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Related Concept Videos

The DNA Helix01:16

The DNA Helix

Overview
Chromatin Packaging02:21

Chromatin Packaging

Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order structures.
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...
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...
Chromatin Packaging01:32

Chromatin Packaging

Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...
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...

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Related Experiment Video

Updated: Jul 6, 2026

Studying DNA Looping by Single-Molecule FRET
11:27

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

Weakly bound water molecules shorten single-stranded DNA.

Shuxun Cui1, Christian Albrecht, Ferdinand Kühner

  • 1Lehrstuhl für Angewandte Physik and Centre for Nanoscience, Ludwig-Maximilians Universität München, Amalienstrasse 54, 80799 München, Germany. cuisx@scu.edu.cn

Journal of the American Chemical Society
|May 18, 2006
PubMed
Summary

We measured single-stranded DNA elasticity in water and organic solvents, finding water bridges around DNA significantly alter its elasticity. Breaking these H-bond bridges is key to understanding DNA behavior in different environments.

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Published on: May 31, 2024

Area of Science:

  • Biophysics
  • Physical Chemistry
  • Materials Science

Background:

  • Understanding the mechanical properties of single-stranded DNA (ssDNA) is crucial for molecular biology.
  • The influence of solvent environment on polymer elasticity is not fully understood.
  • Water's role in mediating interactions with biomolecules like DNA requires further investigation.

Purpose of the Study:

  • To measure and compare the single-chain elasticity of ssDNA in aqueous and nonaqueous environments.
  • To elucidate the contribution of water bridges to the observed differences in ssDNA elasticity.
  • To develop a theoretical model that accurately describes ssDNA elasticity in different solvents.

Main Methods:

  • Atomic Force Microscopy (AFM)-based single-molecule force spectroscopy was employed to measure ssDNA elasticity.
  • Experiments were conducted in both aqueous and nonaqueous, apolar liquid environments.
  • Ab initio quantum mechanics calculations were performed to support experimental findings.

Main Results:

  • A marked deviation in force-extension relationships was observed between aqueous and nonaqueous conditions.
  • This deviation was attributed to the energy required to break H-bond-directed water bridges around the ssDNA chain in aqueous solutions.
  • Results in 8 M guanidine-HCl further supported the role of water bridges.
  • A parameter-free freely rotating chain model perfectly matched experimental data in organic solvents.

Conclusions:

  • Water bridges formed by H-bonding between ssDNA and water molecules significantly impact ssDNA elasticity.
  • The absence of these water bridges in organic solvents leads to different elastic behavior.
  • Weak H-bonding between ssDNA and water may be essential for the stability of double-stranded DNA in aqueous solutions.