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Related Concept Videos

Single-Strand DNA Binding Proteins01:03

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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.
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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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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...
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DNA replication is initiated at sites containing predefined DNA sequences known as origins of replication. DNA is unwound at these sites by the minichromosome maintenance (MCM) helicase and other factors such as Cdc45 and the associated GINS complex.The unwound single strands are protected by replication protein A (RPA) until DNA polymerase starts synthesizing DNA at the 5’ end of the strand in the same direction as the replication fork. To prevent the replication fork from falling apart,...
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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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Updated: Nov 6, 2025

Nanomanipulation of Single RNA Molecules by Optical Tweezers
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Sugar-Pucker Force-Induced Transition in Single-Stranded DNA.

Xavier Viader-Godoy1, Maria Manosas1, Felix Ritort1

  • 1Small Biosystems Lab, Condensed Matter Physics Department, Universitat de Barcelona, Carrer de Martí i Franquès 1, 08028 Barcelona, Spain.

International Journal of Molecular Sciences
|May 5, 2021
PubMed
Summary

Single-stranded DNA (ssDNA) elasticity depends on molecule length. Shorter ssDNA exhibits greater persistence length due to force-induced sugar pucker transitions, impacting molecular reaction thermodynamics.

Keywords:
elastic modelselasticityforce-spectroscopynucleic acidsoptical tweezerssingle-moleculessDNAsugar pucker

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Area of Science:

  • Biophysics
  • Molecular Biology
  • Polymer Physics

Background:

  • Accurate elastic properties of single-stranded DNA (ssDNA) are crucial for understanding DNA mechanics.
  • Force spectroscopy methods are widely used to study ssDNA elasticity, but results vary with molecule length.
  • Previous studies reported a dispersion in ssDNA elasticity, with shorter molecules showing larger persistence lengths.

Purpose of the Study:

  • To precisely characterize the elastic response of ssDNA across a wide range of lengths (60 bases to 14 kilobases).
  • To investigate the length-dependent elasticity of ssDNA using optical tweezers.
  • To elucidate the underlying molecular mechanisms responsible for observed elasticity trends.

Main Methods:

  • Utilized optical tweezers to perform pulling experiments on ssDNA molecules.
  • Measured the force-extension curves (FECs) of ssDNA over three orders of magnitude in length.
  • Applied the Worm-Like Chain (WLC) model to analyze the elastic response and determine persistence length.

Main Results:

  • Confirmed that ssDNA persistence length nearly doubles for short molecules (60 bases) compared to long molecules (14 kilobases).
  • Identified two distinct elastic regimes at low and high forces, attributed to different force regimes analyzed.
  • Observed a length-dependent elastic behavior consistent across a broad range of ssDNA lengths.

Conclusions:

  • The observed length-dependent elasticity of ssDNA is an artifact of fitting different force regimes.
  • A force-induced sugar pucker transition (C3'-endo to C2'-endo) explains the distinct elastic behaviors at low and high forces.
  • Understanding ssDNA elasticity is vital for characterizing DNA-protein interactions and DNA-based molecular machines.