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Atomic Force Microscopy01:08

Atomic Force Microscopy

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Atomic force microscopy (AFM) is a type of scanning probe microscopy that can analyze topographic details of various specimens like ceramics, glass, polymers, and biological samples. AFM offers over 1000 times more resolution than the optical imaging system. Images generated from AFM are three-dimensional surface profiles, offering an advantage over the flat, two-dimensional images from other imaging techniques.
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Atoms and molecules interact through bonds (or forces): intramolecular and intermolecular. The forces are electrostatic as they arise from interactions (attractive or repulsive) between charged species (permanent, partial, or temporary charges) and exist with varying strengths between ions, polar, nonpolar, and neutral molecules. The different types of intermolecular forces are ion–dipole, dipole–dipole, hydrogen bonds, and dispersion; among these, dipole–dipole, hydrogen...
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An atomic orbital represents the three-dimensional regions in an atom where an electron has the highest probability to reside. The radial distribution function indicates the total probability of finding an electron within the thin shell at a distance r from the nucleus. The atomic orbitals have distinct shapes which are determined by l, the angular momentum quantum number. The orbitals are often drawn with a boundary surface, enclosing densest regions of the cloud.
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In an atom, the negatively charged electrons are attracted to the positively charged nucleus. In a multielectron atom, electron-electron repulsions are also observed. The attractive and repulsive forces are dependent on the distance between the particles, as well as the sign and magnitude of the charges on the individual particles. When the charges on the particles are opposite, they attract each other. If both particles have the same charge, they repel each other.
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Intermolecular forces (IMF) are electrostatic attractions arising from charge-charge interactions between molecules. The strength of the intermolecular force is influenced by the distance of separation between molecules. The forces significantly affect the interactions in solids and liquids, where the molecules are close together. In gases, IMFs become important only under high-pressure conditions (due to the proximity of gas molecules). Intermolecular forces dictate the physical properties of...
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Atomic Structure01:33

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Updated: Feb 14, 2026

Visualization of Recombinant DNA and Protein Complexes Using Atomic Force Microscopy
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CTCF-Induced Circular DNA Complexes Observed by Atomic Force Microscopy.

Matthew T Mawhinney1, Runcong Liu1, Fang Lu2

  • 1Department of Physics, Drexel University, Philadelphia, PA 19104, USA.

Journal of Molecular Biology
|February 8, 2018
PubMed
Summary
This summary is machine-generated.

The CTCF protein

Keywords:
CTCFDNADNA loop formationatomic force microscopyprotein–DNA interactions

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Area of Science:

  • Genomics and molecular biology
  • Structural biology
  • Biophysics

Background:

  • CTCF is a key protein in genome organization, hypothesized to initiate DNA looping.
  • The 11 zinc finger (11 ZF) domain of CTCF is crucial for DNA binding.
  • Direct evidence for CTCF-induced DNA loop formation remains elusive.

Purpose of the Study:

  • To investigate the role of CTCF's 11 ZF and 3 ZF domains in DNA morphology using atomic force microscopy.
  • To provide direct evidence for CTCF-mediated DNA loop formation.

Main Methods:

  • Atomic force microscopy (AFM) was employed to visualize DNA-protein interactions.
  • The study examined the effects of the full 11 ZF CTCF domain and a truncated 6-8 ZF CTCF domain on DNA structure.

Main Results:

  • Both CTCF domains altered DNA from relaxed to compact circular complexes, meshes, and networks.
  • The 11 ZF CTCF domain formed quasi-circular DNA/CTCF complexes, destabilized by the 6-8 ZF CTCF domain.
  • Non-specific binding dominated circular complex formation, with DNA appearing twice wrapped around the protein.

Conclusions:

  • The 11 ZF domain of CTCF plays a critical role in DNA loop formation.
  • CTCF exhibits multivalent binding characteristics influencing DNA architecture.
  • AFM provides insights into the structural mechanisms of genome organization by CTCF.