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Related Concept Videos

DNA Packaging00:58

DNA Packaging

Overview
DNA Packaging00:58

DNA Packaging

Overview
Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
Chromatin Packaging01:32

Chromatin Packaging

Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...
Chromatin Packaging02:21

Chromatin Packaging

Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order structures.
The Nucleosome01:19

The Nucleosome

Human DNA is almost two meters long. However, it is compressed inside a tiny nucleus measuring only a few microns in diameter. To make this degree of compaction possible, DNA is organized into several sequential levels so that it can fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
In a chromosome, DNA is wound twice around a protein complex called a histone octamer core, which consists of 8 histone proteins. This...

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Visualization of DNA Compaction in Cyanobacteria by High-voltage Cryo-electron Tomography
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DNA compaction by a dendrimer.

Bidisha Nandy1, Prabal K Maiti

  • 1Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, 560012, India.

The Journal of Physical Chemistry. B
|December 22, 2010
PubMed
Summary
This summary is machine-generated.

Positively charged polyamidoamine (PAMAM) dendrimers compact double-stranded DNA (dsDNA) rapidly. This complexation, driven by electrostatics, shows optimal DNA wrapping with higher dendrimer generations and preserves DNA structure for gene delivery applications.

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Area of Science:

  • Biophysical Chemistry
  • Materials Science
  • Nanotechnology

Background:

  • Polyamidoamine (PAMAM) dendrimers are positively charged at physiological pH, enabling binding with negatively charged double-stranded DNA (dsDNA).
  • Understanding this complexation is crucial for applications in gene delivery and DNA sensing.
  • PAMAM dendrimers offer a model for studying complex biological interactions.

Purpose of the Study:

  • To investigate the complexation between dsDNA and various generations of PAMAM dendrimers (G3-G5).
  • To elucidate the binding modes, dynamics, and structural effects of this interaction using molecular dynamics simulations.
  • To evaluate the potential of PAMAM dendrimers as gene delivery vehicles.

Main Methods:

  • Atomistic molecular dynamics (MD) simulations were employed.
  • Simulations were conducted in aqueous solution with physiological ions.
  • Analysis included binding modes, DNA compaction, counterion release, binding energies, and DNA helical parameters.

Main Results:

  • Rapid compaction of dsDNA by PAMAM dendrimers was observed on a nanosecond timescale.
  • Electrostatic interactions drive binding, with affinity increasing with dendrimer charge (G5 > G4 > G3).
  • Optimal DNA wrapping occurred at charge ratios greater than 1; DNA's B-form structure was preserved.

Conclusions:

  • PAMAM dendrimers effectively complex and compact dsDNA through electrostatic interactions.
  • Counterion release contributes to the binding thermodynamics via entropic gain.
  • The preservation of DNA's B-form structure supports the suitability of PAMAM dendrimers for gene delivery.