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Related Concept Videos

Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

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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...
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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
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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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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...
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DNA Helicases

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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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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.
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Related Experiment Video

Updated: Oct 11, 2025

Studying DNA Looping by Single-Molecule FRET
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Sequence-dependent twist-bend coupling in DNA minicircles.

Minjung Kim1, Sehui Bae1, Inrok Oh2

  • 1Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea. jkim@ewha.ac.kr.

Nanoscale
|November 30, 2021
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Summary

DNA minicircles are key for nanotechnology, but sharp bends can cause defects. This study reveals sequence-dependent DNA structural responses to bending, identifying specific sequences that influence stability in nanoscale DNA applications.

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Related Experiment Videos

Last Updated: Oct 11, 2025

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Area of Science:

  • Biophysics
  • Molecular Biology
  • Nanotechnology

Background:

  • Double-stranded DNA can form minicircles, catenanes, and rotaxanes for DNA nanotechnologies.
  • Sharp DNA bending can alter helical structure, leading to defects that hinder nanoscale applications.

Purpose of the Study:

  • To investigate local helical twist variations in sharply bent DNA minicircles.
  • To understand the sequence dependence of twist-bend coupling in DNA.

Main Methods:

  • Microsecond-long all-atom molecular dynamics simulations of six DNA minicircles.
  • Analysis of twist angles between base pairs at different locations relative to DNA bending.

Main Results:

  • Identified four dinucleotide steps with strong twist-bend coupling: TA/TA, CG/CG, CA/TG, and GA/TC.
  • Demonstrated sequence-dependent structural responses of DNA to mechanical deformation.

Conclusions:

  • Provides molecular-level insights into the structure and stability of sharply bent DNA.
  • Findings are crucial for optimizing DNA minicircles, catenanes, and rotaxanes in nanoscale DNA applications.