Assembling on DNA

Single-Molecule Imaging of EWS-FLI1 Condensates Assembling on DNA

Published on: September 8, 2021

Main Results:

MeCP2 significantly compacts DNA.
MBD2 binding does not alter DNA configuration.
MeCP2 compaction occurs via DNA bridging and loop formation.

Conclusions:

Full-length 5-methylcytosine-binding proteins exhibit varied DNA interaction effects.
MeCP2 strongly compacts DNA, while MBD2 shows no large-scale impact.
ATTO 565-labeled MBD2 is a promising tool for epigenetic mapping.