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Related Concept Videos

Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
DNA as a Genetic Template02:05

DNA as a Genetic Template

Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
DNA Topoisomerases02:02

DNA Topoisomerases

Topoisomerases are enzymes that relax overwound DNA molecules during various cell processes, including DNA replication and transcription. These enzymes regulate positive and negative DNA supercoiling without changing the nucleotide sequence. DNA overwinding in a clockwise direction results in positively supercoiled DNA, whereas underwinding in a counterclockwise direction produces negatively supercoiled DNA.
Types and Mechanism of action
Topoisomerases are divided into two main types.  Type I...
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...
Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
DNA Helicases00:55

DNA Helicases

DNA unwinding helicase enzymes are a type of motor protein. Motor proteins can translocate along filaments or polymers using energy generated from ATP hydrolysis. Helicases are involved in all the important cellular processes where DNA unwinding is required, such as DNA replication, repair, recombination, and transcription. They are present in all living organisms, but vary in their structure, function, and mechanism of action. For example, in prokaryotes, DnaB helicase binds and translocates...

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Updated: May 14, 2026

Studying DNA Looping by Single-Molecule FRET
11:27

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

Molecular basis for sequence-dependent induced DNA bending.

Michael Rettig1, Markus W Germann, Shuo Wang

  • 1Department of Chemistry, Georgia State University, Atlanta, GA 30302, USA.

Chembiochem : a European Journal of Chemical Biology
|January 29, 2013
PubMed
Summary
This summary is machine-generated.

Alternating AT DNA exhibits unique structural flexibility. Binding with agents like netropsin induces significant changes in its minor groove width and bending, crucial for molecular recognition.

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Last Updated: May 14, 2026

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Published on: May 24, 2017

Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biophysics

Background:

  • Subtle DNA microstructural variations are key to molecular recognition and function.
  • A-tract DNA has a narrow minor groove and bent conformation, but alternating AT DNA structure is less understood.
  • Alternating AT DNA shows polymorphism and reduced mobility with minor-groove binders, suggesting bending.

Purpose of the Study:

  • To elucidate the solution structures of alternating AT DNA with and without netropsin.
  • To evaluate the molecular basis of binding-induced conformational changes in alternating AT DNA.
  • To understand the role of conformational features in AT DNA molecular recognition.

Main Methods:

  • Nuclear Magnetic Resonance (NMR) spectroscopy
  • Residual dipolar coupling (RDC) analysis
  • Restrained molecular-dynamics simulations

Main Results:

  • Free alternating AT DNA exhibits a slight bend towards the major groove.
  • Netropsin binding causes significant minor groove narrowing and a pronounced bend towards the minor groove.
  • Conformational malleability of AT sequences is essential for molecular recognition.

Conclusions:

  • Alternating AT DNA undergoes significant conformational changes upon binding with minor-groove agents.
  • These findings highlight the importance of DNA sequence-specific structures in molecular interactions.
  • The study opens new avenues for targeting novel DNA sequences based on their structural properties.