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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...
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...
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...
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...
Nucleosome Remodeling02:54

Nucleosome Remodeling

Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
Nucleosome remodeling complex
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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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Related Experiment Video

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Studying DNA Looping by Single-Molecule FRET
11:27

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

Sequence-specific B-DNA flexibility modulates Z-DNA formation.

Jameson R Bothe1, Ky Lowenhaupt, Hashim M Al-Hashimi

  • 1Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States.

Journal of the American Chemical Society
|February 1, 2011
PubMed
Summary
This summary is machine-generated.

DNA structural transitions, like B-DNA to Z-DNA, are crucial for gene regulation. This study reveals how DNA flexibility influences Z-DNA formation and B/Z junction location, with CG-repeats playing a key role.

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Last Updated: Jun 4, 2026

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Published on: March 1, 2022

Area of Science:

  • Molecular Biology
  • Biophysics
  • Genetics

Background:

  • The transition between right-handed B-DNA and left-handed Z-DNA is a significant structural change in biology.
  • Z-DNA formation is essential for gene expression and regulation, but requires energetically costly B/Z junctions.

Purpose of the Study:

  • To investigate how sequence-specific B-DNA flexibility affects the thermodynamic propensity for Z-DNA formation.
  • To determine the role of B-DNA flexibility in the localization of B/Z junctions.

Main Methods:

  • Natural abundance NMR R(1ρ) carbon relaxation measurements.
  • Circular Dichroism (CD) spectroscopy.

Main Results:

  • Sequence-specific B-DNA flexibility, observed on fast (ps-ns) and slow (micros-ms) timescales, modulates Z-DNA formation.
  • This flexibility is localized at the B/Z junction sites.
  • CG-repeats actively tune the intrinsic flexibility of B-DNA.

Conclusions:

  • Sequence-specific B-DNA flexibility is a key factor influencing Z-DNA formation and junction positioning within genomes.
  • This flexibility may serve as a regulatory mechanism for controlling Z-DNA length and location.