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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...
Nucleic Acid Structure01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...
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...
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...
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...
The DNA Helix01:07

The DNA Helix

Deoxyribonucleic acid, or DNA, is the genetic material responsible for passing traits from generation to generation in all organisms and most viruses. DNA is composed of two strands of nucleotides that wind around each other to form a spring-like structure called a double helix. However, the double helix is not perfectly symmetrical. Instead, there are regularly occurring grooves in the structure. The major groove occurs where the sugar-phosphate backbones are relatively far apart. This space...

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Related Experiment Video

Updated: Jun 3, 2026

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

Formation of stable DNA triplexes.

Keith R Fox1, Tom Brown

  • 1School of Biological Sciences, Life Science Building 85, University of Southampton, Southampton SO17 1BJ, UK. K.R.Fox@soton.ac.uk

Biochemical Society Transactions
|March 25, 2011
PubMed
Summary
This summary is machine-generated.

Modified oligonucleotides overcome limitations in triple-helix formation, enabling high-affinity binding to DNA at physiological pH. This advancement enhances sequence-specific DNA targeting for potential therapeutic applications.

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Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids
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In Vitro Chemical Mapping of G-Quadruplex DNA Structures by Bis-3-Chloropiperidines
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In Vitro Chemical Mapping of G-Quadruplex DNA Structures by Bis-3-Chloropiperidines

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Last Updated: Jun 3, 2026

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

Published on: April 4, 2025

Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids
09:04

Sequence-specific and Selective Recognition of Double-stranded RNAs over Single-stranded RNAs by Chemically Modified Peptide Nucleic Acids

Published on: September 21, 2017

In Vitro Chemical Mapping of G-Quadruplex DNA Structures by Bis-3-Chloropiperidines
05:32

In Vitro Chemical Mapping of G-Quadruplex DNA Structures by Bis-3-Chloropiperidines

Published on: May 12, 2023

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Medicinal Chemistry

Background:

  • Triple-helical nucleic acids form when an oligonucleotide binds to the major groove of duplex DNA.
  • This DNA triplex formation offers potential for sequence-specific oligonucleotide binding.
  • Natural triple-helix formation is hindered by low pH requirements, homopurine target sequences, and low binding affinity.

Purpose of the Study:

  • To overcome the limitations of natural triple-helix formation.
  • To develop modified oligonucleotides for enhanced DNA triplex formation.
  • To achieve high-affinity DNA triplex binding at physiological pH and with sequence variations.

Main Methods:

  • Preparation of modified oligonucleotides with added positive charges on sugar and/or base.
  • Inclusion of cytosine analogues and nucleosides for pyrimidine sequence recognition.
  • Attachment of cross-linking groups to stabilize the DNA triplex structure.

Main Results:

  • Modified oligonucleotides successfully generated triple-helical structures (triplexes).
  • These modified triplexes exhibit high binding affinities.
  • Effective triplex formation was achieved at physiological pH and in sequences with pyrimidine interruptions.

Conclusions:

  • Modified oligonucleotides can overcome the limitations of natural DNA triplex formation.
  • The developed strategies enable high-affinity, sequence-specific DNA binding under physiological conditions.
  • These findings pave the way for advanced applications in DNA targeting and therapeutics.