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Related Concept Videos

The DNA Replication Fork01:02

The DNA Replication Fork

An organism’s genome needs to be duplicated in an efficient and error-free manner for its growth and survival. The replication fork is a Y-shaped active region where two strands of DNA are separated and replicated continuously. The coupling of DNA unzipping and complementary strand synthesis is a characteristic feature of a replication fork.   Organisms with small circular DNA, such as E. coli, often have a single origin of replication; therefore, they have only two replication forks, one in...
Lagging Strand Synthesis01:59

Lagging Strand Synthesis

During replication, the complementary strands in double-stranded DNA are synthesized at different rates. Replication first begins on the leading strand. Replication starts later, occurs more slowly, and proceeds discontinuously on the lagging strand.
There are several major differences between synthesis of the leading strand and synthesis of the lagging strand. 1) Leading strand synthesis happens in the direction of replication fork opening, whereas lagging strand synthesis happens in the...
The Replisome03:01

The Replisome

DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with the...
Translesion DNA Polymerases02:10

Translesion DNA Polymerases

Translesion (TLS) polymerases rescue stalled DNA polymerases at sites of damaged bases by replacing the replicative polymerase and installing a nucleotide across the damaged site. Doing so, TLS allows additional time for the cell to repair the damage before resuming regular DNA replication.
TLS polymerases are found in all three domains of life - archaea, bacteria, and eukaryotes. Of the different classes of TLS polymerases, members of the Y family are fitted with specialized structures that...
Fixing Double-strand Breaks02:04

Fixing Double-strand Breaks

The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...
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...

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Related Experiment Video

Updated: Jul 28, 2026

Direct Observation of Enzymes Replicating DNA Using a Single-molecule DNA Stretching Assay
17:03

Direct Observation of Enzymes Replicating DNA Using a Single-molecule DNA Stretching Assay

Published on: March 23, 2010

Flexibility of duplex DNA on the submicrosecond timescale.

T M Okonogi1, A W Reese, S C Alley

  • 1Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA.

Biophysical Journal
|December 10, 1999
PubMed
Summary

This study reveals new insights into DNA flexibility using Electron Paramagnetic Resonance (EPR). The research determined a dynamic bending persistence length for duplex DNA, offering a deeper understanding of its structural dynamics.

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Studying DNA Looping by Single-Molecule FRET
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Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

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Last Updated: Jul 28, 2026

Direct Observation of Enzymes Replicating DNA Using a Single-molecule DNA Stretching Assay
17:03

Direct Observation of Enzymes Replicating DNA Using a Single-molecule DNA Stretching Assay

Published on: March 23, 2010

Studying DNA Looping by Single-Molecule FRET
11:27

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
05:37

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Published on: April 4, 2025

Area of Science:

  • Biophysics
  • Molecular Biology
  • Spectroscopy

Background:

  • Understanding DNA's dynamic flexibility is crucial for molecular biology.
  • Previous studies often assumed rapid internal motions in DNA, leading to averaged spin interactions.

Purpose of the Study:

  • To investigate the internal dynamics of duplex DNA in solution.
  • To determine the dynamic bending persistence length of DNA using a novel spin probe.

Main Methods:

  • Utilized a site-specific Electron Paramagnetic Resonance (EPR)-active spin probe for rigid DNA attachment.
  • Acquired and simulated EPR spectra of DNA using the stochastic Liouville equation.
  • Modified the weakly bending rod model to include finite relaxation times of internal modes.

Main Results:

  • Found that rapid motion averaging is inconsistent with experimental data.
  • The modified weakly bending rod model accurately predicted probe oscillation amplitude dependence.
  • Determined a submicrosecond dynamic bending persistence length of approximately 1500-1700 Å for duplex DNA.

Conclusions:

  • The measured dynamic persistence length suggests longer-timescale DNA conformations beyond linear CW-EPR accessibility.
  • This study provides the first direct determination of duplex DNA's dynamic flexibility in 0.1 M salt.
  • Findings challenge previous assumptions about DNA internal motion timescales.