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Related Concept Videos

Mismatch Repair01:20

Mismatch Repair

Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
Mismatch Repair01:36

Mismatch Repair

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Mismatch Repair01:36

Mismatch Repair

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Improving Translational Accuracy02:07

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
DNA Base Pairing02:27

DNA Base Pairing

Erwin Chargaff’s rules on DNA equivalence paved the way for the discovery of base pairing in DNA. Chargaff’s rules state that in a double-stranded DNA molecule,
DNA Base Pairing02:27

DNA Base Pairing

Erwin Chargaff’s rules on DNA equivalence paved the way for the discovery of base pairing in DNA. Chargaff’s rules state that in a double-stranded DNA molecule,

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Related Experiment Video

Updated: Jul 18, 2026

Proofreading and DNA Repair Assay Using Single Nucleotide Extension and MALDI-TOF Mass Spectrometry Analysis
11:08

Proofreading and DNA Repair Assay Using Single Nucleotide Extension and MALDI-TOF Mass Spectrometry Analysis

Published on: June 19, 2018

Computational evaluation of the specific interaction between cation and mismatch base pair.

Hajime Sugiyama1, Nobue Adachi, Susumu Kawauchi

  • 1Fujitsu Limited, 1-9-3 Nakase, Chiba 261-8588, Japan.

Nucleic Acids Symposium Series (2004)
|December 8, 2006
PubMed
Summary

Silver cation (Ag(I)) binding to cytosine is more stable than hydrate states. Mercury cation (Hg(II)) binding to thymine was also studied using ab initio calculations.

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Real-time Observation of the DNA Strand Exchange Reaction Mediated by Rad51
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Real-time Observation of the DNA Strand Exchange Reaction Mediated by Rad51

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Last Updated: Jul 18, 2026

Proofreading and DNA Repair Assay Using Single Nucleotide Extension and MALDI-TOF Mass Spectrometry Analysis
11:08

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Real-time Observation of the DNA Strand Exchange Reaction Mediated by Rad51
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Published on: February 13, 2019

Area of Science:

  • Computational chemistry
  • Biophysical chemistry
  • Quantum chemistry

Background:

  • Metal-modified DNA base pairs are crucial in understanding DNA damage and repair.
  • Silver (Ag(I)) and mercury (Hg(II)) cations are known to interact with DNA bases.
  • Cytosine and thymine are fundamental DNA nucleobases.

Purpose of the Study:

  • To characterize the structure and energetics of silver-cytosine and mercury-thymine complexes.
  • To investigate metal-mediated crosslinks in DNA base pairs.
  • To compare the stability of metal-coordinated base pairs versus hydrated states.

Main Methods:

  • Ab initio calculations were employed to optimize the geometry of the complexes.
  • The Hatree-Fock (HF) method was utilized without symmetry constraints.
  • Interaction energies were calculated to assess complex stability.

Main Results:

  • Optimized structures for silver(I) with cytosine (O2(C):Ag:O2(C)) and mercury(II) with thymine (N3(T):Hg:N3(T)) were obtained.
  • The silver(I)-cytosine complex demonstrated higher stability compared to its hydrated form.
  • Calculations provided insights into the energetic favorability of metal-nucleobase interactions.

Conclusions:

  • Coordination of silver(I) to cytosine is energetically more favorable than hydration.
  • The study provides a theoretical basis for understanding metal-DNA interactions.
  • Computational methods offer valuable tools for predicting the behavior of metal cations with DNA bases.