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Single-Strand DNA Binding Proteins

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 Topoisomerases

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 Replication Fork

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...

Fixing Double-strand Breaks

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...

Fixing Double-strand Breaks

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 Recombination

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...

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Related Experiment Video

Updated: May 23, 2026

Studying DNA Looping by Single-Molecule FRET

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

Enhanced bubble formation in looped short double-stranded DNA.

O-chul Lee¹, Wokyung Sung

¹Department of Physics and PCTP, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea. ochul lee@postech.ac.kr

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics

|April 3, 2012

Summary

Short double-stranded (ds) DNA loops form bubbles more easily, releasing bending energy. This leads to DNA melting at lower temperatures and shorter lengths compared to linear DNA.

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Last Updated: May 23, 2026

Studying DNA Looping by Single-Molecule FRET

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Published on: June 28, 2014

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Published on: September 11, 2022

Area of Science:

Molecular Biology
Biophysics
Computational Biology

Background:

Double-stranded (ds) DNA exhibits unexpected bending and looping at scales shorter than its persistence length.
Understanding DNA structural dynamics is crucial for various biological processes and biotechnological applications.

Purpose of the Study:

To investigate the phenomenon of bubble formation in short ds DNA loops.
To analyze how loop conformation influences DNA's thermal stability and melting behavior.

Main Methods:

Simulated the breathing DNA model to study short ds DNA loops.
Analyzed bubble size distributions and melting curves for varying contour lengths.
Compared looped DNA behavior with linear DNA of identical lengths.
Performed analytical evaluation of free energies for DNA bending and bubble formation.

Main Results:

Shorter looped DNA facilitates easier bubble initiation and formation.
Bubble formation in loops serves to release significant bending energy.
Looped DNA exhibits melting at lower temperatures and shorter contour lengths than linear DNA.

Conclusions:

The enhanced propensity for bubble formation in short DNA loops is driven by the release of bending energy.
DNA looping significantly impacts thermal stability, lowering the melting point.
Findings provide insights into the structural flexibility and stability of DNA under conformational constraints.